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gyrolab user guide

1. V Gyrolab Evaluator Gyrolab LIMS v Gyrolab Report Pie be la e Copy file s to disk LIMS result folder ramData Gyros Gyrolab Results user date run _ time Browse LIMS result file name Gyrolab LIMS CD1_ run _ date _ time ext Info This target generates a result file from a Gyralab run for further analysis in a LIMS system The result file is copied to the selected file destination The user sets the name and destination for the result folder and file name The settings from the last run of the current user will be pre selected Note that Gyrolab LIMS result files are always saved in Gyrolab Result Database Import Target Settings Export Target Settings Files are saved to the location specified in LIMS result folder field and with the name specified in LIMS result file name Settings are preserved from the user s last Run To import default settings for LIMS result folder and LIMS result file name Click Import Target Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Default Settings select LIMSTargetSettings xml and click Import e To customize settings for LIMS result folder and LIMS result file name e To edit LIMS result folder click Browse Browse and click Select to set new folder in the Select folder dialog To edit LIMS result file name click in the field and edi
2. A report file that holds method information can be generated To import default settings for report file Stylesheet and Destination lick Import Output Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Default Settings select ReportSettings xml and click Import e If no report file is wanted select the file present in Stylesheet and click on Remove button TIP Customized reports can be generated Contact Gyros for information Click OK and proceed to Chapter By 1 1 sample and reagents preparations Macros for creating names for folders and files macros unique names for results files and folders will be created automatically without having to change the settings for different Runs A selection of macros are provided for this Insert macros by typing them into folder and result file name fields Macro user run cdid date S time Description Expands to the full user name Expands to the Run name Expands to the CD id for example 1234567 123 Expands to the executed Run start date Expands to the executed Run start time Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B 31 B3 Design run B3 2 Instructions for Gyrolab xPlore B3 2 1 Wizard run design introduction The two workflow Wizard and LIMS differ in run design Design of runs are described in separate chapters Chapter B3 2 and Chapter B3 Sample preparations run star
3. Sample identity Sample subgroup as set during Run set up refer to Chap ter D2 2 2 Yes Integrated volume of the fluorescent binding surface of a reac tion in a microstructure Yes Average of response values for replicates of a sample sample group or sample subgroup The standard deviation of responses of sample replicates Coefficient of variation of response of replicates of a sample Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D 31 D 32 D2 Gyrolab ADA Software Column heading Inhibition Dilution CD ID CD Structure Cut Point Log of Response Log of Aver age Response MP Identity MP Well Detect Result Sample Type Needle ID Notes Original view Yes Yes Yes Yes Yes Description Inhibition is calculated as Inhibition 1 response for spiked samples response for unspiked samples Dilution factor for Unknown samples is entered in the Sample List For ADA control samples the dilution factor is entered during Run set up refer to Chapter D2 2 If no Dilution Factor value has been assigned a factor of 1 will automatically be used Identity of Gyrolab CD microlaboratory used to process the sam ples Identity of structure on Gyrolab CD microlaboratory where the sample was processed Describes whether sample response is above or below cut point Negative or positive The logarithm of Response value The logarithm of A
4. cece ee eee eee eeeeeeee ees A 6 AD 2271 Gyrolab XP siseccccccgacdietincsetcnnddvesedbentens cer sesevecdetepaeusticaes A 6 A2 22 2 Gyrolab XPIOSCisccscecsceessewacissesvercsewsnasgoubacestadesped cama dens A 8 A2 3 Gyrolab instrument rear view cceeceeeeeceeceeeeeeeees A 10 AD 3 1 GYtOlaD XP scsi coi as ccese esis mares Tas mesas aaa dada RERNE A 10 AD 3 2 Gyrolab XPlore ass cccsswssckwadsceesdanssdisvags eves e E NERE A 12 A2 4 Gyrolab CD microlaboratories cccccceseeeceeceeeeeeeeees A 13 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A A2 5 A2 6 A2 4 1 Gyrolab Bioaffy CDS cece eee e cece eeeceeeeeeeeeeeeneees A 13 A242 Gyrolab MIXING CD ccscdicsantisooseteensocsiaateues vavastentactedaiuss A 14 REXXID DUTTON renens a sendin ERRE ORREN A 15 Gyrolab SOWA E ss csssasccidwesesscansseesesscaesesesasxeaweesese sees A 15 A2 6 1 Standard SOFtWALE ccccccccccceecceceecceeeecseeeeceseeceeens A 15 A2 6 2 Additional SOftWALE cc cece cece eeecceeeecseeeeceeeeceeees A 15 A2 6 3 Gyrolab software user levels eee eeeeeeeeeeeeeeeees A 16 A2 6 4 Gyrolab software terminology list cceeeeeeeeeeeeeees A 16 Gyrolab immunoassay workflow A719 A3 1 A3 2 A3 3 A3 4 Gyrolab workflow options ccccceecesceeceeceeseeseeees A 19 Baa Wizard RUM ess cece csieccsecesenel sdasbetcsiocd Sana seda ras da sses asus A 19 A312
5. Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H2 Custom Run workflow Example 2 Two Reagent combinations ie Po Mapping Pr ist im CD Type 0 Bioaff M Mandator Op Detection LJ Lui LJ Kd jo jo jo Jo jo Jo jo no gt PO PO Po jo Po Po gt fame jea fae fee lee le le aja oe je fee fee ite lee tI Structure niet Curve tB eI Structureintct Curve Standort ts Semeei Curve t Standarde Js I Structureinict Curve t stondaa Ps Structureinlet Curve 1 Blank 6 Structureinlet Curve i Standard tI Structureiniet Curve t Standard Pgs Structurcinfet Curv Standard 3 Pt I Structure inet Curve Blank i Je Structureinict Curve 2 Standard Js Structureiniot Curve 2 Standard 2 o o OE 4 Js Structurciniot cure 2 Bonk Js Structureintot Curve 2 Standard Jt Structureintot T Curve 2 Standard Js Structurcinlet Curve 2 Standard 3 O EPE eT Figure 10 Example of two Reagent combinations in the transfer list A Run using this transfer list will generate following in Gyrolab Evaluator Two different Reagent combinations Capture 1 Detection 1 Capture 2 Detection 2 Two standard curves in duplicates One for each Reagent combination Samples 1 and 2 will be quantified against both standard curves 1 and 2 Reagent combination 1 Capture 1 Detection 1 and Reagent co
6. Browse for desired folder location and click Export A User List in xml for mat is created Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 43 F2 Gyrolab Administration Tool Button Action Audit Trail Select a desired user and click Audit Trail button x Audit trail for user mial micke 2009 03 09 22 22 59 Edit user User Administrator Changed Password Change 2009 03 09 22 23 29 Edit user User Administrator Changed Password Change A record of all user editing that has occurred for the selected user is dis played e Click Export to export a text file of the user editing record e Click Close to close the Audit Trail dialog Disable Disable is used to disable an existing user Disabling a user will lock the account and prevent the user from logging into Gyrolab software e Select a user in the Users screen lists e Click Disable e Click OK in the Disable User dialog to confirm The selected user is kept in the Users screen list but when the disabled user is selected information about is displayed To re enable a disabled user assign the user a new password se Create User part in this table Click on Close in the top right hand corner of the Users screen to exit F 44 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2 Gyrolab Administration Tool F2 2 6 1 User level descriptions User level System Adm
7. Comments Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A H 15 H2 Custom Run workflow Step Action 4 Click Set to select Method The Select Method dialog is opened Select method and click OK Select Method Approved and Draft m E Custom methods Bioaffy 1000 amp Root BioaffyiCustom methodsiBioaffy 200 Bios fy 20 HC Content O folders 8 methods Runs Attribute Folders draft methods and approved methods allowed Wizard methods Service a Bioaffy 200 1 step v1 re Bioaffy 200 2 step C AD v1 aja a a a Bioaffy 200 2 step C D v1 a Bioaffy 200 3 step C A D low PMT v1 aja a Bioaffy 200 3 step C 4 D v1 F Bioaffy 200 4 step 2xC A D v1 a a a a Bioaffy 200 4 step C A 2xD v1 re Bioaffy 200 wash station 2 v1 a a 5 Click Import under Reagent List and the Import Reagent List dialog opens Browse to locate the desired Reagent list file prepared in Chapter H2 4 2 and click Import Import Reagent List AGyrolab CustomRuntists z Reagents_list_ProteinQuantification_3 xls E Reagent_list_ xls 12 Reagent_list_Protein Quantification 4 xls a Sample list Protein Quantification 4 xls H Sample list ProteinQuantification 3 xls H Transfer list Protein Quantification 4 xls Transfer list ProteinQuantification 3 xs File name Reagent _lst_Protein Quantification 4 xls Files of type fal fi
8. Example of error message Examples of error message below Possible cause Dislocated Controller cables Check the connection between the computer and the instrument Restart the instrument and the com puter If you cannot identify the problem or if the problem remains please contact Gyros for support Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A G 5 G 6 G1 Instrument issues Error message Possible cause Action PA Gyrolab Control P initializing System DETECTOR 0 initialization failed Station 1 initialized successfully SMARTLABEL O initialized successfully Station 3 initialized successfully INSTRUMENT 0 initialized successfully ROBOT O initialized successfully HEAD 0 initialized successfully SPINNER O initialized successfully SYRINGES O initialized successfully PINS 0 initialized successfully WASH O initialized successfully DRY O initialized successfully WASTE O initialized successfully CAROUSEL O initialized successfully WASH 1 initialized successfully BARCODE O initialized successfully Station 4 initialized successfully Station 5 initialized successfully DETECTOR O initialization failed Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A G1 Instrument issues G1 2 Instrument computer contact If the instrument looses contact with the computer an ongoing run will continue until it has finished The user inter
9. F 29 3 Gyrolab Result Database Explorer F 57 4 Gyrolab Database Backup Manager F 65 5 Gyrolab Set System Time F 67 Troubleshooting 1 Instrument issues c ccccccccccc cc coco G 3 2 Software issues cece e eres cece eee G 9 3 Application issues cece eee c cence G n Appendices 1 Products accessories and consumables H 3 2 Custom Run workflow eeceecceeees H 7 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A GYROLAB USER GUIDE A Introduction Contents A1 Az Important user information 008 A 3 ALA USEF MANUAIS sais cocvesccivecserscass casvedessascenvevccuseseaeevens cons A 3 Ats2 Intended USE oaccsisiesciccigacaceatsacenecertecsesacsteaeesacessaesbens A 3 A13 DISCIAIME sisends es ccesnatis soadsnseessaas ser nieessseaseaevereiesisaaseas A 3 Aile SYMBOL Seueri aa Era san ga data a pads elecountesauacentesaeaacs A 3 ATS User TAIN Gs us saccdendied vats se inss des EE EEEE AEAEE Sage A 4 ALG Trademarks essciscccsceacscotsccsenteasdacssseasseeetseebancadensedecsens A 4 Aky Patents cenana E R EAR A 4 A1 8 D SIBMATION cassa sas sum acer me sieniaa engana sa AAEE A 4 Introduction to the Gyrolab platform A 5 A2 1 Products included on purchase of a Gyrolab Instrument A 5 A2 1 1 GL Degasser Gyrolab XP sccccesecceececeesceeeecesenceneues A 5 A2 2 Gyrolab instrument front view
10. F Gyrolab Evaluator Results Explorer 04 11 54 45 AM e Select the new parent Folder and click OK e For Projects Enter a reason for the move The description is saved in the Audit trail Click Move Move Description Describe the reasons for your changes Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C 13 C2 Log in main menu functions and analysis administration Step Action 5 To rename an existing Folder or Project right click on the Folder or the Project and select Rename EE Gyrolab Evaluator Results Explorer Enter the new Folder or Project name and click OK E Rename Project 6 To remove an existing Folder or Project right click on the Folder or the Project and select Remove F Gyrolab Evaluator Results Explorer For Projects enter a reason for the removal The description is saved in the audit trail Click Remove E Remove Description Describe the reasons for your changes NOTE Folders can only be removed if they are empty C 14 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A C2 Log in main menu functions and analysis administration 2 2 3 3 Create new Project Step 1 2 3 Le 5 Action Click Manage in Gyrolab Evaluator start view and click Create Project in the Manage window The Save window opens In the folder structure in the left panel browse to des
11. File Thursday arco KB g Recycle Bin EB Gyrolab Result Database Explorer a B Main View E A CC 2009 01 29012 53 gr E BB 1 2009 01 29014 13 26 E DD 2009 01 29 15_44_35 E cc tonna ni anna na 237 Available files CD images file s are named according CD identity number Contains fluores cence images from the CD in a ZIP file e MainResult xml is the archive file It contains all results from a Run processed for further use by Gyrolab Evaluator or for export to a LIMS e Gyrolab Evaluator is the result file NOTE Files in Gyrolab Result Database have read only status Make a copy if editing is desired open the file click Save as and save a working copy of the file at a desired folder System Log holds the Audit Trail for a specific system All instrument events are logged Files in the System Log may be useful during troubleshooting Click File Close to close Gyrolab Result Database Explorer Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F3 3 F3 Gyrolab Result Database Explorer Customize database view It is possible to create a customized database view by filtering for result files with specific properties Customized views minimizes time consuming browsing for result files when Gyrolab Result Database holds a large quantity of results Step 1 Action To open Gyrolab Result Database Explorer Open Windows Explorer e Right click on Gyrolab Result Data
12. Supported design types Custom Wizard G Gyrolab Evaluator It is possible to perform four different administration actions Import Export Export Readable and Delete NOTE Select a target in the list to activate inaccessible task buttons Button Action Import Import is used to import a Target to Administration Tool to make it avail able for use in Gyrolab Control e Click Import to open Import Targets dialog Browse and select desired Target Targets must be in zm1 format e Click Import e Click OK in the Import Target dialog to confirm import The selected Target is now present in the list in the Targets screen Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 53 F 54 F2 Gyrolab Administration Tool Button Action Export Export is used to export Targets from Administration Tool Exported target can be imported into another Gyrolab system Select Target to export in the Target screen list e Click Export to open Export Targets window Browse and select desired export folder e Click Export e Click OK in the Export Targets dialog to confirm export The selected Target is now present in the selected export folder Export Export Readable is used to export a readable copy of a target This copy readable cannot be used in Gyrolab Control but it can be useful for example when contacting Gyros for support Select Target in the Target screen list e Click Export read
13. Browse Gyrolab evaluator result file name EvaluatorResult_ run _ date _ time xml Info This target generates a result file from a Gyrolab run for further analysis in Gyrolab Evaluator The result file is copied to the selected file destination The user sets the name and destination for the result folder and file name The settings from the last run of the current user will be pre selected Note that result files are always saved in Gyrolab Result Database ingot Taget Satins Expo Target seios Files are saved to the location specified in Gyrolab Evaluator result folder field and with the name specified in Gyrolab Evaluator result file name Settings are pre served from the user s last Run To import default settings for Gyrolab Evaluator result folder and Gyrolab Eval uator result file name lick Import Target Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Default Settings select GyrolabEvaluatorTargetSet tings xml and click Import To customize settings for Gyrolab Evaluator result folder and Gyrolab Evaluator result file name e To edit Gyrolab Evaluator result folder click Browse Browse and click Select to set new folder in the Select folder dialog To edit Gyrolab Evaluator result file name click in the field and edit TIP Macros can be used to construct file names and locations
14. e Browse the folder structure to the left in the Folders screen to locate a destination folder Select folder e Click Paste The folder is now located in its new folder structure position To paste a folder into another the destination folder must have status Allow folder refer to Edit folder on page 34 below Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 33 F 34 F2 Gyrolab Administration Tool Button Delete Create folder Edit folder Action Delete is used to delete folders from the folder structure e Select folder to be deleted in the folder structure in the left panel of the Folders screen e Click Delete e Click OK in the Delete Folder dialog to confirm folder deletion The folder is now removed from the folder structure Create folder is used to create new folders e Select a parent folder in the folder structure in the left panel of the Folders screen e Click Create folder e Inthe Create folder window give the new folder a name and set allow or deny status for Folders Runs Draft Methods and Approved Methods for the new folder e lick OK in the Create Folder dialog to confirm folder creation The new folder is now present in its specified folder position within the folder structure Edit folder is used to change folder name and to change status for allow or deny Folders Runs Draft Methods and Approved Methods in the folder Select folder to edit i
15. 14900 nM The concentration of biotinylated capture reagent should be high enough to satu rate the streptavidin column Normally concentrations of around 700 nM of bioti nylated protein is enough to saturate the column Fluorophore labeling of detection reagent The following solutions and consumables are required Desired Fluorophore labeling kit e Alexa Fluor 647 Monoclonal Antibody Labeling Kit 100 ug proteins gt 30 kDa e Alexa Fluor 647 Microscale Protein Labeling Kit 20 100 Lg proteins 20 150 kDa DyLight 649 Microscale Antibody Labeling Kit 100 ug 50 150 kDa Detection reagent Required solutions and consumables depend on which fluorophore labeling kit is used Please refer to supplier provided instructions for the fluorophore labeling kit Step 1 Action Preparation of detection reagent Refer to instructions for the fluorophore labeling kit for details The protocol in this chapter follows instructions given in Alexa FluorM 647 Monoclonal Antibody Label ing Kit Molecular Probes for antibodies and proteins gt 30 kDa Use 100 pl of 1 mg ml detection reagent antibody or other suitable detecting reagent for fluorophore labeling The reagent to be fluorophore labeled must be in a buffer free of stabilizing proteins for example BSA ammonium ions primary amines and sodium azide to obtain the best possible degree of labeling e Ifthe concentration of sodium azide in detection reagent solution is g
16. BL STD STD STD STD STD STD STD STD STD STD STD STD STD STA Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Sample 6 Sample 7 Sample 8 Standard A_Blank Standard A_Blank Standard A_1 Standard A_1 Standard A_2 Standard A_2 Standard A_3 Standard A_3 Standard A_4 Standard A_4 Standard A_5 Standard A_5 Standard A_6 Standard A_6 Standard A_7 Standard amp 7 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 MP1 lIndex M Sample Ty Sample Id Sample Gr Sample St Dilution F MP Identi Well M D1 D2 D3 D4 D5 D6 D7 D8 Al A2 A3 A4 A5 A6 A7 As A9 A10 A11 A12 B1 B2 B3 B 41 B3 Design run Step Action 2 Edit sample information as desired make sure that data is in accordance with Table B3 3 on page 42 e By default all samples and reagents of all types will be located on the same Sample Microplate To have Unknown samples on the Sample Microplate and place all other sample types on a Reagent Microplate delete all samples but unknowns from the generated Sample List The software will automatically place deleted samples on a Reagent Microplate during Loading List generation refer to Chapter B3 2 4 When evaluating results in Gyrolab Evaluator refer to Chapter C samples are sorted based on sample identity group and subgroup refer to Table B3 4 on page 43 for details Statistics such as average standard deviation and CV are available f
17. Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Step 3 Bs Start Run procedures Action Open the aluminium pouch and place the CD in loading position refer to Chap ter A2 2 1 Touch only the outer edge of the CDs Do not touch the surface of the CD Start the Run within 15 minutes after the CD has been taken out from its pouch Protect the CD from extended illumination from indoor lighting or sunlight since this may affect data quality Click Load in Load dialog or press CD button on the instrument refer to Chap ter A2 2 1 The system identifies the CD and the CD identity appears in the list on screen Repeat for all CDs NOTE The number of CDs required and the number that have been loaded are displayed at the bottom of the screen The LED will not be lit until all required CDs have been loaded B5 1 2 1 Confirm Wash Station Solutions and Pump Liquid If solutions and liquids are available Wash Station Solutions Wash Station Bioaffy wash station soluti 1 Confirm Connect Pump Liquids aa 1 7 HH Bioaffy pump liquid Confirm Connect Action Make sure tubings for wash station solution and pump liquid are connected and system is primed according to Chapter B2 4 Under Wash Station Solutions Highlight the Wash Station Solution and click Con firm Under Pump Liquid section Highlight the Bioaffy Pump Liquid and click Confirm Copyright 2015 Gyros Gyrolab User
18. Doo23573 A B 69 B6 After Run procedures and result export B6 1 3 Generated Gyrolab Control files There are four types of files generated by Gyrolab Control Files are available in the Gyrolab database and accessible through Gyrolab Database Explorer Copies of files may be available in other locations as set during run preparations The locations are displayed in the log panel after a Run Processing information 3 7 09 12 46 47 PM CET CD 0001020 001 Analysis of Detect PMT 25 completed Wrote C Gyrolab Results EvaluatorResult_ProteinQuantification 2_2009 03 07_12_42_10 xml Wrote C Gyrolab Results Administrator 2009 03 07 ProteinQuantification 2_12_42_10 GyrolabReport_ProteinQuantificati Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect ba Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect ba Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect ba Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect Ph Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect Ph Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect Ph Data moved successfully Files generated Run execution finished Hatc
19. F 66 O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F5 Gyrolab Set System Time Gyrolab Set System Time F5 1 Gyrolab Set System Time introduction Gyrolab Set System Time is a software tool that enables Gyrolab users to change system time in a controlled manner All changes of system time will be recorded in the audit trail Only System Administrators can change system time The System Administrator must also have Windows system privileges for the computer F5 2 Perform logged system time change Action Close all open Gyrolab software applications open including the server Select Start All Programs Gyros Gyrolab Control Gyrolab Set System Time Enter user name and password in the Login dialog box and click OK The user name and password is the same for all Gyrolab software For further infor mation on user and password administration refer to Chapter F2 2 6 Password must be changed if requested by the software for example when a new user logs in or if 90 days have passed since last password change Password may also be changed when desired by the user To change password e Mark the check box Change Password Enter current password in Password field new password in New Password field and confirm new password in Confirm Password field e Click OK NOTE User name and password are case sensitive NOTE The software will request the user to log in anew when the system has been inactive for 31 minu
20. NOTE Be careful using any manipulations of analysis settings and exclusions to avoid any undesired implications on reported analyte concentrations NOTE All changes of parameters are recorded in the Audit Trail Chapter C3 10 to enable full traceability of results Parameter Comment Evaluation Include blanks in Blanks included or excluded in curve fitting curve fitting Fit model The following fit models are available Five parameter logistic curve default e Four parameter logistic curve Straight line e Exponential curve e MMF curve Morgan Mercer Flodin Refer to Chapter C4 4 1 for descriptions and recommendation when to use which fit model Weight Following options are available e None e Concentration e Response default e Standard deviation response In general a weighted fit is more appropriate than an unweighted fit Limit of detection Following options are available factor e 2 standard deviations default value e 3 standard deviations Acceptance Criteria Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A C 41 C4 Analyze data Parameter LLOQ conc ULOQ conc T Test CV conc Average Bias Matrix Settings Neat Diluted Comment Lower limit of Quantification For Unknown samples the LLOQ defines the lowest level of analyte concentration measurable e For Standards Quality Controls and Calibration Controls the LLOQ defines the border b
21. P0004354 H D0023573 A B 73 B6 After Run procedures and result export B 74 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A GYROLAB USER GUIDE C Data analysis Contents 1 Introduction to data evaluation 5 1 1 Gyrolab Evaluator introduction ccccescesceeceeeeeeeees 5 2 Gyrolab Evaluator main features cccceeceeceeceeeeeeeees 5 1 21 Data analysis sssesecasesaspesosasesasnaai dis polpan stages cousveesancese 5 122 2 Analysis SCTUINGS scsceciciesssipcsteecstbescdbavendewsastaaedpercioateces 5 1 2 3 Storage Of AMAlYSES ce ceeeee tec eeeeceeeeceseeeesoeeteeeeteees 6 1 2 4 Traceability of analyses cee eeeeeeeeeeeeeeeeeeeeeeneeeenes 6 C1225 Exportof reports ses civ sccencdivvessivess ied EEEE EE OTER eaa C 6 Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A C2 Log in main menu functions and analysis administration C7 Qa Startand IOBAN ies sesedsdadiscaceceedstcdcdacstause OE ENEA 7 2 2 Main Menu FUNCTIONS cece cece ce eececeeesceeceeesceeeeees C 9 2 2 1 New Analysis menu sssssssssssssssssssssssssssesssseesssseeesesses C 9 2 2 2 Open Project MeNu eee ee cece ececeeeeeececeeeececeertceees C 10 2 23 Manage MENU uses scien esc gases dives deesieds alec sales edeesaavencen C 10 2 2 4 Recent Runs menu ccccscececscscecscorercenracceseseneneners 16 2 3
22. Poooy354 H D0023573 A F 5 Fi Gyrolab Control Step Action E Click OK to log in or Exit to close the dialog box without logging in Once logged in the main menu will appear ul F1 1 2 Gyrolab Control main menu F1 1 2 1 Main menu overview The start screen in Gyrolab Control holds the main menu from which all actions are initiated The main menu also displays instrument access status refer to Chapter F1 1 3 instrument mode refer to Chapter F1 1 3 14 and functionality for alarm handling GYROS Figure 1 Main menu The main functions of Gyrolab Control are represented by buttons on the main menu Only one function at a time can be activated Select a function by clicking on the function button and the panel for the selected function is displayed on the screen Buttons may be accessible in the example above Initialize System inaccessible in the example above Prime button or hidden in the example above Execute Run button F1 1 3 Main menu functions Button LED Function Design Method _ Launches the Design Method screen to create new methods edit method refer to Chapter F1 1 3 1 Design Run Launches the Design Run screen to create new edit delete Runs refer to Chapter F1 1 3 2 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Button LED Execute Run Prime Maintenance Initialize System Configure System CD Information Logout Help About View Alarm Instrument
23. Quality Controls and Unknown samples and their replicates are defined in the worklists Note that your LIMS must generate worklists in certain formats in order to be able to interact with Gyrolab Control software Contact Gyros for more information It is possible to make one LIMS worklist per CD or one LIMS worklist for all CDs in a Run Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A D 41 D 42 D3 Gyrolab LIMS Interface D3 4 Prepare LIMS Run Step 1 2 Action Click Execute Run on the Main menu Browse and select desired Run from the list and click OK Runs that are not complete and thus not ready to execute are marked with a zigzag line More information is needed before the Run can be 9 executed A screen is opened LIMS license and Run data is displayed Run LIMS Run 001 One Work List per CD M List Loader workListLoader X Number of samples O Segments Used VI KA 0 Info Work List File Clear E J AB m pm PA J o Info Work List File Clear PA KA o into Work List Fie dem NY VON Ay j o mno Work List Fie cem KY o o mo Work List File cem X gt One MP per CD IV Loading List e List Loader file sets rules for how to import worklists Choose the WorkList Loader option in the drop down menu Define number of work lists e Check One Work List per CD box if multiple work lists one per CD has been defined in the LI
24. This column is only shown for Unknown and Quality Control samples and only if there are any samples with Group information in the Experiment The standard deviation of calculated analyte concentrations of replicates of a sample group or sample subgroup NOTE This column is only shown for Unknown and Quality Control samples and only if there are any samples with Group information in the Experiment It is possible to add comments to individual samples Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Cy Analyze data 4 4 Analysis settings The finding of optimal curve fit model and other analysis settings are important for accurate calculation of results It is possible to modify different settings and evaluate the analysis results For example different algorithms can be selected and outliers in Standard series can be excluded It is recommended to use similar Settings in routine analyses as was found to be optimal during assay development It is possible to lock settings for a Project to ensure identical analysis settings on all samples performed within that project We use the Levenberg Marquardt algorithm LVM which minimizes the sum of squares of the vertical distance between the observed data and the curve or fitted data residuals When weighting is used the following is minimized in order to find best curve fit gt Ydata Yfit Weight 2 It can also be expressed as X Ydata Yfit 2 x 1 Weight2
25. Wash solutions For recipe refer to Chapter E1 Cover filled wells temporarily during preparation of microplates for example with PCR lids to avoid evaporation When a microplate is loaded apply Microplate Foil using a Microplate Foil Adapter Instruction is supplied together with Microplate Foil Adapter Centrifuge microplates at 3000 x g for two minutes This is done to eliminate bubbles in the microplate wells and to ensure that the samples are at the bottom of the wells Examine microplates after centrifugation to make sure that no bubbles are present Do not stack microplate foil sealed microplates on top of each other The microplate foil may get perforated which may cause evaporation from wells Contamination risk Microplate wells must not contain more than 100 pl of any solution Needles are not washed higher than 1 cm Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 51 Bu Prepare samples and reagents B4 2 Instructions for Gyrolab xPlore By 2 1 Reagents and samples By 2 1 1 Capture reagent 1 Vortex Capture reagent stock solution gently 2 Dilute in PBS T or Rexxip to working concentration usually 700 nM for an antibody this corresponds to 0 1 mg ml For minimum required reagent volumes please refer to the Gyrolab Control Loading list Chapter B3 2 4 NOTE Use fresh Capture reagent Use new aliquots from the Capture reagent stock solution kept in refrigerator or freezer at least ever
26. a Standard series Unknown Calibration Control Quality Control sample is repeated on different CDs it must be placed in separate wells in the reagent microplate and on separate rows in the Reagent list in order to avoid evaporation during the run The number of wells for each Standard series Unknown Calibration Control Quality Control sample shall correspond to the number of CDs in the Run on which the sample should be used on Each row in the Reagent list must have unique name Refer to examples in Chapter H2 9 2 It is possible to group reagent combination together for subsequent data analysis by use of a common Experiment name refer to Chapter H2 4 4 and Chap ter for details Enter reagent type or sample type for reagents and samples For more information on sample types refer to Chapter A3 3 2 e RR Reagent regular wash etc RB Reagent biomolecule capture or detection reagent e STD Standard series e C Calibration Control e BL Blank e QC Quality Control Enter the concentration for each reagent Mandatory for Standard series STD Blank BL Calibration Control CC and Quality Control QC Not applicable for Reagent regular RR and Reagent biomolecule RB reagents e For Quality Control QC samples enter the undi luted concentration if diluted Enter the dilution factor in column E Enter the unit of concentration for example pM mg ml Mandatory for Standard series STD Bla
27. labelled M are mandatory columns labelled 0 are optional and columns labelled N A are not used es jun 4 us na Figure H2 2 Reagent list template NOTE Cells with a red mark in the upper right hand corner have a comment attached The comment is a description of the information to be included in the column cell 3 Fill in reagent information according to Table H2 1 4 Click File Save As to save the Reagent list in a folder accessible by the Gyrolab com puter Do not save the file in the C ProgramData Gyros Gyrolab Tem plates Lists folder This folder should be kept for list templates only 5 Click File Close to close the Reagent list Reagent List Mandatory Information item Optional MP type Mandatory Type of microplate NOTE Use only microplates recommended by Cell B1 Gyros that is MP96 PCR Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H2 Custom Run workflow Reagent List Mandatory item Optional Name Mandatory Column A Type Mandatory Column B Concentration Mandatory NIA Column C Unit Column D Information This name is the identity of the reagent and must cor respond to the name specified in the transfer list The name of the reagent is defined by the user It is case sensitive so take care to copy it exactly Enter each reagent name on a new row Check cell A2 Name for list of allowed characters For multi CD runs If designing multiple CD Run where
28. 0 lew Y coordinate value 31 5 Alignment of Needle 9 started lignment of Needle 9 completed hen X coordinate value 0 0 lew Y coordinate value 36 0 Alignment of Needle 10 started lignment of Needle 10 completed hew X coordinate value 0 0 lew Y coordinate value 40 5 Alignment of Needles finished Hatch unlocked 2 Click Finish If the alignment process fails repeatedly please contact your local Gyros office refer to www gyros com for contact details F1 2 3 8 CD information CD Information is used to read the information stored in the CD tag Step Action 1 Click CD information The CD information screen opens 1 Place CD on loading postion in Gyrolab and close the hatch 2 Read CD 3 CD information Type Identity Number of free segments CD is expired Process status 2 Place CD of interest in the instrument CD loading position and close the hatch refer to Chapter A2 2 2 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 25 Fi Gyrolab Control Step Action 3 Click Read CD The following information of the CD is given Type type of CD e Identity identification number of CD Number of free segments number of unused segments on the CD e CD is expired Do not use the CD if the CD is expired Process status Do not use the CD if the status is Unknown 4 Open the hatch and remove the CD from the Gyrolab ins
29. 10 1 0 5 Oracle Net ORANNZSBB10 DLL Shared dll 3 0 10 97 Shared Syncfusion GridCommon WPF dll 7 103 0 21 Synefusion GridCammon WPF NOTE a a E 5 a 8 Logic dil 3 0 10 97 M Logic AuditTrail dil 3 0 10 97 AuditTrail databaseConfig XML Document K Extreme Numerics dll 3 1 8350 0 Extreme Numerics oraoccit0 dll 10 1 0 5 Oracle C Call InterFace sha a a Syncfusion Core dil 7 103 0 21 Synefusion Core teechart wpF dll 35 3274 30664 Steema TeeChart WPF Components dll 3 0 10 97 Components DatabaseConfigTool DatabaseConfigTool Gyros AB Gyrolab Evaluator Gyrolab Evaluator Gyros AB An 1 04 Oracle Call Interface oraociei10 dll 0 0 0 0 Oraele Call Interface Instant Syncfusion Grid WPF dll 7 103 0 21 Synefusion Grids WPF Windows Vista and Windows 7 UAC User Application Control may not allow to select DatabaseConfigTool Right click on the DatabaseConfig Tool icon administrator user privileges required to Right click on the DatabaseConfig Tool icon Run as administrator and select to allow database configuration in the dialogs that follow Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C5 Gyrolab Evaluator installation on office computer Step Action 2 The Database Config Tool opens Database Config Tool x Host localhost Enter the name of the Gyrolab database in the Host field e If Gyrolab
30. 6 Sample and reagents preparations This chapter describes preparation of capture and detection reagents standard sample series Calibration Controls Quality Controls and unknown samples as well as the distribution of samples and reagents in microplates For preparing reagents for a multi CD Run refer to Chapter H2 9 2 for details The following solutions and reagents are required e PBS T for recipe refer to Chapter E1 2 e Capture and Detection reagents Standard Protein e Rexxip buffer Refer to Product information sheet for Rexxip buffers for recommendations on buffer selection H2 6 1 Capture reagent and detection reagent Prepare capture reagent and detection reagent according to Chapter H2 6 1 and Chapter H2 6 2 respectively For minimum required reagent volumes use formula below Reagent volume 2 5 pl x Number of segments 15 ul For correct number of segments refer to Transfer list Chapter H2 4 3 NOTE In multiple CD Runs reagents that are used on more than one CD must be placed in different microplate wells one per CD refer to Chapter H2 4 2 Calculate minimum required volume per well using the formulas above H2 6 2 Standard series and Calibration Controls Prepare Standard series and Calibration Controls according to Chapter H2 6 2 For minimum required sample volumes use formulas below For Bioaffy 20 HC and Bioaffy 200 e Standard volume 0 5 pl x Number of replicates 2 5 pl For Bioaffy 1
31. A WARNING Sodium azide NaN is very toxic Handle with care Composition 150 mM phosphate buffer 1 5 M NaCl 0 2 NaN 150 mM PBS Chemicals required 3 4 g NaH PO Mw 120 g mol 1000 ml 17 3 g Na HPO Mw 142 g mol 87 6 g NaCl Mw 58 44 g mol To prepare 1000 ml Dissolve all chemicals in 1000 ml deionized distilled water Add 10 ml 20 NaN pH 1x PBS should have pH 7 4 Storage Store at room temperature Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A E 3 E Recipes 10x PBS Composition Chemicals required 1000 ml To prepare 1000 ml pH Storage 150 mM phosphate buffer 1 5 M NaCl 150 mM PBS 3 4 g NaH PO Mw 120 g mol 17 3 g Na HPO Mw 142 g mol 87 6 g NaCl Mw 58 44 g mol e Dissolve all chemicals in 1000 ml deionized distilled water Filter buffer through 0 22 pm filter and store at room tempera ture 1x PBS should have pH 7 4 Store at room temperature Use of pre made PBS 1x or 10x Pre made PBS can be used in the Gyrolab instrument provided that the buffer composition is according to our recommendations stated above Additional important aspects regarding pre made PBS buffer e It should be free of Ca and Mg Add Sodium azide prior to connecting the PBS buffer to the Gyrolab instrument NOTE For PBS buffers ensure they are filtered through 0 22 um filter prior to connection to the Gyrolab instrument Store at room temperature 1
32. ADA Software and receive a licence To register the licence Save the licence file to the hard drive of the instrument computer at the destination C ProgramData Gyros Licenses Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 35 D2 Gyrolab ADA Software D 36 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D3 Gyrolab LIMS Interface Gyrolab LIMS Interface Visit www gyros com for the latest updates on available software modules D3 1 Introduction to Gyrolab LIMS Interface workflow Gyrolab LIMS Interface is a software add on module for Gyrolab Control version 5 2 or higher and is compatible with the generic raw data file for Watson LIMS 6 4 The software module is designed to support users that carry out experiment set up and data analysis within a LIMS system Worktist defined in Gyrolab LIMS interface Raw data stored in Raw data stored and Watson LIMS checks the list Gyrolab database analyzed in Watson LIMS Gyrolab database The LIMS workflow Chapter D3 differs from the standard Wizard run design Chapter B Sample preparations run start and run finish procedures are the same for both workflows and described in Chapter By Chapter B6 Hence only LIMS module specific parts of performing a run is described in this section Step LIMS Run Create or Edit e Select Wizard Run design type e Select LIMS Run design type Run Enter experiment parameters Enter experiment pa
33. Delete Action Export is used to export Microplate files from Administration Tool Exported microplate can be imported into another Gyrolab instrument e Select Microplate file to export in the Microplate screen list Click Export to open Export Microplate window e Browse and select desired export folder e Click Export e Click OK in the Export Microplates dialog to confirm export The selected Microplate file is now present in the selected export folder Export Readable is used to export a readable copy of a microplate This copy cannot be used in Gyrolab Control but it can be useful for example when contacting Gyros for support e Select Microplate in the Microplate screen list Click Export readable to open Export Microplate in readable format dialog Browse and select desired export folder e Click Export readable e Click OK in the Export Readable Microplate dialog to confirm export readable The selected Microplate file is now present in a readable format in the selected export folder Delete is used to delete microplate files Select Microplate file to be deleted from Microplate screen list e Click Delete e Click OK in the Delete Microplate dialog to confirm deletion The selected Microplate file is now deleted from the Microplates screen list Click on Close in the top right hand corner of the Microplates screen to exit Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2
34. Delete Delete is used to delete CD files Select item to be deleted from CD screen list Click Delete Click OK in the Delete CD dialog to confirm deletion The selected CD is now deleted from the CDs screen list Click on Close in the top right hand corner of the CDs screen to exit Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2 Gyrolab Administration Tool F2 2 8 Microplates Click on Microplates on the main menu to access the Microplates screen The Microplates screen lists available Microplates Close gt Microplates System version supported 1 2 MP96 PCR Version Not valid System version 1 gz A MP96 PCR It is possible to perform four different administration actions Import Export Export Readable and Delete NOTE Select a microplate in the list to activate inaccessible task buttons Button Action Import Import is used to import a Microplate file to Administration Tool to make it available for use in Gyrolab Control lick Import to open Import Microplate dialog Browse and select desired Microplate file Microplate files must be in zml format Click Import e Click OK in the Import Microplate dialog to confirm import The selected Microplate file is now present in the list in the Microplates screen Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A F 49 F 50 F2 Gyrolab Administration Tool Button Export Export readable
35. Function Maintenance Launches the Maintenance screen to perform instrument prim ing and or a cleaning method refer to Chapter Fi 2 3 5 Initialize System Starts system initialization refer to Chapter F1 2 3 6 Configure System Launches the Configure System screen to change the system configuration refer to Chapter F1 2 3 7 CD Information Launches functionality to read information from a CD tag Logout Logout from Gyrolab Control Help Launches the help system refer to Chapter F1 2 3 10 About Displays information on software versions and licences refer to Chapter F1 2 3 11 View Alarm Displays information about alarms refer to Chapter F1 2 3 12 Instrument access LED Indicates instrument access status refer to Chapter F1 2 3 13 Instrument mode LED Indicates instrument mode refer to Chapter F1 2 3 14 F1 2 3 1 Design Method Design Method function is used for setting up new or edit existing Methods to be used in Runs Methods can be customized by Gyros to suit specific needs Contact Gyros for more information F1 2 3 2 Design Run The information required to perform an immunoassay on the Gyrolab instrument is collected in a Run The function Design Run is used to create edit and delete Runs Input data for a Run differs depending on which design type which type of Run is used e Fora detailed description of how to create or edit Wizard Runs refer to Chapter B3 2 2 e Fora detailed description of how to create or edit LIM
36. Gyrolab Evaluator Audit trail cece ccc eceeeeneeeeeeeees 16 2 4 Close Gyrolab Evaluator cccccesceeceeeceeceeceeseeeseesees 16 Manage analysis projects 0ee eee C 17 317 Project ViEWesercrisciiriiicccsinrginceienie n n aas C 17 3 2 Add and remove run in Project ssssessssssssssssseeessssess C 19 3 3 Add remove and export analyses in a Project C 19 3 4 Open d Projeclas sasesessisa restantes temer EE NTN ada 20 3 5 Savea Projet cieren ci vinici iei en ee seria va rann teats C 20 3 6 COSE d Projet cccccissidsccvaveradsaaiievacenceechase E EEk C 21 3 7 Approve Unapprove a Project ssssssssssssssssssessseesssseees C 21 3 8 Set analysis settings for a Project sssssssssssssssesessesess C 22 3 9 Manage Folder Structure sssssssssssssssssssssssseeesessssses 26 3 10 Audit trail for Projects ccccccesceeceeeceeceeeeesseeseeees 26 3 11 Reports and report data export sssssssssesssssseessssssees 27 C3 1t 1 Report contenta css cise sdavecdessees seineadeies dies a vendo Cones dc ose 27 3 11 2 View print and export report data ecce ee 27 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Analyze Wald 22244440005 ia EERE E SERED 29 Cy 1 Quantification module ccc cce eee e eee eeceeeeeeeeeseeees 29 4 2 Data Comparison MOMUIE cceecceecesceeceeeeeeeeeseeecs 34 C4 3 Result d
37. Gyrolab software This User has user level System Administrator and that user can create and edit other users with different user levels NOTE Service personnel from Gyros must be given access as a local administrator if requested EEE O Users System version supported 1 Q mial Name micke Role System Administrator System version 1 Gyros AB Gyros AB Operator admin Administrator System Administrator mial micke System Administrator service Service Service It is possible to perform six different administration tasks Create User Edit User Disable User Export User List and Audit trail NOTE Select a user in the list to activate inaccessible task buttons Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Button Create User Edit User Export User List F2 Gyrolab Administration Tool Action Create User is used to create a new user This action requires System Administrator privileges e Click Create User User name Your current password Not applicable C Name New password cce Role fOperator Confirm new password Role privileges IE Open Method EE Delet IB create New Method EE Edit Mathod EE confina Suctom E Evaruta Run e In the Create New User dialog Enter User Name Short name of user Enter Name Complete name of user Select Role user level Select one user privilege category of System Administrator Method Developer Project Ma
38. M Sodium bicarbonate buffer stock Composition To prepare 1 ml Storage 1M NaHCO Add 1 ml deionized water to 85 mg of NaHCO Store at 4 C for maximum two weeks Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A E1 Recipes E1 2 Working solutions F1 2 1 Bioaffy Pump Liquid 1x PBS 0 02 NaN3 0 01 Tween 20 Purpose Used for the five Syringe Pumps Composition 15 mM phosphate buffer 150 mM NaCl 0 02 NaN 0 01 Tween 20 To prepare 250 ml Mix 25 ml 10x PBS with 0 2 NaN with 225 ml deionized dis tilled water Add 250 pl 10 Tween 20 Required volume 250 ml is needed for 1 5 CDs F1 2 2 Bioaffy Wash Station Solution 1 1x PBS 0 02 NaN3 0 01 Tween 20 Purpose Used for the Wash Station Composition 15 mM phosphate buffer 150 mM NaCl 0 02 NaN3 0 01 Tween 20 To prepare 1000 ml Mix 100 ml 10x PBS with 0 2 NaN with 900 ml deionized dis tilled water e Add1ml10 Tween 20 Required volume 1000 ml for1 CD 2000 ml for 2 5 CDs E1 2 3 Bioaffy Wash Station Solution 2 Select option depending on application Gyrolab Wash Buffer pH 11 Purpose Used for the Wash Station 2 Composition Gyrolab Wash Buffer pH 11 To prepare 1000 ml Dissolve one pack 10 g of Gyrolab Wash buffer pH 11 powder in 1000 ml deionized destilled water e Filter 0 22 um Required volume e 1000 ml for1 CD 2000 ml for 2 5 CDs O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D00
39. Maintenance 5 To Remove a property from the Property list Select the property to remove Application Bioaffy 20 HC SIA Method Bioaffy 20 HC v1 SIA appl User Jan Henriksson e Click Remove button The selected item is now removed from the Property list 6 Click OK when all wanted properties are Included and or Excluded 7 The customized database view including corresponding Results and System Log folders is now available below the main view in the tree structure in Gyrolab Result Database Explorer window Gyrolab Result Database Explorer View of NOT User Administrator System Log BIA 4 Gyrolab Result Database Explorer Wiew of NOT User Administrator System Log se Local Disk C o mw10029 DVD RAM Drive D o Gyrolabws 01 E amp Control Panel a q My Network Places yg Recycle Bin EB Gyrolab Result Database Explorer E EB main view E us Results E ias System Log a B View of NOT User Administrator E os Rest F 60 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A F3 Gyrolab Result Database Explorer Step Action 8 To remove a customized database view Right click on the customized database view to be removed Select Remove View 9 Gyrolab Result Database Explorer Main View Results a My Documents a p My Computer Local Disk C 3 DVD RAM Drive D G Control Panel g My Network Places E Recycle
40. Note that identical Standard Calibration Control concentrations are distributed to separate microplate wells for each CD in experiments using more than one CD B4 1 1 4 Unknown samples and Quality Controls Quality Controls are prepared in the same manner as Unknown samples Step 1 Action Thaw sample vials completely on ice NOTE Avoid repeated freeze and thaw cycles of samples Aliqout samples before freezing Vortex the vials gently For serum and plasma samples and all other samples that may contain particulate matter with cell debris or pellet centrifuge 3000 x g for 15 min at 8 C Dilute samples to concentration specified in the Loading List using appropriate Rexxip buffer The dilution factor needs to be optimized for each analyte assay format and matrix Dilution should be made so that buffer characteristics are as similar as pos sible for all samples Ensure sufficient mixing Use microtubes for mixing of small samples volumes Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B4 1 2 Step 1 NOTE NOTE B4 Prepare samples and reagents Load microplates Action Add reagents samples and solutions to microplates Sample volume microplate name and microplate well is specified in Gyrolab Control Loading list Chap ter B3 1 4 e Capture reagent e Detection reagent Unknown samples e Quality Controls e Standard series samples e Calibration Controls e Blanks
41. Poooy354 H D0023573 A A3 Gyrolab immunoassay workflow A3 3 Run setup and recommendations A Run is a collection of information required to perform a set of experiments using the Gyrolab platform The run is designed in and executed by Gyrolab Control software After each Run results and statistics are analyzed with Gyrolab Evaluator software Resulting column profiles can be examined using Gyrolab Viewer to facilitate assay optimization and evaluation of possible outliers The concentration of analyte in each unknown sample is quantified against a standard curve It is also possible to include quality control samples in a run Refer to Chapter A3 3 1 Chapter for recommendations on how to set up a run that contribute to good data quality and facilitates data analysis A3 3 1 Standard samples and Blanks In general using Standard samples with many different concentrations in a Standard series facilitates generation of a high quality standard curve However this requires a larger number of microstructures on the CDs leaving fewer microstructures available for analysis of unknown samples Set the highest and lowest concentration in a Standard series to be higher and lower respectively than the expected concentration range of the Unknown samples This ensures the standard curve to be in a range where unknown concentrations can be determined Use serial dilution steps of five or lower In addition to the Standard concentrations at leas
42. Run NOTE Following examples refers to the use of CDs with 14 segments available Example 1 2 CDs Run with standard curve repeated for each CD Figures included in this section show reagent and transfer lists from a Run with the purpose to use the same Standard series on a different CDs in a multiple CD Run This requires that the Standard series samples and reagents are given different names in the reagent list different Reagent combination names and are put in different wells in the micro plate even though it has the same content By giving the different Reagent combinations the same Experiment name they will be analyzed as one entity in Gyrolab Evaluator Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H 25 H2 Custom Run workflow Curve CD 1 Standard 1 Curve CD 1 Standard 2 cD Curve CD 2 Standard 1 Curve CD 2 Standard 2 Curve CD 2 Standard 3 Figure 13 Reagent list with the same Standard series repeated on a different CD in the same Run RE Ds Tomei cme core o Tomei Tomo o PR O PR s Seneuna ouve coraan somone cue corn 6 Tomei Tomo r RO oue corsas Pg Tome ou corsara n RA O RT o Tomei Tomei L e RR PT E RR PR s RA owe ooze gente Tome r foneeme foume coz sunao O e er ouve coz sunao ee Figure 14 Transfer list with the same standard curve repeated on a different CD in the same Run A 2 CD Run using a reagent an
43. Run execution started 3 7 09 12 42 10 PM CET CD 0001020 001 Initial needle wash started 3 7 09 12 42 10 PM CET CD 0001020 001 Initial needle wash completed 3 7 09 12 42 15 PM CET CD 0001020 001 Particle wash 1 started 3 7 09 12 42 22 PM CET CD 0001020 001 Particle wash 1 completed 3 7 09 12 42 22 PM CET CD 0001020 001 Particle wash spin 1 started 3 7 09 12 42 23 PM CET CD 0001020 001 Particle wash spin 1 completed 3 7 09 12 42 28 PM CET CD 0001020 001 Particle wash 2 structure started 3 It is possible to pause or abort an ongoing run e To stop an ongoing Run click Abort The Run is immediately terminated and cannot be resumed Remove all CDs and microplates as described in Chap ter B6 1 1 Do not use results or CDs from aborted Runs as there is a risk that data or the CDs may have been corrupted The pause an ongoing run click Pause To resume the Run click Resume 4 The system stops automatically when the run is completed Click Finish Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Bs Start Run procedures B5 2 Instructions for Gyrolab xPlore B5 2 1 Load Gyrolab instrument Before starting the instrument loading procedure ensure that run preparations and sample and reagent preparations have been performed according to Chapter B3 and Chapter Bu Step Action 1 The following screen should be shown after the clicking OK in the last step in Ch
44. Select a CD in the list to activate inaccessible task buttons Button Action Import Import is used to import a CD into Administration Tool to make it available for use in Gyrolab Control e Click Import to open Import CD dialog Browse and select desired CD CDs must be in zm1 format e Click Import e Click OK in the Import CD dialog to confirm import The selected CD is now present in the list in the CDs screen Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A F 47 F 48 F2 Gyrolab Administration Tool Button Action Export Export is used to export CDs from Administration Tool Exported CD can be imported into another Gyrolab instrument Select CD to export in the CD screen list Click Export to open Export CD window Browse and select desired export folder Click Export Click OK in the Export CDs dialog to confirm export The selected CD is now present in the selected export folder Export Export Readable is used to export a readable copy of a CD This copy cannot readable be used in Gyrolab Control but it can be useful for example when contact ing Gyros for support Select CD in the CD screen list Click Export readable to open Export CD in readable format dialog Browse and select desired export folder Click Export readable Click OK in the Export Readable CD dialog to confirm export readable The selected CD is now present in a readable format in the selected export folder
45. Serial number GW10159 and higher El CO CO o 6 Figure 4 Gyrolab xP instrument rear view serial number GW10159 and higher No av FUN Part Power switch 0 Off On Power cable connection VGA connection Network connection RJ45 USB connectors 3 pcs USB for instrument control For service purposes only Co pyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A A2 Introduction to the Gyrolab platform A2 3 2 Gyrolab xPlore Figure 5 Gyrolab xPlore instrument rear view No Part 1 Instrument label 2 Mains power switch 0 Off On 3 Power cable connection 4 USB for instrument control A 12 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A2 Introduction to the Gyrolab platform A2 4 Gyrolab CD microlaboratories Gyrolab CD microlaboratories have been designed for efficient assay development and simple optimization for different analytes and different assay formats All steps in a traditional immunoassay are automated miniaturized and integrated into the CD Within each CD specific functional units in microstructures perform the individual assay steps required Microstructure columns are pre packed with streptavidin coated beads The specificity of the microstructure is determined by addition of biotinylated reagents allowing for total flexibility in assay design For more detailed CD specifications and recommendations ref
46. and choose between avail able file formats Excel XML Spreadsheet xIs or Text file txt Click Save The exported data can be used to create 2D overlay plots in other analysis software for example Microsoft Excel 8 Click Cancel to close the Gyrolab Viewer window and return to the analysis module window Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D1 Gyrolab Viewer D1 3 Interpreting Gyrolab Viewer images All interactions in the CD microstructure is generated under controlled flow conditions The binding profiles produced by Gyrolab Viewer is a representation of the signal intensity in each Gyrolab CD microstructure and illustrates the analyte s position in the microstructure Interaction between the capture reagent and the analyte molecule affects profile characteristics Characteristics of an ideal binding profile The signal is not saturated i e the maximum signal intensity within the binding profile is lower than 1 The binding profile has a sharp peak and has a narrow distribution in the radial direction indicating high affinity between capture reagent and analyte e No signal spikes are visible within the binding profile Figure 1 Example of desired binding profile in Gyrolab Viewer D1 3 1 Using Gyrolab Viewer to optimize PMT setting for a run The images produced in Gyrolab Viewer are useful when selecting the optimum PMT setting for a Gyrolab Run The fluorescent signal fro
47. and vacuum of the CD stations Step Action 1 Close the Gyrolab instrument hatch if open Click Initialize System on the Main menu The Initializing System dialog box is dis played as initialization proceeds F Initializing System Home positioning started Details of the initialization can be viewed by clicking on the Details button NOTE To re initialize the system click on Logout in the Main menu Choose Restart from the drop down menu in the Shut Down dialog then click OK 2 Click Finish when initialization is complete F1 1 3 7 Configure System The Gyrolab instrument is delivered with a pre programmed configuration set up and system priming protocol This section explains how to configure the system and alter these settings CAUTION Contact Gyros before changing any configuration default settings NOTE Only user with user levels Method Developer or System Administrator can configure the system refer to Chapter F2 2 6 Access the Configure System screen Step Action 1 If the instrument is not initialized click Initialize on the main menu NOTE The system must be initialized in order to access the Configure System screen 2 Click the Configure System button on the main menu Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Fi Gyrolab Control Step Action 3 Select desired tab refer to chapters Configure Syringe Pumps on page 9 to Con figure CD stations on page 1
48. are included in the Audit Trail Significant digits or number of decimals can be set for the current Project e If Lock all settings box is ticked the Analysis settings are locked for all analyses within the project and for all users Only users with user level System Adminis trator can edit Analysis settings or change Lock all settings status 8 In Plug in Selection tab mark the check boxes to select what software modules and plug ins to be available in the specific Project Analysis Settings ADA Analysis Quantification General Plugin Selecton Check the plug ins to use E Quantification Serial Dilution Data Comparison 7 ADA Analysis 9 Click OK Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C 25 3 Manage analysis projects Step Action 10 The Save Description window opens Enter a change description in the text box e Click Save The settings made will be applied on all new analyses made within the selected Project 3 9 Manage Folder structure Projects are saved in a Folder structure Only user with user levels Project Manager or System Administrator can make changes in the folder structure Refer to Chapter 2 2 3 for more information on Folder structure 3 10 Audit trail for Projects All Projects modifications for example adding removing Runs changing Run data with analysis modules etc are logged together with information on user identity time
49. between runs over extended periods of time A set of Quality Controls should be acquitted and stored under the same conditions as your unknown samples Selected Quality Controls should be prepared independently from each other and from Standard series samples Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A 21 A3 Gyrolab immunoassay workflow A3 4 Assay optimization To ensure the best possible data quality each assay must be optimized A3 4 1 Capture reagent concentration A concentration of 700 nM biotinylated capture reagent is sufficient to saturate the column For each new batch of capture reagent perform a test run analyzing samples with known concentration Study resulting column profiles using Gyrolab Viewer refer to Chapter D1 to ensure that the target protein is sufficiently enriched at the top of the column A3 4 2 Detection reagent concentration The degree of detection reagent fluorophor labeling may affect immunoassay performance When developing a new assay perform a titration to determine the optimal detection reagent for the specific assay When labelling a fresh batch of detection reagent for an assay that has already been optimized a titration is not needed provided that the fluorophor to protein ratio is within recommended values Chapter B1 2 A lower detection reagent concentration gives lower background noise which allows for increased assay sensitivity If the desired measurement is higher
50. dialog opens Connect tubings for Standby solutions and click OK Standby procedures will start Standby procedures means priming Syringe Pumps and Wash Stations with Standby Solution It is recommended to put system in Standby mode at least three times a week For more information refer to Gyrolab Instrument Guide for Gyrolab xP B6 1 2 How to turn Gyrolab off Before turning the instrument off for a longer period of time it is recommended to put the instrument in Standby mode see Gyrolab Instrument Guide for Gyrolab xP Step Action 1 Right click on the Gyrolab server icon and select Instrument Go to Offline state This is required before the instrument controller computer can be shut down 2 Press OK to Acknowledge Instrument Offline State 3 After about 10 seconds right click on the Gyrolab server icon and select Instru ment Shutdown This will power off the instrument controller computer in a con trolled way 4 Press OK to shut down the instrument 5 After about 30 seconds a dialog box will appear e Press OK and wait at least 20 seconds before turning off the instrument via the power switch In addition for instruments below Serial Number GW10159 power off the white instrument controller Right click on the Server icon the Instrument line will no longer be present and click on Shut down Gyrolab Server Click on the Yes button in the resulting pop up box Copyright 2015 Gyros Gyrolab User Guide P0004354 H
51. entries are the reagent or sample name from the Reagent list or Sample list This specifies where the reagent or sample will be placed on the CD and in which operation it will be used Table H2 2 Specification for Transfer list Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A H2 Custom Run workflow H2 4 4 Create or edit Run There are three options available when setting up a new Run Create a new Run proceed with Chapter H2 4 4 Edit an existing Run use when similar but not identical experiment design is wanted proceed with Chapter H2 4 4 Use an existing Run use when identical experiment design is wanted go to Chapter H2 5 Step Action 1 Click Design Run on the Main menu The Design Run screen appears amp Root Content 2 folders O runs Attribute Folders and Runs allowed EO Bioaffy O Service e To create a new Run click New Give the Run a name To edit an existing Run browse to locate the desired Run select the Run and click Open Follow instructions below from step 4 and edit items to be changed and leave the other items unedited Select Custom Run in the Design type list and click Select button Custom Run panel can now be seen Run name Protein Quantification 4 Bl Design type Custom NE Select Reselect Custom Q Method Reagent list Transfer list Experiment mapping Reagent combination Experiment name
52. for a Project already opened click View Analysis Settings and follow step 5 to step 10 below To edit and set analysis settings for a Project not opened click Manage in Gyro lab Evaluator start view and follow step 2 to step 10 below 2 Click Edit Analysis Settings in the Manage window The Manage window is avail able from Gyrolab Evaluator main menu The Edit Settings window opens 3 In the folder structure browse to the Folder that contains the Project for which analysis settings are to be changed and click to highlight that Folder F Edit Settings 4 Click to highlight desired Project Click Edit Settings Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 3 Manage analysis projects Step Action 5 The Analysis Settings window opens showing a number of tabs The ADA Analysis tab is specific for and only used with the software module Gyrolab ADA Software Analysis Settings e Functionalities to use Mark check boxes to select what ADA analyis functional ities to be available in the specific project Screening settings Confirmation Settings and Quantification Settings Refer to Chapter D2 4 for information on analysis settings To import the settings used in a previous run e Click Template Run button Template Run in respective analysis section Select a run from which to import analysis settings for the project Select a run to use as a template for the setting
53. for any critical updates to the NET Framework Caneel 11 Check Windows Update for available updates for Microsoft NET Framework 4 12 When the installation is finished eject the CD 13 Restart the computer after installation Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A C 49 C5 Gyrolab Evaluator installation on office computer 5 5 Database configuration Gyrolab Evaluator is designed to evaluate results processed by Gyrolab Control The result files are stored in Gyrolab Result Database The Gyrolab instrument computer is installed with the Windows firewall enabled To allow communication between the Gyrolab instrument computer and an office computer contact the local system administrator This chapter describes how to configure and set up Gyrolab database communication between the Gyrolab instrument computer and another computer in the same network Step Action In Windows Explorer browse to the Gyrolab Evaluator installation folder The location for this folder was set during installation refer to Chapter 5 4 step 8 1 j e Click to open DatabaseConfigTool Cis lab Evaluator 3 0 10 97 Os pas Eees E Ts Address C Program Files Gyros Gyrolab Evaluator 3 0 10 97 ae Images License C 50 modules Datadiccess dll 30 10 97 DataAccess DataTypes dll 3 0 10 97 DataTypes Tonic Utils Zip dill 1 5 2 Tonic s Zip Library orannzsbb10 dll
54. for the Run Select folder e Click Paste The Run is now located in the new folder NOTE To paste a Run into a folder the folder must have status Allow Run refer to Chapter F2 2 2 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 35 F2 Gyrolab Administration Tool Button Action Delete Delete is used to delete a Run e Browse the folder structure to the left in the Runs screen to locate the folder that holds the Run to be deleted Select folder e Select the Run to be deleted in the Run list to the right in the Runs screen e Click Delete e Click OK in the Delete Run dialog to confirm deletion The selected Run is now deleted from the Runs list Import Import is used to import Runs into the Administration Tool to make them available for use in Gyrolab Control Browse the folder structure to the left in the Runs screen to locate the folder into which the Run is to be imported Select folder e Click Import to open Import Runs dialog Browse and select desired Run Runs must be in zm1 format e Click Import e Click OK in the Import Runs dialog to confirm import The selected Run is now present in Runs list Export Export is used to export Runs from the Administration Tool Exported Run can be imported into another Gyrolab instrument e Browse the folder structure to the left in the Runs screen to locate the folder that holds the Run to be exported Select folder Select Run t
55. in Gyrolab Evaluator runs must be performed using the Gyrolab Mixing CD and its specific methods The Gyrolab ADA product portfolio enables measurement of anti drug antibodies ADAs in the presence of excess amounts of drug Samples are treated with acid in an automated procedure to allow drug ADA complexes to dissociate and then neutralized just before analysis preventing complexes from reforming The acid pre treatment of the ADA drug complex increases the drug tolerance of the assay a term used to describe its capability to detect ADAs in the presence of drug in the sample Recommendations on assay development and sample and reagent preparations are found in the Gyrolab ADA assay protocol included in the purchase of Gyrolab ADA Software During clinical ADA analysis samples are screened for ADA positives in a Screening assay Confirmation assays are performed to investigate whether positive samples from screening are true positives Evaluation functionalities are available in Gyrolab ADA Software to support these analyses D2 2 Run set up D2 2 1 Design Method The Gyrolab Mixing CD contains 48 microstructures all with individual mixing chambers upstream of the capture column The mixing chamber allows for rapid mixing of liquids added according to the Gyrolab method Mixing is followed by incubation steps to get the full effect of sample acidification to dissociate ADA drug complexes or neutralization to form complexes necessary f
56. is the concentration value after dilution Applied to the Unspiked Results column and reflected in the Checked Unspiked Result column The upper limit for the assay The value is the concentration value after dilution Applied to the Unspiked Results column and reflected in the Checked Unspiked Result column Highest acceptable value for the spiked recovery percentage Lowest acceptable value for the spiked recovery percentage The maximal acceptable CV The concentration in the spike that was added to the sample 1000 ng mL in the example below Example The initial spiked sample dilution is prepared by adding 50 uL of sample 50 ul of 2000 ng mL protein X for a final concentration of spike 1000 ng mL The unspiked sample is prepared by adding 50 pL of sample 50 pL of sample diluent The initial dilution is then serially diluted 2 fold twice The spiked concen tration in the second dilution should be 500 ng mL and 250 ng mL in the third The prefix used to identify spiked samples Specified in the Sub group column in the Sample list used when executing the Run The prefix used to identify unspiked samples Specified in the Subgroup column in the Sample list used when executing the Run The PMT setting that the analysis will be performed on Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D5 Gyrolab Serial Dilution Analysis D5 6 Installation of Gyrolab Serial Dilution Analysis The Gyrol
57. list Click Export to open Export Liquids window Browse and select desired export folder e Click Export Click OK in the Export Liquids dialog to confirm export The selected Liquid is now present in the selected export folder Export Readable is used to export a readable copy of a liquid This copy cannot be used in Gyrolab Control but it can be useful for example when contacting Gyros for support Select Liquid in the Liquid screen list e Click Export readable to open Export Liquid in readable format dialog Browse and select desired export folder e Click Export readable Click OK in the Export Readable Liquid dialog to confirm export read able The selected Liquid is now present in a readable format in the selected export folder Delete is used to delete Liquid files Select item to be deleted from Liquid screen list e Click Delete Click OK in the Delete Liquid dialog to confirm deletion The selected Liquid is now deleted from the Liquids screen list Click on Close in the top right hand corner of the Liquids screen to exit Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2 Gyrolab Administration Tool F2 2 10 Targets Click on Targets on the main menu to access the Targets screen The Targets screen lists available Targets Targets System version supported 1 GC Gyrolab Evaluator Description Target for Gyrolab Evaluator System version 1 Version 5 0
58. or click on z button to export the report to xps format Microsoft s electronic paper format NOTE When analyzing data in Quantification or Data Comparison modules it is possible to export the data to xis or XML format refer to Chapter C4 1 and Chapter 4 2 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Cy Analyze data Analyze data 4 1 Quantification module The Quantification module is used to quantify samples by analyzing results from Gyrolab Runs Several evaluation functions and setting options are available to achieve optimal quantification results For an introduction to quantification analyses of Gyrolab Runs refer to Chapter 1 To set analysis parameters and or to lock the settings for a Project refer to Chapter 3 8 Analysis parameters can also be set or modified during the quantification analysis procedure refer to step 2 below Step Action 1 In Gyrolab Evaluator Project view Chapter 3 1 click the Quantification button 2 The Quantification Analysis Setup window opens BE Quantification Runs Select run to perform analyss on E GentgG QC samples 2010 MAR 05 03 40 54 PM Analysis Settings Dirce blanks n curve fitting LLOQ tone ULOQ conc jr Trez 6 e Inthe Runs section select desired Run for quantification analysis Inthe Analysis Settings section set or edit Analysis setting for Evaluation Matrix Settings and Acceptance Criteria refer to Chapter Cy 4 f
59. patents and or proprietary intellectual property rights All infringements are prohibited and will be prosecuted Please contact Gyros AB for further details A1 8 Designation The Product model name and commercial name for the Gyrolab xP system is Gyrolab xP The Gyrolab xPlore system has the commercial name Gyrolab xPlore and Product model name Gyrolab xPS Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A2 A2 Introduction to the Gyrolab platform Introduction to the Gyrolab platform A2 1 Products included on purchase of a Gyrolab Instrument The Gyrolab Instrument is delivered with equipment and software needed for installation and usage of the system Additional products can be ordered Purchase of a Gyrolab Instrument includes e Gyrolab instrument GL Degasser only for Gyrolab xP e Wash solution bottles pump liquid bottles and tubings e Waste container e Gyrolab User Guide Gyrolab Instrument Guide and Gyrolab Quick Guide e Start up kit of Microplates Microplate foil and Microplate foil adaptor e Software Gyrolab Control Gyrolab Evaluator and administration software Four user licenses e USB stick 1 GB NOTE A computer is required to control Gyrolab Instrument The computer is purchased separately See Gyrolab Instrument Guide for further information A2 1 1 GL Degasser Gyrolab xP NOTE GL degasser is embedded in Gyrolab xPlore GL Degasser is delivered with the Gyrolab syste
60. reagents or wash solutions Figure 4 Example of binding profile with spike irregularities To prevent this and similar issues it is important that all liquids entering the microstructures reagents samples and buffers are prepared according to recommendations These procedures include centrifugation filtration and storage Refer to Chapter B1 for recommendation on reagent labelling Chapter B4 for recommendations on sample and reagent preparation and to Gyrolab Instrument Guide Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 11 D1 Gyrolab Viewer D1 4 Installation of Gyrolab Viewer The Gyrolab Viewer software module is available for Gyrolab Evaluator version 3 2 or higher and is activated by the user with a licence key Licences are instrument specific Contact Gyros to purchase Gyrolab Viewer and receive a license To register the license Save the license file to the hard disk of the computer at a user defined destination for example C ProgramData Gyros Licenses D 12 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 D2 Gyrolab ADA Software Gyrolab ADA Software Visit www gyros com for the latest updates on available software modules D2 1 Introduction to Gyrolab ADA Software workflow Gyrolab ADA Software is a software add on module for Gyrolab Control version 5 4 and Gyrolab Evaluator version 3 3 or higher To enable data analysis in the Gyrolab ADA Software module
61. reduce the risk or errors Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Step Action 14 Save the Run 15 Click Close to finish the Design Run procedure B3 2 3 Sample List completion B3 Design run A Sample List is designed to transfer important sample information from run design phase to run execution phase in Gyrolab Control All samples types Unknown samples Standard samples Quality Control samples Calibration Control samples defined in the Run are included in the Sample List The automatically generated Sample list is a template the final numbers of samples and replicates in a run are set when the Sample list is imported prior to run start refer to Chapter B3 2 4 Step Action 1 Open the Sample List location defined in Chapter B3 2 2 step 10 in Microsoft Excel From row 8 and below one row represents one sample Data is mandatory in columns labelled M and optional in columns labelled 0 Columns labelled N A are not used Example of automatically generated Sample List E A c D E 1 Template Sample3 0 Sample list info 2 M Manda Sample M MP96 PCR 3 O Option Result File Name 0 4 N A Not Result File Path O 1 9 2 10 3 11 4 12 85 13 6 14 7 15 8 Ts E 18 19 20 a 2 23 24 25 26 27 28 29 30 zal Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A UNK UNK UNK UNK UNK UNK UNK UNK BL
62. refer to Chap ter B3 2 5 for a list of available macros TIP The settings in the Targets tab can be exported and imported which enables settings to be shared between users instruments and projects 8 The Targets tab Gyrolab Report section contains settings specific for the software module Gyrolab Control Report and is only available if a licence for Gyrolab Control Report has been acquired Refer to Chapter D4 2 for more information B 46 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Step 9 10 B3 2 5 By using B3 Design run Action Open Reports tab Targets Reports F ProgramData Gyros Gyrolab Templates C ProgramData Gyros Gyrolab Resuits user i d 4 i I Fls i le ad Import Output Settings Export Output Settings A report file that holds method information can be generated To import default settings for report file Stylesheet and Destination lick Import Output Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Default Settings select ReportSettings xml and click Import e If no report file is wanted select the file present in Stylesheet and click on Remove button TIP Customized reports can be generated Contact Gyros for information Click OK and proceed to Chapter By 1 1 sample and reagents preparations Macros for creating names for folders and files macros
63. that opens B5 2 1 3 Load reagent microplate Step Action 1 Click Load in the Reagents section The Define Reagent Microplate dialog box is displayed 2 Load reagents as defined by the selected MP type as pi we A B c D E F G H rjo jnimjolo m OODOODOO OODDODOO OODOODODOO OODODODOO OODOODOO OODOODODOO DODDODOO 2 QQQQQOQQQ OQQQQOQOQQ e 00000000 00000000 5 OOOOOOOO 8 a nm we Select Deselect 2 Verify that the reagents are placed correctly in the microplate according to the Gyrolab Control Loading list Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A B 63 Bs Start Run procedures Step Action 3 Click OK The load reagent microplate dialog appears 1 Enter microplate identity or use barcode reader DLE ue 2 Insert microplate at the postion indicated by the light diode into Gyrolab and confirm e Either scan the barcode ID or click Enter ID Manually and enter microplate ID as stated in the Loading List Insert sample microplate in loading position indicated by the light LED Chap ter A2 2 2 e Click Confirm The microplate ID will appear in the list on screen 4 Repeat for each reagent microplate until all reagent microplates are loaded Ensure the BCR is configured so that Enter or Carriage Return is not added when
64. the Analyte bar e Add additional Experiments to an Analyte by clicking ca in the Analyte bar e Delete Experiment by clicking x in the Experiment bar Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B 40 B3 Design run Step Action 13 Select Generate Sample List template Number of unknowns 0 v Unknown replicates 2 v v Ensure compatibility with single CD instrument Include limited CD Number of free segments Use spiked unspiked Number of unknowns is doubled and subgroup set to spiked unspiked in sample list Generate Template Save the Run e To save a new Wizard Run click Save Browse to select folder and click Save To save an edited Wizard Run click Save as Name the Run browse to select folder and click Save If Save is clicked the information on the original Run will be replaced with the edited information e Ifany information added to the Wizard Run is incomplete or erratic an error message will be presented The specified issues must be addressed before it is possible to save Specify number of samples to be analyzed Unknown samples in the Number of unknowns list Specify number of sample replicates in the Unknown replicates list Highest number of replicates are 8 Ensure compatibility with single CD instrument checkbox Purpose of this function is to help the user to ensure that the run can be ex
65. the Maximum Needle Volume in ul F 22 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A Fi Gyrolab Control Step Action 8 Click Standby Liquid The standby liquid is the solution used to put the system in Standby mode The Pump Liquids dialog displays a list of available liquids Wash station sanitize solution 1 New Wash Station Solution Delete Wash Station Solution 9 Select Standby Solution by clicking its name in the list To add new liquids to the list click New Pump Liquid Type a new name and click OK e To remove a liquid from the list select a name in the list and click Delete Pump Liquid and click OK to confirm deletion 10 Click Set The standby liquid appears on the tab 11 Click Save to save syringe pump settings Configure Wash Stations The system is equipped with two wash station pumps one for each Wash Station The wash station pumps are primed with wash station solutions The two Wash Stations are configured on the Wash Stations tab in the Configure System screen Syringe Pumps Wash Stations Needles Prime Volume Wash station 1 NO ui Wash station 2 100000 0 ul General wash station settings Standby Solution Standby solution Prompt for priming wash stations before run execution Figure 10 Example of Wash Station configuration tab Step Acti
66. the Number of free segments list e The Use spiked unspiked check box is specific for the software module Gyrolab ADA Software Refer to Chapter D2 2 for more information e Click Generate template e Browse to select Sample List location and click Save A Sample List is generated The Sample List contains all necessary sample informa tion defined in the run design It also holds a suggestion for sample placement within the microplate NOTE The procedure described in this step is the most convenient way to gen erate a Sample List Sample Lists can created manually and automati cally generated lists can be edited prior to run start refer to Chapter B3 1 3 However Gyros recommends using the automatically generated Sample Lists as this will reduce the risk or errors 14 Save the Run 15 Click Close to finish the Design Run procedure B 24 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B3 1 3 B3 Design run Sample List completion A Sample List is designed to transfer important sample information from run design phase to run execution phase in Gyrolab Control All samples types Unknown samples Standard samples Quality Control samples Calibration Control samples defined in the Run are included in the Sample List The automatically generated Sample list is a template the final numbers of samples and replicates in a run are set when the Sample list is imported prior to run start refer to Chapter B3 1
67. the column only after a proper separation of compounds in the bioti nylation mixture is confirmed NOTE This protocol step is only valid for proteins larger than 7kD For smaller proteins use another method for removal of free biotin for example Nanosep Pall Life Sciences with a suitable cutoff Concentration measurement of biotinylated reagent Measure absorbance A so of the biotinylated reagent Dilute an aliquot of the biotinylated reagent 1 10 in PBS for absorbance measurement Calculate reagent concentration mg ml Reagent concentration mg ml Ago x dilution factor e x L e 1 38 cm mg ml L cuvette length in cm 1 cm NOTE The extinction coefficient s for IgG is 1 38 cm mg ml other values may be valid for other reagents Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Step 6 TIP TIP B1 2 B1 Labelling of capture and detection reagents Action Storage of biotinylated reagent Aliquot and store the biotinylated capture reagent at 4 C or 20 C long term storage Verify biotinylation Perform a Run using 700 nM of the biotinylated molecule for an antibody this cor responds to 0 1 mg ml Evaluate results to verify a successful biotinylation Recalculations of concentration from g L to molar terms Formula M protein g L protein MW g mol mol L protein Example For 1 mg mL of BSA MW 67000 g mol M BSA 1 g L 67000 g mol 0 0000149 M
68. used to delete List Loader files Select item to be deleted from SampleListLoader screen list e Click Delete Click OK in the Delete List Loader dialog to confirm deletion The selected Target is now deleted from the SampleListLoader screen list Click on Close in the top right hand corner of the SampleListLoader screen to exit F2 2 12 About function Click About to get information about the software versions and licences for Administration Tool F2 2 13 Logout Click Logout to log out and shut down Administration Tool F2 2 14 Help To access the help section a pdf version of Gyrolab User Guide click Help on the main menu and browse for needed Gyrolab User Guide chapter F 56 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F3 Gyrolab Result Database Explorer Gyrolab Result Database Explorer F3 1 Introduction Files that are generated by Gyrolab Control during a Run are saved in Gyrolab Result Database The files are kept in a read only state and can not be changed moved or deleted Use Gyrolab Result Database Explorer to view database files Chapter F3 2 e customize database view Chapter F3 3 e export copies of Result files and Report files Chapter F3 4 e generate status reports Chapter F3 5 F3 2 View database files Step Action 1 To open Gyrolab Result Database Explorer Open Windows Explorer e Click on Gyrolab Result Database Explorer 2 Gyr
69. using Nanosep G3 5 Poor precision and bad reproducibility between runs G3 6 Increased background in lower parts of the CD column Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Gi Instrument issues G1 Instrument issues This section contains information on how to diagnose and possibly solve problems related to all Gyrolab instrument Always start the troubleshooting by checking the connection between the computer and the instrument and restart the instrument and the computer If you cannot identify the problem or if the problem remains please contact Gyros for support G1 1 Instrument initialization problems The instrument initialization problems described in this section applies for all Gyrolab Instruments Error message Possible cause Action GYROS Example of error message Check the connection between the com 3 puter and the instrument No instrument access see 3 e R hei nt Initialize System button disabled greyed Ae mamen out e If still no instrument connection restart i m r Possible cause the compute Ifyou cannot identify the problem or if the problem remains please contact Gyros for support e Gyrolab Control software turned on without restarting the instrument The instrument initialization problems described in this section applies for Gyrolab Instruments with serial numbers up to 158 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D
70. workflow Step Action 1 Click Design Run on the Main menu of Gyrolab Control refer to Chapter F1 1 2 The Run screen appears 2 e To create a new Run click New and continue with step step 3 To edit an existing Run browse and select the desired Run and click Open Change desired parameters For instructions refer to step step 3 to step 16 3 Enter a Run name in the Run Name field Select Wizard in the Design Type list and click Select The Wizard panel appears Mme i dee FRE met Wizard O Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A D 15 D2 Gyrolab ADA Software Step Action 4 5 In the Method section click Select Qa i The Select Method dialog is opened amp RootIADA methods Content 1 folders 7 methods Attribute Folders draft methods and approved methods allowed Browse and select desired ADA Method Click OK The selected method is added to the run design and method information is displayed Qr ADA 1W 001 A Eee p Method information Name Root ADA methods ADA 1W 001 A CD Gyrolab ADA CD Description Bioaffy ADA CD 1 step capture analyte detection in one step wizard run Wash 1 solution used for all needle washes PBS Tween 0 01 e eT os E n E n SE Initial needle wash 2 column washes e Acid dissociation step Neutralization step Neutralizing buffer including capture and detection r
71. 0 Number of replicates is 8 or less Sample volume 2 5 pl x Number of replicates 5 0 ul Number of replicates is 8 or more Sample volume 2 5 pl x Number of replicates 10 0 ul NOTE In multiple CD Runs samples that are used on more than one CD must be placed in different microplate wells one per CD refer to Chapter H2 4 1 Calculate minimum required volume per well using the formulas above NOTE If more than 41 replicates are used on a Bioaffy 1000 CD the sample liquid must be divided into more than one well H2 6 4 Microplates Prepare microplates according to Chapter By 2 2 Prepare reagent microplate Reagent microplate contains e Capture reagent e Detection reagent e Standard series samples including blank samples e Quality Control samples e Calibration Control samples The volumes and microplate positions are specified in the Reagent List Chapter H2 4 2 and Transfer List prepared in Chapter H2 4 3 Prepare sample microplate Sample microplate contains e Unknown samples Transfer the samples as prepared in Chapter H2 6 3 to wells in the sample microplate according to the order stated in the Sample List prepared in Chapter H2 4 1 H2 7 Start Run procedures Please refer to Chapter B5 H2 8 After Run procedures and result export Please refer to Chapter B6 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H 21 H2 Custom Run workflow H2 9 Examples of run set up and exp
72. 000 Number of replicates is 8 or less Standard volume 2 5 pl x Number of replicates 5 0 pl Number of replicates is 8 or more Standard volume 2 5 pl x Number of replicates 10 0 pl For correct number of replicates refer to Transfer list prepared in Chapter H2 4 3 NOTE In multiple CD Runs samples that are used on more than one CD must be placed in different microplate wells one per CD refer to Chapter H2 4 2 Calculate minimum required volume per well using the formulas above NOTE Calibration Controls can be used in multiple CD runs and are selected points in the Standard series When calibration Controls are used one must prepare extra volume of Standard series samples to ensure that the volume is sufficient for both the Standard series sample and Calibration Control It is very important that the Standard series and Calibration Control samples are from the identical Standard series dilution NOTE If more than 41 replicates are used on a Bioaffy 1000 CD the sample liquid must be divided into more than one well Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A H2 Custom Run workflow H2 6 3 Unknown Samples and Quality Controls Prepare Standard series and Calibration Controls according to Chapter H2 6 3 For minimum required sample volumes use formula below For Bioaffy 20 HC and Bioaffy 200 Sample volume 0 5 pl x Number of replicates 2 5 pl For Bioaffy 100
73. 0020034 P0004824 Po004825 P0020027 P0020096 Pooo5002 P0003697 P0004955 P0020028 P0020025 P0005028 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Gyrolab Bioaffy 20HC Gyrolab Bioaffy 200 Gyrolab Bioaffy 1000 Gyrolab Mixing CD Microplate Foil PCR Plate 96 Rexxip A Rexxip A max Rexxip H Rexxip H max Rexxip AN Rexxip AN max Rexxip HN Rexxip HN max Rexxip HX Rexxip HX max Rexxip CCS Rexxip F Rexxip ADA Gyrolab Wash Buffer pH 11 Gyrolab Functionality Check Kit Microplate Foil Adapter Gyrolab User Licenses Gyrolab Viewer Gyrolab ADA Software Gyrolab LIMS interface Content One piece CD One piece CD One piece CD One piece CD Pack of 50 Pack of 25 One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 25 ml One piece 10 ml One piece 25 ml Pack of 10 10x10 gram One piece Kit One piece Pack of 5 One piece Software One piece Software One piece Software H 3 H1 Products accessories and consumables Product Content number P0020006 Gyrolab Control Report One piece Software P0005016 Gyrolab Serial Dilution Analysis One piece Software P0000007 Syringe pump external tubing One set of PEEK tubings 5 x 1 m assembly PEEK with fittings and connectors Pooo0009 Wash tubing assembly One set of w
74. 0023573 A G 3 G1 Instrument issues Error message Possible cause Examples of error messages Robot Carousel or CD arm timed out Software error No immediate action sug gestion available example in figure below Possible cause e Dislocated Controller cables wi Gyrolab Control Action e Check Controller cable 1 refer to Chap ter A2 3 Disconnect and reconnect the cable e Retry instrument initiation If problem remains check and refit other cables controller cables and USB cable If problems still remain contact Gyros Failed to move Robot or CD arm to home position internal Galil error No immediate action suggestion available Examples of error messages e Needles correlated error messages or that the instrument failures initialization example in figure below Possible cause Dislocated Controller cables al Initializing System INSTRUMENT 0 initialized successfully Initializing System Station O initialized successfully Station 1 initialized successfully Station 2 initialized successfully VACUUMARM O initialized successfully SMARTLABEL O initialized successfully Station 3 initialized successfully INSTRUMENT O initialized successfully Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A e Check Controller cable 2 refer to Chap ter A2 3 e Disconnect and reconnect the cable e Retry instrument initiation If problem rem
75. 1 1 1 and Chapter B5 1 2 2 Gyrolab xP or Chap ter B5 2 1 1 and Chapter B5 2 1 3 Gyrolab xPlore Unexpected appearance of standard curve Laboratory and instrument generated errors Action Refer to Chapter B4 1 2 Gyrolab xP or Chap ter By 2 2 Gyrolab xPlore for details To remove air bubbles centrifuge microplate at 3000 x g for two minutes If bubbles still remain increase time or speed until all bub bles are gone Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A G 11 G3 Application issues Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Possible cause Were there any air bubbles in the Syringe Pumps G3 2 2 Low response Possible cause Were Unknown and Standard series sam ples handled and stored appropriately Where correct Rexxip buffers and solu tions used according to Gyros recommen dations Are reagents freshly prepared Where the reagents stored according to recommen dations If using a freshly labeled detection reagent Is the optimal concentration used If using a freshly labeled detection reagent Was unbound labeling reagent sufficiently removed Is the optimal reagent pair used in the assay G3 2 3 Extensive variation Possible cause Was the detection reagent centrifuged before use Where the reagent stored according to recommendations Was enough Wash Station Solution con nected to the system Ensure that the degas
76. 18 Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Fi Gyrolab Control F1 2 2 Gyrolab Control main menu F1 2 2 1 Main menu overview The start screen in Gyrolab Control holds the main menu from which all actions are initiated The main menu also displays instrument access status refer to Chapter F1 1 3 instrument mode refer to Chapter F1 1 3 14 and functionality for alarm handling GYROS Figure 8 Main menu The main functions of Gyrolab Control are represented by buttons on the main menu Only one function at a time can be activated Select a function by clicking on the function button and the panel for the selected function is displayed on the screen Buttons may be accessible in the example above Initialize System inaccessible in the example above Prime button or hidden in the example above Execute Run button F 2 3 Main menu functions Button LED Function Design Method Launches the Design Method screen to create new methods edit method refer to Chapter F1 2 3 1 Design Run Launches the Design Run screen to create newledit delete Runs _ refer to Chapter F1 2 3 2 Execute Run Launches the Execute Run screen to prepare and start a Run Chapter F1 2 3 3 Prime Launches the Prime screen to set priming parameters perform instrument priming refer to Chapter F1 2 3 4 Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A F 19 Fi Gyrolab Control Button LED
77. 2 2 e Click Confirm The microplate ID will appear in the list on screen 2 Repeat for each sample microplate until all sample microplates are loaded Ensure the BCR is configured so that Enter or Carriage Return is not added when scanning the identity of a MP B5 2 1 2 Confirm Wash Station Solutions and Pump Liquid If solutions and liquids are available o Wash Station Solutions Solution Wash Station Confirm Connect o Pump Liquids P Confirm Connect Step Action 1 Make sure tubings for wash station solution and pump liquid are connected and system is primed according to Chapter B2 4 2 Under Wash Station Solutions Highlight the Wash Station Solution and click Con firm 3 Under Pump Liquid section Highlight the Bioaffy Pump Liquid and click Confirm Chapter A2 2 2 B 62 Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Bs Start Run procedures If solutions and liquids are not available O wash Station Solutions Solution Wash Station Confirm Connect O mus Confirm Connect Step Action 1 Make sure tubings for wash station solution and pump liquid are connected and system is primed according to Chapter B2 4 2 Under Wash Station Solutions Click Connect Click OK in the Connect Wash Station dialog that opens 3 Under Pump Liquids Click Connect e lick Confirm in the Pump Liquid dialog
78. 23573 A E 5 E Recipes 50 mM Glycin pH 9 5 with 0 5 Dodecylsulfate sodium salt SDS Purpose Used for the Wash Station 2 Composition 50 mM Glycin pH 9 5 with 0 5 Dodecylsulfate sodium salt SDS To prepare 1000 ml e Dissolve 3 75 g Glycin in approximate 800 ml deionized dis tilled water e Adjust to pH 9 5 using sodium hydroxide e Filter 0 22 pm e Dissolve 5 g Dodecylsulfate sodium salt SDS Mw 288 38 g mol and adjust the volume to 1000 ml Required volume 1000 ml for1 CD 2000 ml for 2 5 CDs 1 5 M NaCl 20 ethanol Purpose Used for the Wash Station 2 Composition 1 5 M NaCl in 20 ethanol To prepare 1000 ml e Mix 200 ml 95 ethanol with 800 ml deionized distilled water Dissolve 87 66 g NaCl Mw 58 44 g mol e Filter 0 22 um Required volume 1000 ml for1 CD e 2000 ml for 2 5 CDs 0 5 Dodecylsulfate sodium salt SDS 20 ethanol Purpose Used for the Wash Station 2 Composition 0 5 SDS in 20 ethanol To prepare 1000 ml Mix 200 ml 95 ethanol with 800 ml deionized distilled water e Dissolve 5 g SDS Mw 288 38 g mol Filter 0 22 um Required volume 1000 ml for1 CD e 2000 ml for 2 5 CDs Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A E1 Recipes E1 2 4 Standby Solution 20 ethanol Purpose To be used in Syringe Pumps Composition 20 ethanol To prepare 250 ml Prepare 20 solution Required volume 250 ml is needed to process 1 5 CDs E1 2 5 Needle Sanitize S
79. 3 166 Setup Wizard The installer will guide you through the steps required to install Gyrolab Evaluator 3 3 3 166 on your computer WARNING This computer program is protected by copyright law and international treaties Unauthorized duplication or distribution of this program or any portion of it may result in severe civil or criminal penalties and will be prosecuted to the maximum extent possible under the law ec past Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A C 47 C5 Gyrolab Evaluator installation on office computer Step Action 7 A Gyrolab Evaluator dialog opens Read the license agreement select Agree and click Next gt If the License agreement can not be accepted click Cancel and contact Gyros Gyrolab Evaluator 3 3 3 E GYROS Please take a momentto read the license agreement now If you accept the terms below click I Agree then Next Otherwise click Cancel License Agreement Software End User License Agreement IMPORTANT PLEASE READ CAREFULLY This is the license agreement the Agreement that you the End User are required to accept before installing and using the software Gyrolab Evaluator including third party software installed using Gyros Installation Packages the Software The Software is licensed to the End User from either A Gyros AB if the Software the Gyrolab system and related Gyrolab products have been provided by Gyros
80. 3 for further instructions Syringe Pumps Wash Stations Needles Configure Syringe Pumps The system is equipped with five Syringe Pumps that control two needles each Pump number 1 controls needles 1 and 2 pump number 2 controls needles 3 and 4 and so on This set up is displayed on the Syringe Pumps tab in the Configure System screen NOTE Different Syringe Pumps can handle different liquids Syringe Pumps Wash Stations Needles CD Stations carves nts Synge vee E Pump 1 v r joo u VER Pump 2 v r foco u Bs 4 Pump 3 F r fioo u Pe Pump 4 id r joo u pa Pump 5 r d joo u po General pump settings Pump to needle prime volume 2000 0 ul Minimum neede volume 0 1 ul Bottle to pump prime volume 6000 0 ul Maximum needle volume 50 0 ul Standby Liquid m Prompt for priming needles before run execution 7 Figure 2 Example of syringe pump configuration tab Step Action Samples and Reagents for each pump 2 Enter the Syringe Volume in ul 3 Enter the Connected Needles if not already completed 4 In the General Pump Settings section enter Pump to Needle Prime Volume in ul The Pump to Needle Prime Volume is the volume used to rinse the tubing between the syringe pump and its connected needles during priming 5 In the General Pump Settings section enter Bottle to Pump Prime Volume in ul The Bottle to Pump prime Volume is the volume used to rinse the tubing between the pump liquid bottle and the
81. 354 H D0023573 A A2 Introduction to the Gyrolab platform A2 2 22 Gyrolab xPlore Figure 2 Gyrolab xPlore instrument front view No Part 1 Hatch 2 CD loading position and spinning unit with protective casing Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A No A2 Introduction to the Gyrolab platform Part Instrument Ready LED Green light indicates that the start up sequence has finished and the instrument is ready for use Instrument Run LED Green light indicates that the instrument is performing a Run Instrument Alarm LED Red light indicates that the instrument is in alarm state Syringe Pumps for the needles Power button Microplate locking lever Liquid transfer device Wash Stations Connecting panel for external tubing Peristaltic pumps for Wash Stations and waste Microplate positions positions 1 2 and 3 Fluorescence detector Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A2 Introduction to the Gyrolab platform A2 3 Gyrolab instrument rear view A2 3 1 Gyrolab xP A2 3 1 1 Serial number less than GW10159 2 3 4 Figure 3 Gyrolab xP instrument rear view serial number less than GW10159 No Part 1 Power switch 0 Off On o Power cable 3 Motor power cables L USB connector 5 Instrument label A 10 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A A2 5 A2 Introduction to the Gyrolab platform 3 1 2
82. 354 H D0023573 A H2 Custom Run workflow Example 4 Two different Standard series and two Reagent combinations Transfer No list info CD 0 Bioaffi M Mandator Op Capture reagent Op Detection Structure M MM addition Dp Analgt tio L Tommena cue stn o onene E re er ET rs re eee rs es ere ewer cuve tants e E O oue runsas DO Toma mermo a RO cueg saras rs ee cuve 2 sunaa L e fonema cuve z sunaa o someone omezem rs ere eee DO E Figure 12 Two different Standard series with for example different standard preparations dilutions with two different Reagent combinations will generate two standard curves A Run using this transfer list will generate following in Gyrolab Evaluator Two Reagent combination e Capture curve1 Detection curve e Capture curve 2 Detection curve 2 Two standard curves in duplicates One for each Reagent combination H2 9 2 Examples of experiment mapping for multi CD Runs Three examples for set up of multi CD Runs are provided NOTE In the following examples Transfer Lists where only transfers to segments 14 and 15 are shown This is to make the examples easy to follow If present in a real Run the Transfer List must also specify transfers to segments 1 13 Otherwise the transfer will occur to segments 1 and 2 on the first CD since segments with no specified transfer will be ignored during the
83. 4 Step 1 Action Open the Sample List location defined in Chapter B3 1 2 step 13 in Microsoft Excel From row 8 and below one row represents one sample Data is mandatory in columns labelled M and optional in columns labelled 0 Columns labelled N A are not used Example of automatically generated Sample List are er FE E F G H _1 Template Sample3 0 2 M Manda Sample M MP96 PCR 3 O Option Result File Name 0 4 N A Not Result File Path O 5 6 7 Index M Sample Ty Sample Id Sample Gi Sample St Dilution F MP Identi Well M Sample list info 8 1 UNK Sample 1 MP1 D1 9 2 UNK Sample 2 MP1 D2 10 3 UNK Sample 3 MP1 D3 11 4 UNK Sample 4 MP1 D4 12 5 UNK Sample 5 MP1 D5 13 6 UNK Sample 6 MP1 D6 14 7 UNK Sample 7 MP1 D7 15 8 UNK Sample 8 MP1 D8 16 BL Standard A_Blank MP1 Al 17 BL Standard A_Blank MP1 A2 18 STD Standard A_1 MP1 A3 EB STD Standard A 1 MP1 A4 20 STD Standard A_2 MP1 A5 21 STD Standard A_2 MP1 A6 22 STD Standard A_3 MP1 A7 23 STD Standard A_3 MP1 A8 24 STD Standard A_4 MP1 A9 25 STD Standard A_4 MP1 A10 26 STD Standard A_5 MP1 A11 27 STD Standard A_5 MP1 A12 28 STD Standard A_6 MP1 B1 29 STD Standard A_6 MP1 B2 30 STD Standard A_7 MP1 B3 21 tn Standard A 7 Mp1 RA Edit sample information as desired make sure that data is in accordance with Table B3 1 on page 26 e By default all samples and reagents of all types will be located on the same Sample Microplate To
84. 5 2 Readable Audit Trail Report System Log Report A readable Audit Trail report is called a System log Report Output format is xML which is a readable format suitable to archive or study at user site Since this report does not contain any run data it can be used when data can not be shared for some reason Step 1 2 Action To open Gyrolab Result Database Explorer open Windows Explorer and click on Gyrolab Result Database Explorer Gyrolab Result Database Explorer window opens Click Folders Ere croa Result Database Explorer Desktop Main View ic My Documents E 3 My Computer E my Network Places E Recycle Bin a Gyrolab Resul Right click Main View and select Generate Status Report Set Start date and End date for the status report Default setting is 10 days from current date Generate Status Report 2007 10 21 2007 10 31 x ca Click OK In the Save As dialog name the status report file and browse for desired location The location must be at the local disc usually the C disc Click Save The exported status report is now found at its specified location The file contains the instrument audit trail system log and is compressed to gyr format F 64 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A Fu Gyrolab Database Backup Manager Gyrolab Database Backup Manager Gyrolab Database Backup Manager is used to back
85. 5 Gyros Gyrolab User Guide Pooo4354 H D0023573 A C2 Log in main menu functions and analysis administration 2 2 Main menu functions 2 2 1 New Analysis menu Step Action 1 Click New Analysis in Gyrolab Evaluator start view 2 A dialog opens Select one or more Runs to be analyzed and click Add Start Time End Time 2009 11 10 15 45 55 2009 11 10 15 53 01 2005 02 26 09 38 18 2009 02 26 20 24 47 2009 02 04 11 54 45 2009 02 04 13 28 51 Show all Runs started by the current user z e Unselect a Run by clicking on the name again Use the list in the lower left corner to view different subsets of Runs or all avail able Runs 3 Gyrolab Evaluator Project view opens For more information on the Project view and how to manage and save the new Project refer to Chapter C3 e To perform data analysis on a Run refer to Chapter Cy 1 and Chapter Cy 2 To discard the project click File Close or the or click Close button K to close the Project Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C2 Log in main menu functions and analysis administration 2 2 2 Open Project menu Step Action 1 Click Open Project in Gyrolab Evaluator start view 2 The Open widow is displayed In the Folder structure browse to find the desired Project Select Project and click Open 3 Gyrolab Evaluator Project view opens To manage and save the Project refer to Chapter C3 To p
86. 5 Gyros Gyrolab User Guide Poooy354 H D0023573 A Fi Gyrolab Control Step Action 1 Enter the Prime Volume in gl for Wash Stations 1 and 2 The Prime Volume is the volume used to rinse the tubing between the wash station bottle and the Wash Station during priming 2 Click Standby Solution at the bottom of the tab The standby liquid is the solution used to put the system in Standby mode The Wash Station Solution dialog is displayed containing a list of available standby solutions Wash Station Solution lt None gt Bioaffy wash station solution 1 Bioaffy wash station solution 2 Needle desorb solution 1 Needle desorb solution 2 Needle sanitize solution Wash station sanitize solution 1 New Wash Station Solution Delete Wash Station Solution 3 Select the Standby Solution to be added by clicking its name in the list To add new liquids to the list click New Wash Station Solution Type a new name and click OK To remove a standby liquid from the list select a name in the list and click Delete Wash Station Solution e Click OK to confirm deletion 4 Click Set The Standby Solution appears on the tab 5 Click Save to save wash station settings Align needles An alignment procedure can be performed to ensure that the needles are correctly aligned i e on target for the wells of a microplate This procedure is normally only performed by Gyros Service staff when needles have been replace
87. AB or a third party DIDo NotAgree lAgree Cancel lt Back Next gt 8 A Gyrolab Evaluator dialog opens e Click Browse to select folder for installation Click Disc Cost to evaluate storage capacity to place software at certain folders Set user access to Gyrolab Evaluator by ticking Everyone or Just me e Click Next gt GYROS The installer will install Gyrolab Evaluator 3 3 3 166 to the following folder Select Installation Folder Ta install in this folder click Next To install to a differentfolder enter it below or click Browse Folder ENPragrem Files Gyros Gyralab Evaluator 3 3 3 166 Browse Disk Cast Install Gyrolab Evaluator 3 3 3 166 for yourself or for anyone who uses this computer Everyone I5 Justme siete C 48 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C5 Gyrolab Evaluator installation on office computer Step Action 9 A Gyrolab Evaluator dialog opens Click Next gt to start the installation Confirm Installation GYROS The installer is ready to install Gyrolab Evaluator 3 3 3 166 on your computer Click Next to start the installation 10 When the installation is completed a Gyrolab Evaluator dialog opens Click Close to exit Installation Complete Gyrolab Evaluator 3 3 3 166 has been successtully installed Click Close to exit Please use Windows Update to check
88. B3 12 UNK Y Spiked_2 10 MP1 B4 Figure 1 Example of a Sample List for a Run analyzed with Gyrolab Serial Dilution Analysis Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 51 D5 Gyrolab Serial Dilution Analysis D5 3 Perform serial dilution analysis To set default analysis parameters and or to lock the settings for a Project refer to Chapter 3 8 Step Action 1 To activate Gyrolab Serial Dilution Analysis go to View Analysis settings and select the tab Plug in Selection and mark the check box Serial Dilution Analysis Settings Close the Analysis settings window 2 In the Project view Chapter 3 1 click the Quantification button i Z Quantification j 3 The Analysis Settings window opens The basic analysis settings are described in Chapter C4 4 Edit settings as desired Click OK Bi Quantification Runs Select run to perform analyss on GenlgG QC samples 2010 MAR 05 03 40 54 PM LLOQ cone ULOQ cone Tres D 52 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D5 Gyrolab Serial Dilution Analysis Step Action 4 The Quantification window opens a This window holds all the same functionality as the Quantification module Left panel shows available experiments and right panel holds analysis settings data tables and a chart It is possible to add notes and to copy data to file Quantification module and available settings and too
89. Bin E Gyrolab Result Database Explorer E EB main view os Results The selected customized database view is now removed from Gyrolab Result Data base Explorer F3 4 Generate Result Reports Result reports contain result and system log files for a specific run and are exported from Gyrolab Result Database Explorer Output format is gyr which is a compressed format suitable to e mail to Gyros support function Step Action 1 To open Gyrolab Result Database Explorer Open Windows Explorer e lick on Gyrolab Result Database Explorer 2 Gyrolab Result Database Explorer window opens Click Folders a Gyrolab Result Database Explorer B Desktop Main view My Documents 3 My Computer E My Network Places 8 Recycle Bin aa Database Explorer E Main view Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A F 61 F 62 F3 Gyrolab Result Database Explorer Step 3 Action Click Main View The folders Results and System log appear 2t Gyrolab Result Database Explorer B Desktop My Documents P My Computer my Network Places 2 System Log It is possible to create customized database views in Gyrolab Result Database Explorer to facilitate finding specific database files refer to Chapter F3 3 NOTE Click Results for a list of Runs stored in the database Click on the icon for the Run of interest Gyrolab Result
90. Database ExploreriMain View Results B Desktop Aa Run Thursday Janu 0 37 06 Administrator E My Documents cc Run Thursday Janu 0 38 56 Administrator m my Computer Mee Run Thursday Janu 0 40 36 Administrator my Network Places Moo Run Thursday Janu 0 41 06 Administrator ig Recycle Bin IGG Run Friday January 0 30 55 Administrator a e Gyrolab Result Database Explorer AH Run Friday January 0 33 42 Administrator a EB main vi Fa Run Friday January 0 59 22 Administrator Results JHH2 Run Friday January 1 02 23 Administrator u System Log gu Run Friday January 0 32 31 Administrator Au Run Friday January 0 38 22 Administrator es Run Monday Febru 0 35 19 Administrator BB 1 Run Monday Febru 0 40 57 Administratoy Highlight the desired Result file right click and select Generate result report In the Save As dialog name the result report file and browse for desired location The location must be at the local disc usually the C disc Click Save The exported result report is now found at its specified location The file contains run results and system log for the specific run and is compressed to gyr format Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F3 Gyrolab Result Database Explorer F3 5 Generate Gyrolab Control Audit Trail report An Audit Trail report includes all system log files within specified dates set by the user No result fi
91. Details button NOTE To re initialize the system click on Logout in the Main menu Choose Restart from the drop down menu in the Shut Down dialog then click OK 2 Click Finish when initialization is complete F1 2 3 7 Configure System The Gyrolab instrument is delivered with a pre programmed configuration set up and system priming protocol This section explains how to configure the system and alter these settings CAUTION Contact Gyros before changing any configuration default settings NOTE Only user with user levels Method Developer or System Administrator can configure the system refer to Chapter F2 2 6 Access the Configure System screen Step Action 1 If the instrument is not initialized click Initialize on the main menu NOTE The system must be initialized in order to access the Configure System screen 2 Click the Configure System button on the main menu 3 Select desired tab refer to chapters Configure Syringe Pumps on page 22 to Align needles on page 24 for further instructions Syringe Pumps Wash Stations Needles Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 21 Fi Gyrolab Control Configure Syringe Pumps The system is equipped with five Syringe Pumps that control two needles each Pump number 1 controls needles 1 and 2 pump number 2 controls needles 3 and 4 and so on This set up is displayed on the Syringe Pumps tab in the Configure System
92. E ste ESERE F u7 F2 2 8 MICrOpIaLeS sms sames cacusesivorend eee nt suisse mana p dessa co mesa amdd F 49 F252 9 Liigid S lt lt ca ssincscnvessswute stews ysatimeneensntes ociet den as eubeeesaneceseees F 51 F252 10 TAR B OTS vi RU ME SRA AR NR RO RT F 53 F2 2 1 Ust L dde Soenen ire arestas asia sia sa st sap these vad ss das seus F 54 F2 2 12 About FUMICEION seca ss does sasas Fase sas soam as asa des asa Pai cs Dad ves F 56 E2 2 13 LOBOUL ss cssiendavtcnsesmcassnsaaemesdie eene sabes ars cesso F 56 E2221 Help ssusadsegacussie sera valsas asma cas RSE EES F 56 Gyrolab Result Database Explorer F 57 F3 1 Introduction 0 0 eee ee ee ee ee F 57 F3 2 View database files 0 0 ccc eee ee eee F 57 F3 3 Customize database view 000 eee eee F 59 F3 4 Generate Result Reports 0 2 eee ee eee F 61 F3 5 Generate Gyrolab Control Audit Trail report F 63 F3 5 1 Compressed Audit Trail report Status Report F 63 F3 5 2 Readable Audit Trail Report System Log Report F 6u Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A FL Gyrolab Database Backup Manager Fy 1 Perform Gyrolab database back Up F4 2 Schedule Gyrolab data base backup cceeeeeeeeees F5 Gyrolab Set System Time 00 F5 1 Gyrolab Set System Time introduction F5 2 Perform logged system time Chan
93. GYROLAB USER GUIDE Original version Copyright 2015 Gyros Poooy354 H Doo23573 A GY RES Content A Introduction 1 Important user information A 3 2 Introduction to the Gyrolab platform A 5 3 Gyrolab immunoassay workflow A 19 Perform immunoassays on Gyrolab In strument 1 Labelling of capture and detection reagents B 5 2 Gyrolab instrument startup procedure B 13 3 Desion Ul oe adia RS De dor a nes B 17 4 Prepare samples and reagents B 49 5 Start Run procedures ccccccccvceee B 55 6 After Run procedures and result export B 67 Data analysis 1 Introduction to data evaluation 5 2 Log in main menu functions and analysis administration C 7 3 Manage analysis projects c C 17 Analyze data s essi e nd DR dp Gard C 29 5 Gyrolab Evaluator installation on office computer C 45 Gyrolab software add on modules 1 Gyrolab Viewer cactecueceedadencyenGoveds D 5 2 Gyrolab ADA Software esssecsscoecesooe D 13 3 Gyrolab LIMS Interface cece eceees D 37 Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A 4 Gyrolab Control Report D 47 5 Gyrolab Serial Dilution Analysis D 51 Recipes 1 RIDER A RR ATER dA E 3 System administration and configura tion 1 Gyrolab Control sa vs se ces pda dO F 5 2 Gyrolab Administration Tool
94. Guide P0004354 H D0023573 A B 57 B 58 Bs Start Run procedures If solutions and liquids are not available Step 1 2 Wash Station Solutions Bioaffy wash station soluti Not Available Pump Liquids UME Bioaffy pump liquid Not Available Action Make sure tubings for wash station solution and pump liquid are connected and system is primed according to Chapter B2 4 Under Wash Station Solutions Click Connect Click OK in the Connect Wash Station dialog that opens Under Pump Liquids Click Connect e lick Confirm in the Pump Liquid dialog that opens B5 1 2 2 Load reagent microplate Step 1 2 Action Click Load in the Reagents section The Define Reagent Microplate dialog box is displayed Define Reagent Microplate 1 Select microplate type Det re 000 QQQ 4 Wash Solution ag e OOO O B Wash Solution Bis c QO O QO c 2 QQQ Q D E QQQ Q E E O00000000000 a vesa 6 O00000000000 H 000900000009 H Verify that the reagents are placed correctly in the microplate according to the Gyrolab Control Loading list Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Bs Start Run procedures Step Action 3 Click OK The load reagent microplate dialog appears Load Reagent Microplate x 1 Enter microplate identity or use barcode reader 2 Insert microplate
95. Gyrolab Administration Tool F2 2 9 Liquids Click on Liquids on the main menu to access the Liquids screen The Liquids screen lists available Liquids lis Liquids lia Bioaffy pump liquid Liquid type Hydraulic E Fr Bioaffy pump liquid Hydraulic lia Bioaffy wash station solution 1 Wash Recipe lia Bioaffy wash station solution 2 Wash Recipe lia Needle desorb solution 1 Wash Recipe lia Needle desorb solution 2 Wash Recipe lia Needle sanitize solution Wash Recipe lia Standby solution Wash Recipe It is possible to perform four different administration actions Import Export Export Readable and Delete NOTE Select a liquid in the list to activate inaccessible task buttons Button Action Import Import is used to import a Liquid to Administration Tool to make it avail able for use in Gyrolab Control e lick Import to open Import Liquid dialog e Browse and select desired Liquid Liquids must be in zm1 format e Click Import e Click OK in the Import Liquid dialog to confirm import The selected Liquid is now present in the list in the Liquids screen Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A F 51 F 52 F2 Gyrolab Administration Tool Button Export Export readable Delete Action Export is used to export Liquids from Administration Tool Exported liquid can be imported into another Gyrolab instrument Select Liquid to export in the Liquid screen
96. Gyrolab methods are designed for one specific D type and Run Design Type The method name describes what it is used for For example 1000 3W 001 A e 1000 is the code for which CD type is used in the method e 20 Gyrolab Bioaffy 20HC e 200 Gyrolab Bioaffy 200 e 1000 Gyrolab Bioaffy 1000 e ADA Gyrolab Mixing CD e 3 defines the number of steps the method has e 3 The standard method 3 step method In this method 3 liquid transfers occur sequentially washes not included There is one capture addition one analyte addi tion and one detection addition e 1 The1 step method In this method only one analyte addition occurs This can for example be applicable when running a homogeneous assay where capture analyte and detection reagent have been pre mixed in a microplate prior to the run e 2 The 2 step method This method contains one capture addition and one analyte addition 4 The 4 step method This method contains two capture additions one analyte addition and one detection addition W defines design type e W wizard design type e C custom design type 001is a unique identity number for a specific combination on CD type number of steps in the method and design type A stands for approved and official method released by Gyros and B for beta method released by Gyros Methods can be customized by Gyros to suit specific needs Contact Gyros for more information Copyright 2015 Gyros Gyrolab User Guide
97. Import Design type dialog Browse and select desired design type Design types must be in zm1l format e Click Import e Click OK in the Import Design type dialog to confirm import The selected design type is now present in the Design type screen list Export Export is used to export design types from Administration Tool in order to for example make the design type available for use on another Gyrolab instrument e Select design type to export e Click Export to open Export Design type dialog e Browse and select desired export folder e Click Export e Click OK in the Export Design type dialog to confirm export The selected design type is now present in the selected export folder Export Export Readable is used when it is desired to have an uncoded readable readable copy of a design type This copy cannot be used in Gyrolab Control but it can be useful when for example contacting Gyros for support e Select design type to export readable e Click Export Readable to open Export Design type in readable format dialog e Browse and select desired export folder e lick Export Readable e Click OK in the Export Readable Design type dialog to confirm export readable The selected design type is now present in a readable format in the selected export folder Delete Delete is used to delete design types Select design type to be deleted from Design type screen list e Click Delete e Click Yes in the Delete Design t
98. Initializing Standby Operating e Power off e Initializing Standby Operating Activated by e Initialization failure e User log out e Switching off the Gyrolab instrument e Critical alarms e User selects Initial ize System and follows the direc tions on the screen e Successful initial ization e Starting a Run e Priming the system e Operator selects Standby and follows the directions on the screen F2 F2 Gyrolab Administration Tool Gyrolab Administration Tool The Administration Tool is used by System Administrators to manage users and various items such as folders targets Runs methods CD types microplate types and liquids F2 1 Login procedure Gyrolab server must be running before the Administration Tool can be started Step Action 1 Start Gyrolab server e Click Start All Programs Gyros Server e Gyrolab Instrument Log is displayed and Gyrolab server icon appears on the task bar L 2 Start Gyrolab Administration Tool Select Start All Programs Gyros Administration Tool 3 Enter user name and password in the Login dialog box and click OK The user name and password is the same for all Gyrolab software For further infor mation on user and password administration refer to Chapter F2 2 6 Password must be changed if requested by the software for example when a new user logs in or if 90 days have passed since last password change Password may also be changed when
99. M Analyses Quantification Quantification 1 analysis name and version Data comparison Data Comparison 1 analysis name and status Description Project position in Folder structure For Projects not yet saved the folder path is missing Version status is increased every time the Project is saved Version o is an unsaved Project Project status Not saved for an unsaved new Project Project status Working for open Projects Project status Replaced for earlier versions of a Projects Refer to Chapter 3 10 for information on how to open previous versions of a Project Not approved status is set for all active Project Approved status locks the Project for further actions Only users with user level System Administrator and Project Manager can change approval status to Approved refer to Chap ter F2 2 6 for more information on user levels Description The Run name is generated during the Run ona Gyrolab instrument and consists of the execu tion name filled in before run start in Gyrolab Control and a time stamp It can not be changed Note Each quantification analysis is given a name which can be changed by the user if desired In brackets the status is given nothing is shown or status New or Changed Version number is available as a tool tip Each Data comparison analysis is given a name which can be changed by the user if desired In brackets the status is given nothing is shown or status New or Chan
100. MS Go to step 4 Un check One Work List per CD box if one worklist is used for all CDs Go to step 5 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A D3 Gyrolab LIMS Interface Step Action 4 Option one Work List per CD For each CD and worklist Click Work List File In the Select Work List File window browse and select Work List for current CD Required CD segments is shown in the CD symbol Click Info for CD of interest to view sample information Check Show replicate ID s box to show information about sample replicates Click Clear to remove a Work List Continue to step 6 Run LIMS Run 001 One Work List per CD List Loader workListLoader z Number of samples 44 Segments Used nu Ce T TX Cc 0 onto work List File Clear 5 Option one Work List for all CDs Click Work List File In the Select Work List File window browse and select Work List Required CD segments per CD are shown in the CD symbols Click Info for CD of interest to view sample information Check Show replicate ID s box to show information about sample replicates Continue to step 6 Trial period until Feb 6 2010 Run LIMS Run 001 One Work List per CD Work List File List Loader workListLoader Number of samples O Segments Used EV LAE o Info T CoO o Info 0 D Info oO o Info f PAL H Info One MP per CD 7 Co
101. Name field To edit an existing Run browse and select the desired Run and click Open D 38 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D3 Gyrolab LIMS Interface Step Action 3 Select LIMS in the Design Type list and click Select The LIMS panel appears Run name LIMS RUN 01 A Design type Lms Select Reselect LIMS Analyte information Analyte name Capture reagent addition Detection reagent addition Advanced settings Process order on CD As Work List x Output format Generic Raw Data Basic format O External format Import Format View Format To change design type highlight the design type in the Design type list and click Reselect Comments for the Run can be made in the Comments window for example what type of assays the run is intended for 4 Select Method and click Select rai Method Select The Select Method dialog opens amp Rooti Bioaffy Wizard methods Bioaffy 200 wizi Coment O folders 4 methods Anritue Folders draft methods and approved methods alowed Browse and select desired Method in the folder structure Click OK NOTE Use the Method that was used during assay development Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A D 39 D3 Gyrolab LIMS Interface Step Action 5 It is now possible to add and edit Method information An
102. S Runs refer to Chapter B3 2 5 F1 2 3 3 Execute Run Runs are prepared loaded executed unloaded and finished in the Execute Run function The run design is completed with sample information Sample List and settings for result and report files Input data and settings differs depending on which design type which type of Run is used e Fora detailed description of how to prepare and execute Wizard Runs refer to Chapter B3 2 4 e Fora detailed description of how to prepare and execute LIMS Runs refer to Chapter D3 e Fora detailed description of how to prepare and execute Custom Runs refer to Chapter B3 2 4 F1 2 3 4 Prime Instrument priming is performed through this function Refer to Gyrolab Instrument Guide F1 2 3 5 Maintenance Maintenance function is used for system maintenance Refer to Gyrolab Instrument Guide for information about specific methods and procedures F 20 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Fi Gyrolab Control F1 2 3 6 Initialize System Hardware tests of the components are performed during initialization for example robot arm movements carousel rotation and vacuum of the CD stations Step Action 1 Close the Gyrolab instrument hatch if open Click Initialize System on the Main menu The Initializing System dialog box is dis played as initialization proceeds Finish Detais v Details of the initialization can be viewed by clicking on the
103. Sample list Choose the SampleList Loader option in the drop down menu Number of Unknown samples will be displayed in the Number of samples field when the desired Sample List is loaded The number of Unknown sample replicates was defined during run design Chapter D2 2 and is displayed in the Sample replicates list Sample replicate number can be changed compared what was defined during the run design e Include limited CD box is ticked if a partially used limited CD was included when the run was designed Chapter D2 2 It will always be the first CD in the Run that is partially used It is possible to remove limited CD or change number of available Mixing CD structures The Gyrolab Mixing CD has 48 structures e Mark Use spiked unspiked check box if this option was used during Run set up Chapter D2 2 The CD structure consumption is calculated based on number of samples and repli cates For all samples position on the CD s is automatically randomized and dis tributed by the software For multiple CD runs If Calibration Controls are used these are placed on each CD that does not have a corresponding Standard series D 22 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software Step Action 4 Click Loading List Gyrolab Control Loading screen is opened Gyrolab Control He View ES SK DM tomlin GYROS Gyrolab Control Loading Pos ample Concentration Page 4
104. Select ADA controls in the ADA control name list s ADA controls specified in step 9 are available D 18 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software Step Action 11 An example of an experiment set up is given below Name ADA 1 Kon Ecreering homogeneous Acidic reagent addition Acid dissociation _HAC 300mM pH 2 Detection reagent mix addition Neutraization_1MTrispH8 0 Number of Standard series 0 M Use on all CDs Number of Quality controls 0 I Use on al CDs Number of ADA controls 5 7 Use on all CDs 12 More analytes and experiments can be added e Add additional Analytes by clicking in the Analytes bar e Delete Analytes by clicking x in the Analyte bar e Add additional Experiments to an Analyte by clicking ES in the Analyte bar Delete Experiment by clicking x in the Experiment bar Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A D 19 D2 Gyrolab ADA Software Step Action 13 Select Generate Sample List template Number of unknowns O Same value must be used when executing run Unknown replicates Same value must be used when executing run Include limited CD Number of free segments Number of unknowns is doubled and subgroup set to Use spiked unspiked C spiked unspiked in sample list Generate Template e Save the Run e To save a new ADA Run click Save Browse to select folder and cli
105. Set if the acceptance criteria LLOQ and ULOQ represents the back calculated Neat i e 100 matrix concentration values or the Diluted concentration values C 42 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Cy Analyze data C4 4 1 Curve fit models Dose response curves are used to calculate concentrations of unknowns in many types of immunoassays The X axis shows concentration of an analyte the substance to be studied The Y axis shows the fluorescent response in the assay Different biological results will fit to varying extent to different curve fit models Testing different curve fit models may identify an improved curve fit With the four parameter logistic curve the change from the initial value and towards the final value is fairly symmetrical When the data does not show this symmetry the resulting fit may not be adequate The five parameter logistic curve remedies this situation by adding an asymmetry factor 4 4 1 1 Four parameter logistic model A dose response curve with fairly symmetrical transition from one response level to another Model equation y A B 1 x Q B Model parameters A The bottom level of the curve i e the minimum level of y B The top level of the curve i e the maximum level of y C The EC50 value represents the x value at which the middle y value is attained D The slope factor A positive value is returned when y is decreasing as x increases and a negative valu
106. Table B3 3 Details for Sample List items Sample identity Column C Used Used Used Used Mandatory Optional Optional Optional for Unknown samples not used for other sample types Mandatory Mandatory Sample group Column D Not used Used Not used Used Table B3 4 Basis for sample statistics B3 Design run Information Sample Subgroup is used to subgroup samples within a Sample Group or Sample identity with common properties for example samples given different treat ment or from different time points Sample subgroup is used as basis for statistical analy sis in Gyrolab Evaluator software Table B3 4 Basis for sample statistics on page 43 below A Microplate identity must be entered Identity of microplate well where the sample is located Sample subgroup Statistics based on Column E Not used Sample identity Not used Sample group Used Sample identity and subgroup Used Sample group and subgroup Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 43 B3 Design run B3 2 4 Prepare Wizard Run Step Action 1 Click Execute Run on the Main menu 2 Browse and select desired Run as set in Chapter B3 2 4 from the list and click OK Runs that are not complete and thus not ready to execute are marked with a zigzag line More information is needed before the Run can be 9 executed 3 A screen is opened Run Protein Quantificati
107. UMS RUM 25055 casada ques tiered attends inca gia gba nas E ealeidlp salen aioe sa sane A 19 A31 3 Custom RUN Lasesauesa nossas Criaa INTE CENA ENE a ads asas dada aio Naa aids A 20 GyrOlab Methods assess amora casaria serasa cessar asi esaerseda sos A 20 Run setup and recommendations cccceeceeceeeeeeees A 21 A3 3 1 Standard samples and Blanks ccescesceeeeceececeeeees A 21 A3 3 2 Calibration Controls c ccc ccccecececeecceeecnseeeceeeesceeess A 21 A3 3 3 UNKNOWN sampleS ssssssssssssssssssseessssseessesssesssssseese A 21 A3 3 4 Quality Controls scienne A 21 ASSAY optimization cece eee eeceeceeceeeceeceeseeeeeeseesees A 22 A3 4 1 Capture reagent concentration eeeeeeeeeeeeeeeeeeeeees A 22 A3 4 2 Detection reagent concentration ssssssssessessssssssseese A 22 A3 4 3 Evaluation of PMT Fluorescence detector settings A 23 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A1 A1 Important user information Important user information A1 1 User manuals Gyrolab Instrument Guide is the main manual for the Gyrolab system It contains basic operational instructions maintenance procedures and safety information It also holds guidance on how to decontaminate the instrument which is mandatory before a service visit if the system has been exposed to biohazards Gyrolab Instrument Guide is found in the instrument binder There are two versions of Gyrola
108. Unknown samples Step Action 1 Thaw sample vials completely on ice NOTE Avoid repeated freeze and thaw cycles of samples Aliqout samples before freezing 2 Vortex the vials gently 3 For serum and plasma samples and all other samples that may contain particulate matter with cell debris or pellet centrifuge 3000 x g for 15 min at 8 C B 52 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Step 4 5 B4 2 2 Step 1 NOTE NOTE By Prepare samples and reagents Action Dilute samples to concentration specified in the Loading List using appropriate Rexxip buffer The dilution factor needs to be optimized for each analyte assay format and matrix Dilution should be made so that buffer characteristics are as similar as pos sible for all samples Ensure sufficient mixing Use microtubes for mixing of small samples volumes Load microplates Action Add reagents samples and solutions to microplates Sample volume microplate name and microplate well is specified in Gyrolab Control Loading list Chap ter B3 2 4 e Capture reagent e Detection reagent Unknown samples e Quality Controls Standard series samples Blanks e Wash solutions For recipe refer to Chapter E1 Cover filled wells temporarily during preparation of microplates for example with PCR lids to avoid evaporation When a microplate is loaded apply Microplate Foil using a Microplate Foil Adapter Instru
109. Working solutions cccccc esc eecceceeeceeceeseesseeseeaeeeseees E 5 1 2 1 Bioaffy Pump Liquid eee ee cece ec eceeeceeeetceeeeneneaees E 5 E1 2 2 Bioaffy Wash Station Solution 1 cece eee cece ee ee ee ee eee E 5 E1 2 3 Bioaffy Wash Station Solution 2 cee eeeeeeeeeeeeeeee ees E 5 E1 2 4 Standby Solution 2 0 cece ceeeeeeeeeeeneeeeeneeeneeseeeeeaeees E 7 E1 2 5 Needle Sanitize Solution ccc ccceeceeeeeesteectenceenceeaee E 7 E1 2 6 Wash Station Sanitize Solution ccceeseeeeeeeeeeeeeeeees E 7 E1 2 7 Needle Desorb Solution cceceeeeeeeeeeeeeeceenensneeenees E 8 E1258 General DUPTEMS isc iiccveceseicssvaeeseeeoweceaseesccedsccs aa Via en ce E 9 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A E1 Recipes E1 Recipes In this chapter recipes for Gyrolab Runs maintenance and sanitization procedures are provided F1 1 Stock solutions 10 Tween 20 To prepare 100 ml Dissolve 10 g Tween 20 in 90 g deionized distilled water Storage Store at room temperature up to six months and keep protected from light 20 sodium azide NaN A WARNING Sodium azide NaN is very toxic Handle with care To prepare 100 ml Add 20 g NaN to 100 g Milli Q water e Stir for 20 hours Storage Store in a hood at room temperature for up to 1 year 10x PBS with sodium azide
110. a particular purpose Neither Gyros nor any party involved in creating producing or delivering this document shall be liable for any damages arising out of access to this document or any errors or omissions in the content thereof A1 4 Symbols The following symbols are used throughout Gyrolab User Guide to draw attention to important usage and safety issues when working with the Gyrolab instrument WARNING Indicates a situation that could result in potential injury to operators of the equipment or those nearby Situations highlighted with these precautionary symbols may also cause mechanical or electrical damage to the Gyrolab instrument CAUTION Indicates an action or condition that could potentially damage equipment data or materials To disregard this caution may cause mechanical damage Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A1 Important user information NOTE Provides and highlights information for the user that will help ensure proper execution of an action or procedure TIP Provides suggestions A1 5 User training Gyros provides Gyrolab user training The system should not be used by personnel which has not been given this training A1 6 Trademarks Gyros Gyrolab Gyrolab xPlore Bioaffy Rexxip and the Gyros logo are trademarks of Gyros Group All other trademarks are the property of their respective owners A1 7 Patents Products and technologies from Gyros are covered by one or more
111. ab Serial Dilution Analyis software module is compatible with Gyrolab Evaluator version 3 2 or higher and is installed by the Gyrolab user Contact Gyros to purchase Gyrolab Serial Dilution Analysis and receive an installation CD Step Action 1 Insert Gyrolab Serial Dilution Analysis installation CD in the CD drive NOTE Gyrolab Evaluator must be installed on the computer prior to installation of Gyrolab Serial Dilution Analysis 2 Gyrolab Serial Dilution Analysis installation screen opens pod Ora Yad If the installation start screen does not appear automatically browse for the CD folder in Windows Explorer and double click on the file splash autorun exe 3 Select Installation Guide to view installation instructions Select User Manual to access Gyrolab User Guide e Select Exit to exit installation procedures Select Install Acrobat Reader and follow the instructions to install Acrobat Reader This is needed only if your system does not have a pdf reader already Select Release Notes to view information on this software release L Select Install Serial Dilution Add on to start installation Follow the instructions in the installation wizard D 58 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A GYROLAB USER GUIDE E Recipes Contents E1 RECIPES a a aoa ratoeira qa aceon ea later hoe eee E 3 E11 STOCK SOIUTIONS asc esesessensnaessess sacvesevesaceevevensevevevevere cents E 3 E1 2
112. ab Tem plates Lists folder This folder should be kept for list templates only Click File Close to close the Transfer list O Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H Doo23573 A H2 Custom Run workflow Transfer List information item Use Exact Specifies if Exact mapping will be used This value can be Yes or No Mapping Yes the number of samples entered must match the number stated in the Sample List Cell B1 e No itis possible to enter the same or a lower number of samples than the number stated in the Sample List CD type Specifies the CD type Cell E1 Segment The segment numbers each refer to a specific segment on a CD microlab oratory The segment are used in order Segment 1 refers to the first Column A available segment on the CD segment 2 means the second available seg ment etc For Bioaffy 20 HC and Bioaffy 200 CDs that have 14 segments on each CD If more than one CDs are used segment 15 means the first seg ment on the second CD segment 16 means the second segment on the second Bioaffy CD microlaboratory etc For Bioaffy 1000 CDs that have 12 segments on each CD If more than one CDs are used segment 13 means the first segment on the second CD segment 14 means the second segment on the second Bioaffy CD microlaboratory etc If partly used CDs are included in the Run there are less than 14 12 for Bioaffy 1000 segments available on those CDs and the numbering of segments will be diffe
113. able to open Export Target in readable format dialog Browse and select desired export folder e Click Export readable e Click OK in the Export Readable Target dialog to confirm export read able The selected Target is now present in a readable format in the selected export folder Delete Delete is used to delete Target files Select item to be deleted from Target screen list e Click Delete e lick OK in the Delete Target dialog to confirm deletion The selected Target is now deleted from the Targets screen list Click on Close in the top right hand corner of the Targets screen to exit F2 2 m List Loaders Click on List Loaders on the main menu to access the SampleListLoader screen The SampleListLoader screen lists available List loader files Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2 Gyrolab Administration Tool List Loader SampleListLoader Description This list loader works with Custom and Wizard design typ System version 1 Version 5 3 0 Supported design types Custom Wizard SampleListLoader WorkListLoader It is possible to perform four different administration actions Import Export Export Readable and Delete NOTE Select a List Loader in the list to activate inaccessible task buttons Button Action Import Import is used to import a List Loader to the Administration Tool to make it available for use in Gyrolab Control Click Import to op
114. access LED Instrument mode LED F1 1 3 1 Fi Gyrolab Control Function Launches the Execute Run screen to prepare and start a Run Chapter F1 1 3 3 Launches the Prime screen to set priming parameters perform instrument priming refer to Chapter F1 1 3 4 Launches the Maintenance screen to perform instrument prim ing and or a cleaning method refer to Chapter F1 1 3 5 Starts system initialization refer to Chapter F1 1 3 6 Launches the Configure System screen to change the system configuration refer to Chapter F1 1 3 7 Launches functionality to read information from a CD tag Logout from Gyrolab Control Launches the help system refer to Chapter F1 1 3 10 Displays information on software versions and licences refer to Chapter F1 1 3 11 Displays information about alarms refer to Chapter F1 1 3 12 Indicates instrument access status refer to Chapter F1 1 3 13 Indicates instrument mode refer to Chapter F1 1 3 14 Design Method Design Method function is used for setting up new or edit existing Methods to be used in Runs Methods can be customized by Gyros to suit specific needs Contact Gyros for more information F1 1 3 2 Design Run The information required to perform an immunoassay on the Gyrolab instrument is collected in a Run The function Design Run is used to create edit and delete Runs Input data for a Run differs depending on which design type which type of Run is used e Fora detailed descriptio
115. ain menu The Run screen appears Root Content 3 folders 4 runs Attribute Folders and Runs allowed Run comete Approved 5 e To create a new Run click New Enter a Run name in the Run Name field To edit an existing Run browse and select the desired Run and click Open 6 Select Wizard in the Design Type list and click Select The Wizard panel appears Run name E Design type wizard Select Reselect To change design type highlight the design type in the Design Type list and click Reselect Comments for the Run can be made in the Comments window for example what type of assays the run is intended for Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A B 19 B3 Design run Step T L 8 S Action Select Method and click Select The Select Method dialog is opened amp RootlBioaffylWizard methods Bioaffy 200 wizi Content O folders 2 methods Attribute Folders draft methods and approved methods allowed II Method Approved Complete 200 3W 001 A lei le 200 3W 002 A w zZ Browse and select desired Method The selected Method must contain W in the name which indicates that it is designed for use with a Wizard run refer to Chap ter A3 2 for more information Click OK The selected method is added to the run design and method i
116. ains check and refit other cables controller cables and USB cable If problems still remain contact Gyros x Finish Details W il Error message Possible cause Example of error message LIF correlated error messages example in figures below Possible cause e Dislocated Controller cables A Gyrolab Control P Initializing System DETECTOR 0 initialization failed Station 1 initialized successfully SMARTLABEL O initialized successfully Station 3 initialized successfully INSTRUMENT 0 initialized successfully ROBOT 0 initialized successfully HEAD O initialized successfully SPINNER O initialized successfully SYRINGES O initialized successfully PINS 0 initialized successfully WASH O initialized successfully DRY O initialized successfully WASTE O initialized successfully CAROUSEL O initialized successfully WASH 1 initialized successfully BARCODE O initialized successfully Station 4 initialized successfully Station 5 initialized successfully DETECTOR O initialization failed One or more module s failed to initialize No immediate action suggestion available Gi Instrument issues Action Check Controller cable 3 Chapter A2 3 Disconnect and reconnect the cable Retry instrument initiation If problem remains check and refit other cables controller cables and USB cable If problems still remain contact Gyros Details W
117. alyte information and Advanced settings Run name LIMS RUN 01 A Design type LIMS v Select _ Reseect LIMS ra Method Bioatfy 200 3 step C A D wiz v1 Select Method information Root Bioaffy Wizard methods Bioaffy 200 wiz Bioaffy 200 3 step C A D wiz v1 Gyrolab Bioaffy 200 1 capture transfer 1 detect transfer Detection setting Detect PMT 1 s Analyte information im Analyte name Capture reagent addition Detection reagent addition Advanced settings Process order on CD By Gyros recommended w Output format Generic Raw Data O Basic format O Extemal format Import Format View Format Comments 6 In the Method information panel select a detection setting from the Detection setting list Result files will only contain data for the selected detection level 7 In Analyte information panel set Analyte name Capture reagent name s Capture reagent addition Detection reagent name s Detection reagent addition NOTE The number of capturing and detecting reagents displayed may differ depending on the Method 1 step 2 step 3 step or 4 step D 40 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D3 Gyrolab LIMS Interface Step Action 8 In Advanced settings panel select Process order on CD The sel
118. anaaaanannaannannuaa O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 45 F 46 F2 Gyrolab Administration Tool User level Method Developer Operator Description A Method Developer can develop methods and configure or align the system In addition a Method Developer can perform all actions of Operators Complete user level privileges are indicated by ticked boxes below You anent pxssword FIT 7 gt FF pen Method F Edt Method F View Software Versio F Vaw Hain Tort F reeet mamen EF Cesto apcrowed Mathie RE Move metros E morto Foge TE ocete c F moot me R Spots E cesto e TE Edt Ad Poker E Est Lovet 1 Folder E idt Level 2 Folders FF Ooloto Rur E Create New fur EE orra syetan 0 reot an CEST FE pert Desg Type E apot Desp Tyee E mrm EE export kuskit mothe E foot Kaki CD E hoot Pie Pury F ioon baai F roo Mantorurcu EF celta Mauntorunra EE import Target EE Sedrun proper EP EvalMaru folder FE Exalta promt E evaaa TE Eva Acristrate project PF Dvd Manage edi tore quant report FF code vt sem o dat F Exsicontgue quant presentanen EE Eyal Export orate E Sjena quint ann das FE Exajuroo setting Re ae setting E Eval View project EE erot toit Kee E noot pate E smart muto An Operator can perform runs but cannot edit existing runs or con figure the system Complete user level privileges are indicated by ticked
119. and version in the Audit trail This is done to ensure full traceability of results It is possible export and print Audit trail reports This chapter describes Audit trail for Projects refer to Chapter 2 3 for information on Audit trail for the Gyrolab Evaluator Step Action 1 Select View Audit trail in Gyrolab Evaluator Project view to display the Audit trail log 2 The Audit Trail window opens W Audit Trail Assay_A2 Project version User Adminstrator 6 7 2031 7 39 22 PM Bice ag entire standard point from standard Project version 3 User Adminstrator 6 7 2011 7 37 27 PM Added curve comparison analysis Project version 2 User Administrator 6 7 2011 7 32 23 PM Removed outlier Project version 2 User Administrator 6 7 2011 7 31 29 PM stew To review details click the Open button for desired Project Version That version of the Project is opened as read only e To view details of an analysis click analysis expander e To export a copy of the Audit trail in text format click the Export button Browse for desired location and click OK 3 Click Close to go back to Gyrolab Evaluator Project view C 26 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 3 Manage analysis projects 3 11 Reports and report data export 3 11 1 Report content A Run report contains Run name and other Run information e Unprocessed data raw data e Version number of the Gyrolab Eva
120. anol Dissolve 8 77 g NaCl Mw 58 44 g mol in 100 ml 20 EtOH Filter through a 0 22 um filter To prepare 100 ml O Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H Doo23573 A E1 2 8 PBS T Purpose Composition To prepare 20 ml Storage PBS 0 2 BSA Purpose Composition To prepare 20 ml Storage 1x PBS Purpose Composition To prepare 20 ml Storage E1 Recipes General buffers PBS T is a buffer for dilution of capture antibody and column wash in CDs 15 mM phosphate buffer 150 mM NaCl 0 02 NaN3 0 01 Tween 20 e Mix 2 ml 10x PBS with 0 2 NaN3 20 ul 10 Tween 20 and 18 ml with deionized water Filter buffer through a 0 22 mm filter Store at 4 C Storage buffer Dilute Detecting reagent to 1000 nM after labeling 15 mM phosphate buffer 150 mM NaCl 0 02 NaN3 0 01 Tween 20 Mix 2 ml 10x PBS with 0 2 NaN3 400 pl 10 BSA with 18 ml with deionized water Filter buffer through a 0 22 mm filter Store at 4 C During labelling of fluorophore and biotinylation 15 mM phosphate buffer 150 mM NaCl 0 01 Tween 20 Mix 2 ml 10x PBS 20 pl 10 Tween 20 and 18 ml deionized water Store at 4 C Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A E1 Recipes ee gt E 10 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A GYROLAB USER GUIDE F System administration and configuration Contents F1 Gyrola B COr
121. ap ter B3 2 4 Run Protein Quantification 2 CD type Gyrolab Bioaffy 200 Execution name RARA O Use MP id Use foi or noid HHH Samples MP type MP96 PCR Identity Loaded No of Samples MP1 No 20 Load Unload O wash Station Solutions Solution Wash Station Confirm Connect pumpliguids Pi Confirm Connect Reagents Name Ideni Available Load Unload EE CD data Identity Segments Status Start Structure Load Unload 1 CD is needed 0 loaded The screen is a check list for the loading steps Upon completion of each step the corresponding green LED on the left panel is lit A Run cannot be started until all LEDs are lit Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A B 61 Bs Start Run procedures B5 2 1 1 Load sample microplates Step Action 1 Click Load in the Samples section The Microplate ID dialog appears 1 Enter microplate identity or use barcode reader 2 Insert microplate at the postion indicated by the light diode into Gyrolab and confirm e Either scan the barcode ID or click Enter ID Manually and enter microplate ID as stated in the Loading List e Insert sample microplate in loading position indicated by the light LED Chap ter A2
122. ash tubing 2 x 1 m Po000010 Waste tubing assembly One set of waste tubing 1 x 2 m H1 2 Recommended consumables Product Recommended supplier Ethanol 95 Albumin bovine serum gt 95 purity Calbiochem Sodium azide e g Aldrich Sodium chloride e g Merck Sodium hypochlorite CAS Number 7681 52 9 e g Aldrich Sodium dihydrogen phosphate NaH PO e g Merck Sodium hydrogen phosphate Na HPO e g Merck Tween 20 e g Merck Virkon S DuPont Syringe filter disposable 0 45 um 0 22 um Syringes 10 ml 50 ml Alexa Fluor 647 Monoclonal Labeling Kit Molecular Probes e Monoclonal antibody labeling kit optimized for labeling of 100 pg antibodies and proteins gt 30 kDa Alexa Fluor 647 Microscale Protein Labeling Kit Molecular Probes e Protein labeling kit optimized for labeling of 20 100 Lg proteins 10 150 kDa Dylight 649 Microscale Antibody Labeling Kit Thermo Scientific Antibody labeling kit optimized for labeling of 100 pg antibodies and proteins 50 150 kDa EZ Link Sulfo NHS LC Biotin Thermo Scientific 8x1 mg microtubes No weight format EZ Link Sulfo NHS LC Biotin Thermo Scientific 100 mg Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Product no 126615 438456 106404 425044 106346 106586 822184 A30009 53051 21327 21335 Product Nanosep 30K OMEGA Centrifugal Devices Note that the size of the filter in the spin column depends on the size of the
123. ata table descriptions ccceceeeeeceeeeeeeeees 38 Cy Analysis settings cccceecescescceeeeecesceeeeeesesseseeeenees C 41 Cel Curve fit IMO EIS ccssecscsecceascive cen decid need Visa doa Ve Nasi nada C 43 Gyrolab Evaluator installation on office computer C 45 5 1 5 2 5 3 5 4 5 5 Gyrolab Evaluator installation package 45 Computer requirements cccceeceecenceeceeecesceeseeeeees C 45 User level requirements ccceecceccecesceeceescesceeseeees C 45 Installation icc sevieve srs iinei aE nese sic se nabaweseses C 46 Database configuration ssssssssssssssssssoseesesessssssseo C 50 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Cu C1 C1 Introduction to data evaluation Introduction to data evaluation This chapter gives an introduction to and describes structure and functionalities available within Gyrolab Evaluator 1 1 Gyrolab Evaluator introduction Gyros provides software to facilitate data evaluation of Runs performed on the Gyrolab instrument e Gyrolab Evaluator is part of the base software package installed on all Gyrolab systems It is designed analyze data from Gyrolab Runs Several evaluation functions and setting options are available to achieve optimal quantification results For an introduction to Gyrolab Evaluator refer to Chapt
124. b Instrument Guide one for Gyrolab xP and one for Gyrolab xPlore Gyrolab User Guide contains detailed information on system usage This Gyrolab User Guide is valid for Gyrolab xP product no Po004943 Gyrolab xPlore product no Poo20300 and Gyrolab Workstation product no Poo01661 with software Gyrolab Control 6 0 and Gyrolab Evaluator 3 3 or higher Gyrolab Quick Guide is a short instruction that describes the most common tasks performed with the Gyrolab system A1 2 Intended use The Gyrolab Instrument is a flexible instrument platform used for running Gyrolab CD microlaboratories The CDs are designed for development and processing of miniaturized immunoassays Products are for research use only Not for use in diagnostic procedures A1 3 Disclaimer Do not use the Gyrolab instrument or other products from Gyros in any way other than described in Gyrolab Instrument Guide or other documentation provided by Gyros The built in safety functions of the system may be reduced if operations not described in Gyrolab Instrument Guide are performed Gyros will use reasonable efforts to include accurate and up to date information in this document but Gyros makes no warranties or representations of any kind as to its accuracy currency or completeness You agree that the use of this document and the content thereof is at your own risk Gyros disclaims all warranties expressed or implied including warranties of satisfactory quality or fitness for
125. b User Guide P0004354 H D0023573 A B3 Design run Statistics based on Sample identity Sample group Sample identity and subgroup Sample group and subgroup B3 Design run B3 1 4 Prepare Wizard Run Step Action 1 2 Click Execute Run on the Main menu Browse and select desired Run as set in Chapter B3 1 4 from the list and click OK with a zigzag line More information is needed before the Run can be lt Runs that are not complete and thus not ready to execute are marked h executed A screen is opened Run Protein Quantification 2 ESA Sample List File C Gyrolab CustomRunLists Sample_list_Protein Quantification 2 8 UNK xIs Cancel List Loader SampleListLoader X Number of samples 8 Sample replicates 2 Use spiked unspiked Only for unknowns Include limited CD 7 Number of free segments 9 Number of CDs 1 Loading List Segments Used Comment To load a Sample List click Sample List file browse and select desired Sample List e List Loader file sets rules for how to import Sample list Choose the SampleList Loader option in the drop down menu Number of Unknown samples will be displayed in the Number of samples field when the desired Sample List is loaded The number of Unknown sample replicates was defined during run design Chapter B3 1 2 and is displayed in the Sample replicates list Sample r
126. base Explorer and select Create view The Create View dialog opens Create View o User Application Folder Method CD Maintenance Process failure Batch Status Type Alarm MP E Em H a a a E E a E E Es A number of filter categories are shown User Design type etc For each category one or more properties are listed Click the expander button for a category to dis play available properties To Include a property in a customized database view Click the icon for the category and select item El User i Administrator e Click Include sutton lll Jan Henriksson e Repeat this procedure to include additional properties All selected items are displayed in the Property list according to Category name Property name User Jan Henriksson Application Folder Method CD Maintenance mMm et O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 59 F3 Gyrolab Result Database Explorer Step Action 4 To Exclude an item in a category from the customized database view Click the icon for the category and select item E User je Administrator e Click Exclude sutton E e Repeat this procedure to exclude additional properties All excluded items are displayed in the Property list according to NOT Category name Property name User jm Administrator NOT User Jan Henriksson Application Folder Method CD
127. biotinylated capture reagent during loading to the capture column and that an insufficient amount of biotinylated capture reagent being loaded Unbound biotin may occupy binding sites on the capture col umn This will dilute the density of spe cific capture reagent and usually lead to less efficient analyte capture and a broader fluorescent column profile Action Discard the biotinylated capture reagent batch and make a new biotinylation refer to chap ter Chapter B1 1 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A G 15 G3 Application issues G 16 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A GYROLAB USER GUIDE H Appendices Contents H1 H2 Products accessories and consumables H 3 Hi Gyros PIOGUCIS rs cacsssecssseaenerscccsvinvesseecsanveervemevexscestedens H 3 H1 2 Recommended cOnMSuMAabDIES ceceeceeeeceeeeeeeeeeeees H 4 Custom Run workflow eee eee eee H 7 H2 1 Introduction to Custom workflow eceeeeeeeeeeeeeeeees H 7 H2 2 Preparation of capture and detection reagents H 7 H2 3 Gyrolab instrument startup procedure H 7 H2 4 Experimental design cece cece ec eceeceeceeeeeneeeeeees H 8 H2 4 1 Create Sample List cece cece cece ee eceeeeeececeeeeeeeteees H 8 H2 4 2 Create Reagent List eee eee ec eee ecencececeeeeeeeteees H 9 H2 4 3 Create Transf
128. boxes below EE Cntete Method EE View Motho E Contige Synem E Eyton tiyr E reer mamen FE Vaw iaio Tor EF Cuesta arqroved Mathod TE Move metros E meet FF income Feo TE Deste co EE asmenetiato uia TE Et Al Potten EF Edt Lovet 1 Folder F Open Run TE Deste Rur F Create Now Pur E Edt te RE Orma Systa F impon un F Mowe tur FE mec Des Tye E Export Desp Twe E manage CO EE export Roseiic o Mother E eun Rescis o a EE tuot pudite Ran EE Expor Readable Design Type F iron Lasd E reset Mantou EE Exmort Target EE Deete Taget FE exalta ot E seda sucerore proper EE Evalimurugo poet EE Eraf dnaisvate project F irain promt FE Eva Maree folder F Evalicui o E fd Moree eine fvdiCortgre wart report OF Crd Edt quent serm o date RE Eval Coriigure cuit erate F exsitortque EE Senon quant awa dats F Evao sonno E tew project R cvai E Ewon natio TE wo patio Beno Mundo do ts Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A F2 Gyrolab Administration Tool F2 2 7 CDs Click on CDs on the main menu to access the CDs screen The CDs screen lists available CD microlaboratories CDs System version supported 1 D Gyrolab Bioaffy 1000 System version 1 Version 1 0 CS Gyrolab Bioaffy 20 HC ED Gyrolab Bioaffy 200 It is possible to perform four different administration tasks Import Export Export Readable and Delete NOTE
129. brane twice Spin up to 11 000 x g for a couple of minutes Do not allow the membrane to dry out prior to use 2 Pipette the required volume of protein 50 to 500 pl into the sample reservoir e Fill up to 400 pl with buffer e Cap the Nanosep device Spin up to 11 000 x g for 2 20 minutes 3 e Wash 2 3 times with 200 400 ul buffer Spin up to 11 000 x g for 2 20 minutes 4 If the reagent appears to have spun dry in the device the reagent is easily recov ered by pipetting several times with approximately 50 pl buffer 5 Dilute the reagent with buffer to get a concentration of 1 mg ml Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 9 B1 Labelling of capture and detection reagents B1 3 2 Thermo Scientific spin column protocol The protocol is copied from Thermo Scientific Protein Desalting Spin Columns product number 89849 which is designed for use on proteins with a My gt 7000 Da Follow this protocol when using Desalting spin column for buffer exchange and azide removal The following solutions and material are required Thermo Scientific Protein Desalting Spin Column e Variable speed bench top microcentrifuge e 1 5 2 ml microcentrifuge collection tubes e Equilibration buffer PBS A Protein Desalting Spin Columns Preparation Step Action 1 Prepare the protein desalting spin column e Invert column to suspend slurry e Twist off bottom closure and loosed cap e Place col
130. cientific spin column protocol B 10 B1 3 3 Concentrate reagent solution ssssssssssesssssssesseresseese B 11 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B2 Gyrolab instrument startup procedure B 13 B2 1 B2 2 B2 3 B2 4 Turn on instrument and GL Degasser ccceeeeeseeeees B 13 Start Gyrolab Control SoftWare ccccccescesceeceeseeeeeees B 13 Initialize the system ccceeccesceeceeceesceeceeeeesseeseeeees B 15 Prime IMSEFUMENL cccccscscescscccsescessnccescsssacessesessens B 16 B3 Design TUN iad ve a kad Be ee ewe ee ees B 17 B3 1 Instructions for Gyrolab xP B3 1 1 Wizard run design introduction eceeeeeeeeeeeeeeeeee B 17 B3 1 2 Create or edit a Wizard Run c cece ecceeeeeceeeeceeeeeuee B 18 B3 1 3 Sample List completion cece eeeee ee eec eet eeceeeeeeeeees B 25 B3 1 4 Prepare Wizard RUN ccecescecceceecescenceeeeeeeenceeseees B 28 B3 1 5 Macros for creating names for folders and files B 31 B3 2 Instructions for Gyrolab xPlore ccecceeceeceeeeeeeeeeees B 32 B3 2 1 Wizard run design introductiOon cccesceseeeeeeseeenes B 32 B3 2 2 Create or edit a Wizard RUN cc cece eceeeceeseeeeeeeeneees B 32 B3 2 3 Sample List completion cece sc eececeeceececeeeeseeseeees B 41 B3 2 4 Prepare Wizard Run sssssssessssssssssssesessssssseesessee
131. ck Import to open Import Maintenance dialog Browse and select desired Maintenance method Maintenance methods must be in zm1 format e Click Import e Click OK in the Import Maintenance dialog to confirm import The selected Maintenance method is now present in the Maintenance method list F 40 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Button Export Export readable F2 Gyrolab Administration Tool Action Export is used to export Maintenance methods from Administration Tool Exported Maintenance method can be imported into another Gyrolab instrument Browse the folder structure to the left panel in the Maintenance screen to locate the folder that holds the Maintenance method to be exported Select Maintenance method to be exported in the list to the right in the Maintenance screen Click Export to open Export Maintenance dialog Browse and select desired export folder Click Export Click OK in the Export Maintenance dialog to confirm export The selected Maintenance method is now present in the selected export folder Export Readable is used to export a readable copy of a Maintenance method This copy cannot be used in Gyrolab Control but it can be useful for example when contacting Gyros for support Browse the folder structure to the left panel in the Maintenance screen to locate the folder that holds the Maintenance method to be exported Select Maintenance method to be expo
132. ck Save To save an edited ADA Run click Save as Name the Run browse to select folder and click Save If Save is clicked the information on the original Run will be replaced with the edited information If any information added to the ADA Run is incomplete or erratic an error message will be presented The specified issues must be addressed before it is possible to save Specify number of samples to be analyzed Unknown samples in the Number of unknowns list Specify number of sample replicates in the Unknown replicates list Highest number of replicates are 8 e If itis desired to use a CD that previously has been partially used check Include limited CD and define number of available segments in the Number of free segments list e Mark Use spiked unspiked check box when performing confirmation runs This will automatically generate a Sample List where the number of unknown sam ples are doubled and sample subgroup for unknown samples is set to spiked and unspiked respectively within each pair Click Generate template e Browse to select Sample List location and click Save A Sample List is generated The Sample List contains all necessary sample informa tion defined in the run design It also holds a suggestion for sample placement within the microplate NOTE The procedure described in this step is the most convenient way to gen erate a Sample List Sample Lists can created manually and automati call
133. ction is supplied together with Microplate Foil Adapter Centrifuge microplates at 3000 x g for two minutes This is done to eliminate bubbles in the microplate wells and to ensure that the samples are at the bottom of the wells Examine microplates after centrifugation to make sure that no bubbles are present Do not stack microplate foil sealed microplates on top of each other The microplate foil may get perforated which may cause evaporation from wells Contamination risk Microplate wells must not contain more than 100 pl of any solution Needles are not washed higher than 1 cm Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 53 By Prepare samples and reagents B 54 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Bs Start Run procedures Start Run procedures NOTE B5 1 B5 1 1 There are two separate instructions one for Gyrolab xP and one for Gyrolab xPlore Instructions for Gyrolab xP Load Gyrolab instrument Before starting the instrument loading procedure ensure that run preparations and sample and reagent preparations have been performed according to Chapter B3 and Chapter Bu Step 1 Action The following screen should be shown after the clicking OK in the last step in Chap ter B3 1 4 Run ProteinQuantification 2 CD type Gyrolab Bioaffy 200 Execution name 2 E Use MP lid Use foil or ne tid HH Confirm Connect Conn
134. ction reagent at 4 C Q Long term storage of detection reagent at 20 C Response Elevated background 01 1 10 100 1000 Concentration pvi Figure 1 An example of elevated background caused by ageing of detection reagent during storage at 4 OC G 14 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A G3 Application issues G3 3 Problems with outliers Possible cause Contaminated spinner positions CD and LIF Action Perform Clean surfaces in Gyrolab instrument on all surfaces Refer to Gyrolab Instrument Guide It is important also to wipe the LIF spinner position with a fresh lint free cloth without fluorescent material G3 4 Poor recovery of proteins after using Nanosep Possible cause Protein interaction with Nanosep filter Pall Life Sciences Action Surface pretreatment can in some situations increase recovery Contact the supplier for instructions G3 5 Poor precision and bad reproducibility between runs Possible cause Capture reagent dilution problems Action Capture reagent dilution in Rexxip buffer might improve results This is not applicable for antibodies The recommended Rexxip buf fers for this purpose are in recommended order Rexxip F Rexxip A and Rexxip AN PBS T usually works well for monoclonal antibod ies G3 6 Increased background in lower parts of the CD column Possible cause Poor biotinylation This may cause loss of un
135. culated analyte con centration of the neat sample If no Dilution Factor value has been assigned a factor of 1 will automatically be used CD ID Yes Identity of Gyrolab CD microlaboratory used to process the sam ples CD Struct Yes Identity of structure on Gyrolab CD microlaboratory where the sample was processed SD Response The standard deviation of responses of sample replicates SD Conc The standard deviation of calculated concentrations of repli cates of a sample Recovery Recovery is calculated for samples with known concentration Standard sample recovery Calculated concentration Expected concentration x100 e Calibration Control recovery Calculated concentration Average concentration for the standard sample s with same concentration x100 e Quality Control recovery Calculated concentration Expected concentration x100 MP Identity Identity of the microplate where the sample was placed MP Well Well position on the microplate where the sample or standard was placed Detect Result e OK The results are approved Not OK The results are not approved The fluorescence sig nal is of poor quality which may be caused by inadequate PMT setting detector is saturated or errors in sample preparation Sample Type Sample types Standard Blank Quality Control Calibration Control and Unknown sample T test The T test analyzes whether a blank and any single Standard respectively belong to the same
136. d The alignment procedure is controlled from the Needles tab on the Configure System screen The tab holds a list of the needles along with their nominal positions and the allowed deviation ranges NOTE The nominal positions and allowed deviation ranges are set by the manufacturer and cannot be altered Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 11 Fi Gyrolab Control Syringe Pumps Wash Stations Needles cp stations Needle configuration 0 4 0 M D E 3 0 9 0 4 m M 4 0 i 0 4 0 M 5 o 0 4 m M 6 0 0 4 m Vv 7 m 0 4 m M 8 0 0 4 fi Vv 0 0 4 0 Vv 0 0 4 m Vv Figure 4 Needles tab Step Action 1 Click Align The Aligning Needles dialog box is displayed F Needle Alignment J y x Alignment of Needle 5 started Alignment of Needle 5 completed New X coordinate value 0 0 New Y coordinate value 18 0 Alignment of Needle 6 started Alignment of Needle 6 completed New X coordinate value 0 0 New Y coordinate value 22 5 Alignment of Needle 7 started Alignment of Needle 7 completed New X coordinate value 0 0 New Y coordinate value 27 0 Alignment of Needle 8 started Alignment of Needle 8 completed New X coordinate value 0 0 New Y coordinate value 31 5 Alignment of Needle 9 started Alignment of Needle 9 completed New X coordinate value 0 0 New Y coordinate value 36 0 Alignment of Needle 10 started Alig
137. d was placed e OK The results are approved Not OK The results are not approved The fluorescence sig nal is of poor quality which may be caused by inadequate PMT setting detector is saturated or errors in sample preparation For ADA controls Negative control or Positive control For unknown sample Unknown The needle used to transfer the sample from the MP to the CD structure It is possible to add comments to individual samples Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software D2 4 2 Confirmation Confirmation assays are performed to investigate whether positive samples from screening assays are true positives Step Action 1 In the ADA Analysis window Chapter D2 4 click on Confirmation Settings The Confirmation Settings panel opens A Confirmation Settings Cut point value A Help You can enter a value for the cut point Note All numeric values must be written in american English e g decimal point not decimal comma Spiked Unspiked Sample Tags Subgroup Spiked Unspiked spiked Oo unspiked F 4 CV unknown samples e In the Evaluation section enter cut point value in the Cut point value field A help section is available with explanations on how to enter numerical values What confirmation cut point to apply for the assay is determined during the assay validation phase For more information o
138. d in Steps 6 to 8 above to be used for the specific experiment To set up an Analyte with one Experiment continue to next step Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B3 Design run Step Action 11 e Select Analyte Analyte 1 Enter a name for the Analyte in the Name text field Select Experiment Experiment 1 Enter a name for the Experiment in the Name text field Select Capture reagent s from the Capture reagent addition list Only Capture reagents specified in step 8 are available Select Detection reagent s from the Detection reagent addition list Only Detect reagents specified in step 8 are available Select number of Standard series in the Number of Standard series list For multi CD runs Tick Use on all CDs to place Standard series on all CDs included in the Run This is only applicable for the Gyrolab xP system When Use on all CDs is ticked unknown samples will be quantified against Standard series on the same CD One analysis per CD will be created If Use on all CDs is not ticked all unknown samples are quantified against the same Standard series NOTE Instead of Standard series on all CDs Calibration Controls can be used Refer to step 7 This is not applicable for the Gyrolab xPlore system Select Standard series in the Standard series name list Only Standard series specified in step 7 are available e Select number of Quality Controls in the Number of Qua
139. d panel appears To change design type highlight the design type in the Design Type list and click Reselect Comments for the Run can be made in the Comments window for example what type of assays the run is intended for Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A B 33 B3 Design run Step Action 4 Select Method and click Select Es Qur The Select Method dialog is opened Foos raoa amp RootlBioaffylWizard methods Bioaffy 200 wizl Content O folders 2 methods Attribute Folders draft methods and approved methods allowed Ill Approved Complete a q Cd ra Browse and select desired Method The selected Method must contain W in the name which indicates that it is designed for use with a Wizard run refer to Chap ter A3 2 for more information Click OK The selected method is added to the run design and method information is displayed ran Method 200 3W 001 A Method information Name Root Bioaffy Wizard methods Bioaffy 200 wiz 200 3W 001 A CD Gyrolab Bioaffy 200 Description Bioaffy 200 CD 3 step capture analyte detection Wizard run One Wash solution used for all needle washes Initial needle wash 2 column washes Capture addition 2 column washes Analyte addition 2 column washes Background detect Detection addition 4 column washes De
140. d prior to dilution refer to Chapter By 1 1 4 Gyrolab xP or Chap ter By 2 1 4 Gyrolab xPlore Ensure to follow Instruction For Use for CDs regarding handling of a partly used CD G 13 G3 Application issues G3 2 5 Elevated background Possible cause Action Was the detecting reagent stored and Refer to Chapter B1 2 for details ding t tions prepared according tocam ndatons In Figure 1 an example of elevated background caused by ageing of detection reagent during storage at 4 2C is shown The Figure shows a comparison of results using two different ali quots of detection reagent from the same labeling analyzed after storage for three months in fridge crosses and freezer circles respectively There is a significantly elevated background after storage at 4 C If using a freshly labeled detection Titrate detection reagent concentration Refer reagent is the optimal concentration to Chapter A3 4 2 for details used Were the correct Rexxip buffers used Refer to Chapter By 1 1 Gyrolab xP or Chap ter By 2 1 Gyrolab xPlore for details Was enough wash solution added to the Refer to Chapter B4 1 2 Gyrolab xP or Chap microplate wells ter By 2 2 Gyrolab xPlore for details Did sample to sample carryover interfere Gyrolab methods with extended wash proce with results dures are available for analytes with specific biochemical properties Contact Gyros for sup port Long term storage of dete
141. d transfer list from current examples will generate following in Gyrolab Evaluator If not using an Experiment name e Capture CD1 Detection CD1 processed on CD 1 Capture CD2 Detection CD 2 processed on CD 2 Two Standard series in duplicates One for each Reagent combination If using an Experiment name One combined set of reagents Experiment name One common Standard series in quadruplicates O Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A H2 Custom Run workflow Example 2 A two CD Run with a common Experiment name One Standard series CD1 e Two Calibration Control samples CD2 Eight Unknown samples four on each CD Sample List not shown The figures included in this example demonstrates Reagent and Transfer lists for a 2 CD Run using one Standard series on CD1 and Calibration Control samples on CD2 Unknown samples are present on both CDs Using this strategy all Unknown samples will be quantified against the Standard series on CD 1 M Mlandator e Iommmene cue coreana A two CD Run using current lists will generate following in Gyrolab Evaluator e One Standard series e Two Calibration Controls Eight Unknown samples quantified against Standard series on CD 1 Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A H 27 H2 Custom Run workflow Example 3 A two CD Run with a common Experiment name Two Standard series CD1 and CD2 e Eight Unknow
142. data population Needle ID The needle used to transfer the sample from the MP to the CD structure Group No Optional information of important sample properties such as common source or treatment Group is only used for Quality Control and Unknown samples refer to Chapter B3 1 3 NOTE This column is only shown for Unknown and Quality Control samples and only if there are any samples with Group information in the Experiment Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C 39 C 40 C4 Analyze data Column heading Subgroup Group aver age conc Notes Original view Description Optional information of important sample properties such as common source or treatment which can be used to sub group samples within a group Subgroup is only used for Quality Con trol and Unknown samples refer to Chapter B3 1 3 NOTE This column is only shown for Unknown and Quality Control samples and only if there are any samples with Group information in the Experiment The average calculated analyte concentration of replicates of a sample group or sample subgroup NOTE This column is only shown for Unknown samples and only if there are any samples with Group information in the Experiment NOTE Even if a group is specified other statistical parame ters is calculated for individual replicates Coefficient of variation of analyte concentration of replicates of a sample group or sample subgroup NOTE
143. database is located on the same computer as Gyrolab Evaluator enter localhost e if the Gyrolab database is located on a different computer than the Gyrolab Evaluator software enter the computer network address for the computer that holds the Gyrolab Result Database e Reset will regenerate the original localhost settings 3 Click Save 4 Press the Test button to verify the connection There should be no red text in the result If there is any text refer to Chapter G2 3 To change database perform step 1 to 3 above and change to desired database in step 2 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C5 Gyrolab Evaluator installation on office computer C 52 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A GYROLAB USER GUIDE D Gyrolab software add on modules Contents D1 Gyrolab VIGWOR quadros ncn E Accs lee de ate we Wd oh Rew D 5 D1 1 Gyrolab Viewer introduction cceceeccecceeceeceeeeeeees D 5 D1 2 View binding profile images sssssssssssssesssssssssssssssess D 5 D1 3 Interpreting Gyrolab Viewer imageS essssssssessesessssees D 10 D1 4 D1 3 1 Using Gyrolab Viewer to optimize PMT setting for a run D 10 D1 3 2 Using Gyrolab Viewer to characterize binding properties D 11 D1 3 3 Using Gyrolab Viewer to investigate outliers D 11 Installation of Gyrolab Viewer ccccecesceeceeseeeeeeeees D 12 O Copyri
144. desired by the user To change password e Mark the check box Change Password e Enter current password in Password field new password in New Password field and confirm new password in Confirm Password field e Click OK NOTE User name and password are case sensitive 4 Click OK to log in or Exit to close the dialog box without logging in Once logged in the Administration Tool main menu will appear 5 Perform the tasks in Gyrolab Administration Tool according to the descriptions below 6 When finished click the Logout button to log out and shut down Gyrolab Adminis tration Tool Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 29 F 30 F2 2 EAEE ET ET ELEVATE au dd F2 Gyrolab Administration Tool GYROS Button Design types Folders Runs Methods Maintenance Users CDs Microplates Liquids Targets List Loaders Logout Help About Gyrolab Administration Tool main menu The start screen in Gyrolab Administration Tool holds the main menu from which all main functions are initiated Only one function at a time can be activated Function Manage different Run design types for example Wizard Run LIMS Run and Custom Run import export export readable and delete Manage folders create edit cut paste and delete Manage Runs import export export readable cut paste and delete Manage Methods import export export readable cut paste and delete Manage main
145. dialog and click Resolve Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 27 Fi Gyrolab Control F1 2 3 13 Instrument access Instrument access status is indicated by a green LED below the function buttons on the main screen o Instrument Access When the instrument access LED is lit the main power is on and the connection between instrument and computer is functioning NOTE methods and Runs can still be created and edited F1 2 3 14 Instrument modes Instrument mode is indicated by a LED below the instrument access LED refer to Chapter F1 1 3 13 in the main menu Even if the instrument access LED is not lit indicating no instrument access o Operating Mode Instrument mode and user privileges refer to Chapter F2 2 6 determine what functions are available in the main menu The change of instrument mode is triggered by actions from the user or the control software These actions differ depending on the status of the Gyrolab instrument Gyrolab instrument modes Mode Power off Initializing Operating Standby Description Gyrolab Con trol software is started Sys tem is ready to be initialized Hardware tests are being performed System is ready for use System has been primed with standby solutions LED appearance off Not indicated by LED On Flashing Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A Accessible from e
146. distilled water Milli Q water to a final concentration of 1 mg ml e Vortex gently Biotin labeling procedure e Mix appropriate volumes of biotinylation reagent and capture reagent solution at a 12 times molar excess of biotinylation reagent compared to capture reagent TIP Formula pmol capture reagent ug capture reagent g mol capture reagent umol Biotin 12 x pmol capture reagent ug Biotin pmol Biotin x g mol Biotin MW Biotin 556 g mol Example For 100 pg of 1 mg ml IgG MW 150 000 g mol add 4 5 ug Biotin reagent umol IgG 100 pg 150 000 g mol 0 000667 pmol IgG umol Biotin 12 x 0 000667 pmol IgG 0 008 pmol Biotin ug Biotin 0 008 pmol Biotin x 556 g mol Biotin 4 5 ug Biotin 4 5 ug Biotin is 4 5 pl of a 1 mg ml Biotin reagent solution e Vortex gently for a few seconds e Incubate 1 hour at room temperature while occasionally shaking the vial gently Removal of unbound biotinylated reagent e Invert the Protein Desalting Spin Column Thermo Scientific to suspend slurry e Place the column in a collection tube and centrifuge at 1500 x g for one minute to remove excess liquid Add the biotinylation mixture to the column center of the compacted resin bed Be careful not to disturb the resin or to allow sample to flow around the resin bed e Centrifuge at 1500 x g for two minutes Biotinylation mixture will be collected in the tube e Put the tube with biotinylation mixture on ice e Discard
147. ditional information such as Standard samples dilution buffer Set Replicates for Blank samples Highest number of replicates is 20 Set Number and Replicates for Standard series samples and Calibration Controls Highest number of replicates is 8 e For each Standard series sample specify the Concentration Specify unit in the Concentration unit text box For multi CD runs the use of calibration controls is added by ticking Calibration check boxes for standard samples of choice A marked check box means that for every CD that does not have a standard curve calibration control s with con centration corresponding to that of the standard sample will be placed instead of the Standard series NOTE Calibration controls are not applicable for the Gyrolab xPlore system It is only applicable when designing a run for a Gyrolab xP system Additional functions e To add additional Standard series click Add To copy settings of one Standard series to a new Standard series highlight desired Standard series and click Copy The new Standard series can be edited and saved by a new name e Highlight Standard series and click Delete to remove a Standard series NOTE Maximum 8 replicates for the same needle can be used in a Gyrolab Bio affy 1000 CD B 36 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B3 Design run Step Action 8 Select Quality Control This step is optional Quality Controls are sample
148. e P0004354 H D0023573 A C 35 C4 Analyze data Step Action 7 In the Data Comparison panel use buttons to display Samples data and overlay chart Overlay chart E Samples data 8 Overlay Chart functionalities oa i 39 10e 1 990 19 000 Curves 5 Cyro 25 cm PMT 1 3 Mousa 25 aM PMT 1 E Semace 25 aM PMT I Click Chart settings above the Overlay Chart to set linear logarithmic scales on the X axis and the Y axis and to edit chart legend Click again to close the Chart settings view To rename curves right click on curve number and select Rename Legend Item Enter new name and click OK to return to default name click OK directly If the curve is not named only the number of the curve is displayed e Overlay Chart zooming Click in the graph and drag cursor down and right to zoom in Zoom out by clicking in the graph and dragging the cursor up and left e Place the cursor on a curve to display a tool tip with the analysis settings used for that curve 9 Click Table Settings to view and edit which Tables and Columns to display Note that only selected tables and columns are included in the Report For data columns definitions refer to Chapter Cy 4 Table Settings Choose Tables Choose Columns E standards dentit S 2 Quality Controls Expacten Coacestratio 2 Calibration Controls P Average Response 4 Unknowns E Average Concentration lal CV Concentration MlAverace Bias E
149. e controls with response below screening cut point are highlighted Refer to Chapter D2 4 1 1 for detailed information on column data e Unknowns Data table with analysis results for unknown samples Samples with results that fall outside of acceptance criteria set in step 1 are highlighted Refer to Chapter D2 4 2 1 for detailed information on column data 3 Click Analysis settings to change settings for the Screening functionality 4 To simplify bar chart view and facilitate data evaluation it is possible to hide unknown samples with response values below the cut point e Mark check box Hide negative unknowns D 26 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D2 Gyrolab ADA Software Step Action 5 General commands for data tables e In the View list select display option for data tables Original A selected number of data columns default Extended All available data columns e Ifthe With replicates box is ticked default all replicates for samples are shown in the table and in the bar chart Untick the box to display average values for samples e Itis possible to include or exclude data points e To exclude a data point right click on the sample and select Exclude To perform this With replicates must be ticked If required by Project settings the reason for inclusion must be specified The change description is included in the Audit Trail To include an excluded sample right click on th
150. e Cut point formula field Enter numbers operators and or parameters or build your cut point for mula using the parameters in the drop down list A help section is available with explanations on available functions For multi CD runs Averages of ADA control response values and standard devia tions can be included in the cut point formula If ADA controls are applied to all CDs in the run check box Use on all CDs is ticked Chapter D2 2 the average ADA control responses and standard deviations will be calculated for each CD individually and resulting cut point used to evaluate samples on that specific CD If ADA Controls are applied only to one CD in the run the average of ADA control results for this CD will be used to calculate a cut point and the same cut point will be used to evaluate all samples on all CDs What screening cut point formula to apply for the assay is determined during the assay validation phase For more information on cut point determination refer to Gyrolab ADA assay protocol NOTE Gyros recommends using floating cut point and to include ADA controls on all CDs in a run In the Acceptance Criteria section add acceptance criteria for ADA controls for precision in the fields Max CV and for response values in fields Lower Limit and Upper Limit Add acceptance criteria for Unknown samples in the field CV unknown samples Values for upper and lower limit can be set for each detect operation in the method C
151. e Project is opened as read only e To view details of an analysis click analysis expander e To export a copy of the Audit trail in text format click the Export button Browse for desired location and click OK 3 Click Close to go back to Gyrolab Evaluator Project view 2 4 Close Gyrolab Evaluator Select File Exit C 16 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 3 3 Manage analysis projects Manage analysis projects This chapter describes how to handle analysis project functionalities within Gyrolab Evaluator All analyses of Gyrolab Runs are organized in Gyrolab Evaluator Projects For an introduction of how to use Projects refer to Chapter 1 2 3 3 1 Project view The Project view is reached by selecting New Analysis or Open Project in the Gyrolab Evaluator Start view described in Chapter C2 In the Project view a number of actions are available refer to Chapter 3 2 to Chapter 3 11 2 for instructions I Assay_NN3_date Gyrolab Evaluato Assay NN3 date Rootj ssay Development lAssay itii po Page N7 2010 01 21 15 3800 Version 1 Working re GYROS Runs Bassey 1 2009 Nov 10 03 45 55 PM Data Comparison Report Analyses RTP Data Comparison 1 Quantification 2 Analysts History Quantification 2 New Crested by Administrator 2010 01 21 15 38 02 ast modifestion by Admiristrator 2010 01 21 15 32 09 Data Comparison Data Comparison 1 New Report C
152. e returned when y is decreasing as x decreases x The known original concentrations y The known responses Fit Method Data is fitted using the Levenburg Marquardt algorithm 4 4 1 2 Five parameter logistic model A dose response curve with asymmetrical transition from one response level to another Model equation y A B 1 x C P E B Model parameters A The bottom level of the curve i e the minimum level of y B The top level of the curve i e the maximum level of y C The EC50 value represents the x concentration value at which the middle y response value is attained for a symmetric curve E 1 D The slope factor A positive value is returned when y is decreasing as x increases and a negative value returned when y is decreasing as x decreases E The symmetry factor x The known original concentrations y The known responses Fit Method Data is fitted using the Levenburg Marquardt algorithm Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C 43 C4 Analyze data 4 4 1 3 Exponential model A curve with exponential growth Model equation y Ae x Model parameters A The point where the curve crosses the y axis B The value of a definite physical constant x The known original concentrations y The known responses Fit method Data is fitted using the Levenburg Marquardt algorithm 4 4 1 4 Straight line Linear model equation y A Bx Model parameters A Linear
153. e sample and select Include To perform this With replicates box must be ticked If required by Project settings the reason for inclusion must be specified The change description is included in the Audit Trail e Itis possible to edit Dilution values If required by Project settings the reason for editing must be specified The change description is included in the Audit Trail e Itis possible to add Notes for individual samples in the right most column if With replicates box is ticked and View list is set to Extended NOTE The number and titles of columns may differ depending on the Run and if replicates are shown or not 6 It is possible to add general experiment comments in the Notes text box located at bottom of the right panel 7 To export data or generate analysis report continue to Chapter D2 4 4 D2 4 1 1 Data table descriptions Screening Columns that are displayed in the Screening view will be included in reports generated If Original view is selected refer to Chapter D2 4 1 step 7 only columns indicated with a Yes below will be displayed If Extended view is selected all available columns are shown Column Original Description heading view Identity Sample identity Subgroup Yes Sample subgroup as set during Run set up refer to Chap ter D2 2 2 Response Yes Integrated volume of the fluorescent binding surface of a reac tion in a microstructure Average Yes Average of response values for replicates of a sa
154. eagent 4 column washes Detect Select Setup D 16 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A D2 Gyrolab ADA Software Step Action 6 Select Reagents The number of reagents may differ depending on what assay for mat and method is used NOTE The software will automatically add reagents to the design depending on selected method The number of reagents can be edited by the user alization tis pH 8 0 Enter Reagent name for reagents The Condition field is optional and can be used for additional information such as concentration value matrix or buffer e Click Add to add more reagents Add and name one reagent in the software for each different reagent required for the assay Highlight reagent and click Delete to remove reagent 7 Select Standard series This step is optional e Standard Series set up is identical to the workflow used with Gyrolab Bioaffy CDs refer to Chapter B3 1 2 Gyrolab xP or Chapter B3 2 2 Gyrolab xPlore 8 Select Quality Control This step is optional e Quality Control set up is identical to the workflow used with Gyrolab Bioaffy CDs refer to Chapter B3 1 2 Gyrolab xP or Chapter B3 2 2 Gyrolab xPlore 9 Enter ADA control name for ADA controls Specify ADA control name for ADA controls e The Dilution field is optional The dilution value is used for concentration calcu lations in the evaluation software The value can be chang
155. eck box Change Password Enter current password in Password field new password in New Password field and confirm new password in Confirm Password field e Click OK NOTE User name and password are case sensitive NOTE The software will request the user to log in anew when the system has been inactive for 31 minutes Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A 2 Log in main menu functions and analysis administration Step Action 3 Gyrolab Evaluator Start view opens Recent Runs Administrator System Administrator The following options are available e Click New Analysis to add Run s to a new Project perform analysis and then save or discard the new Project refer to Chapter 2 2 e Click Open Project to open an existing Project to view or add remove Runs and analysis in the Project refer to Chapter 2 2 2 e Click Manage to create a new Project edit analysis setting for a Project manage the Folder structure or perform searches within Projects refer to Chapter 2 2 3 Access to the Manage menu requires System Administrator or Project Manager user level privileges refer to Chapter F2 2 6 Click on desired Run under Recent Runs to add this run to a new Project refer to Chapter 2 2 4 In the lower left corner current user and its user level is shown Some actions are restricted to certain user levels For information of user levels refer to Chap ter F2 2 6 O Copyright 201
156. ecommended to put the data base backup at a location where regular backup is taken e g on a net work server e Browse for the desired folder and click OK The selected folder is shown in the Backup folder path field Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 65 F4 Gyrolab Database Backup Manager Step Action 3 Check or un check the Use time stamp box If Use time stamp is checked the time and date for the database backup will be included in the database backup file name Each database backup file will have a unique name and the risk of replacing old back up files is minimized If Use time stamp is not checked the database backup file will be saved under the standard name in the selected folder and any previous database backup files without time stamps in the same folder will be replaced The name for the database backup file is shown in the Backup file name field 4 Click Generate backup The back up file is not available in the set folder destination 5 To close Gyrolab Database Backup Manager Click Quit F4 2 Schedule Gyrolab data base backup Database backup can be scheduled as a one time event or as a recurring action using the Windows Task Scheduler Refer to Windows Help for instructions on how to perform a scheduled task Chose Gyrolab Database Backup Manager to run as a recurring task The path to the software is C Program Files Gyros Gyrolab Bin GyrolabDbBackupMan exe
157. ect 1 CD is needed O loaded D The screen is a check list for the loading steps Upon completion of each step the corresponding green LED on the left panel is lit A Run cannot be started until all LEDs are lit Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A B 55 Bs Start Run procedures B5 1 1 1 Load sample microplates Step Action 1 Click Load in the Samples section The Microplate ID dialog appears F Microplate ID 1 Enter microplate identity or use barcode reader es 2 Insert microplate into Gyrolab and confirm or use MP button in instrument to confirm e Either scan the barcode ID or click Enter ID Manually and enter microplate ID as stated in the Loading List Insert sample microplate in loading position Chapter A2 2 1 e Click Confirm The microplate ID will appear in the list on screen 2 Repeat for each sample microplate until all sample microplates are loaded Ensure the BCR is configured so that Enter or Carriage Return is not added when scanning the identity of a MP B5 1 2 Load CDs Step Action 1 Put CDs in room temperature for 30 minutes in the unopened aluminium pouches 2 Click Load in the CD Data section The Load CD dialog opens 1 Insert CD into instrument 2 Press Load or use CD button in instrument to load CD 1CD is required O are loaded Method requires Gyrolab Bioaffy 200 CD id B 56
158. ect Reselect Custom Q Method itom methods Bioaffy 200 Bioaffy 200 3 step C A D v1 Reagent list JReagent_lst_ProteinQuantification 4 View Import Remove Transfer list Transfer list ProteinQuantification 4 E e ere Experiment mapping Reagent combination 2 Capi CD1 Deti CDI 2 Cap1_CD2_Det1_cb2 Comments oats For multi CD runs reagents must be placed in unique microplate wells one per CD and have unique identities even if it is the same reagent Data analysis in Gyrolab Evaluator are based on which reagents Reagent combination that are used for the specific sample It is possible to group sample made with identical reagents but with different reagents names by giving them a common Experiment name Gyrolab Evaluator will analyze all samples with a common Experiment name together if it is present If not present the Reagent combination will be used to group samples Another reason for using an Experiment name is that it is possible to use a simple informative name for example IgG To group reagent combinations for subsequent data analysis Enter identical names in the Experiment name field for regent combinations to be grouped together Experiment mapping Reagent combination 2icapt_CD1_Det1_cD1 2Capi CD2 Deti CD2 IgG To save a new Run click Save Browse to select folder and click Save To save an edited Run click Save as Give the Ru
159. ection defines how samples are distributed on CDs Options available As Work List Select this option to place samples in the order defined in the worklist generated in the LIMS e By Gyros Gyrolab Control distributes samples on CDs to achieve optimal dis tribution of sample replicates Output format Options available Generic Raw Data default All work list information and results are exported in tab delimited text format txt compatible with Watson LIMS Basic format Sample ID and results are exported in tab delimited text for mat txt e External format Click Import Format button to browse and select desired format Click View Format button to view selected format External format is used when a customized output format is required contact Gyros for more information To save a new LIMS Run click Save In the Save as window browse to select folder and click Save To save an edited LIMS Run click Save as Name the Run browse to select folder and click Save If Save is clicked the information on the original Run will be replaced with the edited information NOTE If any information added to the LIMS run is incomplete or erratic an error message will be presented The specified issues must be addressed before it is possible to save 10 Click Close to finish the Design Run procedure D3 3 LIMS worklist generation In your LIMS generate one or more worklists to be processed in the LIMS Run Standards
160. ecuted on a single CD instrument by limiting the Number of unknowns dropbox to not exceed the number of structure on the CD If the checkbox is checked Then the dropbox is limited to one CD If not checked the dropbox is limited to 5 CDs Default values for the checkbox are e If system is initialized it will be checked if the client is connected to a Gyrolab xPlore system Unchecked if connected to Gyrolab xP system e Ifthe system is not initiated a dialog will appear informing the user that configuration is unknown and the checkbox is unchecked If it is desired to use a CD that previously has been partially used check Include limited CD and define number of available segments in the Number of free segments list The Use spiked unspiked check box is specific for the software module Gyrolab ADA Software Refer to Chapter D2 2 for more information Click Generate template Browse to select Sample List location and click Save A Sample List is generated The Sample List contains all necessary sample informa tion defined in the run design It also holds a suggestion for sample placement within the microplate NOTE The procedure described in this step is the most convenient way to gen erate a Sample List Sample Lists can created manually and automati cally generated lists can be edited prior to run start refer to Chapter B3 2 3 However Gyros recommends using the automatically generated Sample Lists as this will
161. ed during data anal ysis Set Type to PC positive control or NC negative control e Mark Use spiked unspiked check box when performing confirmation runs This automatically doubles the number of ADA controls and sample subgroup for ADA controls is set to spiked and unspiked respectively within each pair e Click Add to add more ADA controls e Highlight ADA control and click Delete to remove ADA control Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A D 17 D2 Gyrolab ADA Software Step Action 10 Select Analytes e Analyte and experiment set up is identical to the workflow used with Gyrolab Bioaffy CDs refer to Chapter B3 1 2 Gyrolab xP or Chapter B3 2 2 Gyrolab xPlore except for the addition of a new sample type ADA controls To set up an Analyte with one Experiment e Select Analyte Analyte 1 Enter a name for the Analyte in the Name text field Select Experiment Experiment 1 Enter a name for the Experiment in the Name text field Select reagent s from the drop down lists The number of reagent fields is determined by the number of reagent transfer operations in the method and the reagent field names are determined by the reagent transfer operation names in the method Only reagents specified in step 6 are available in the reagent drop down lists In the example in step 11 there are two reagent transfer operations in the method and therefore two reagent drop do
162. egulations and cannot be edited The report includes raw data and general information about the run and experimental details The software was developed to support users whose workflows require non editable and printable raw data reports Dy 2 Perform run using Gyrolab Control Report After installation of Gyrolab Control Report module during preparation of the first Gyrolab run it is necessary to import target settings for the Gyrolab Control Report module Unless it is desired to change location for the Gyrolab Control Report file at a later time these settings need only be performed once for each user Step Action 41 Prepare the run and edit settings for targets as described in Chapter B3 1 4 Gyrolab xP or Chapter B3 2 4 Gyrolab xPlore When the target screen is reached go to tar get tab Gyrolab Report Gyrolab Control Report result files from the run are always saved in Gyrolab Result Database To create local copies of the result files optional mark the check box Copy file s to disc Targets Reports v Gyrolab Evaluator w Gyrolab Report Process this target v Copy file s to disk Gyrolab Report result folder ramData Gyros Gyrolab Results user date run _ time Browse Gyrolab Report result file name Gyrolabreport run date tme pdf Info This target generates a non editable raw data report in pd
163. em Refer to Chapter D3 for details e Gyrolab Control Report The Gyrolab Control Report module for Gyrolab Control version 5 2 or higher that enables automatic generation a condensed printable raw data report in pdf format after each run on the Gyrolab instrument The generated report is compliant with 21 CFR Part 11 regulations and cannot be edited The report includes raw data and general information about the run and experimental details Refer to Chapter Dy for details e Gyrolab Serial Dilution Analysis The Gyrolab Serial Dilution Analysis module for Gyrolab Evaluator version 3 2 or higher is used for automatic evaluation of spike recovery to verify the sample analysis accuracy using dilution series of spiked and unspiked unknown samples Refer to Chapter D5 for details A2 6 3 Gyrolab software user levels The users of Gyrolab software are given certain user levels each user level given certain user rights privilege depending on their role in the laboratory flow and result generation There are four user levels available System Administrator Project Manager Method Developer and Operator One additional user level is available for Gyros service personnel only refer to Chapter F1 1 3 for details A2 6 4 Gyrolab software terminology list Terminology used in the Gyrolab software and throughout this manual is explained in the list below Term Description Design Type There are a number of workflows or Design Types available fo
164. en Import Rulfile dialog e Browse and select desired List Loader file List loaders must be in zml format e Click Import e Click OK in the Import Rulfile dialog to confirm import The selected List Loader is now present in the list in the SampleListLoader screen Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 55 F2 Gyrolab Administration Tool Button Action Export Export is used to export List Loaders from the Administration Tool Exported List Loader can be imported into another Gyrolab system Select List Loader to export in the SampleListLoader screen list e Click Export to open Export List Loader window e Browse and select desired export folder e Click Export e Click OK in the Export List Loader dialog to confirm export The selected List Loader is now present in the selected export folder Export Export Readable is used to export a readable copy of a List Loader This readable copy cannot be used in Gyrolab Control but it can be useful for example when contacting Gyros for support Select List Loader in the SampleListLoader screen list e Click Export readable to open Export Target in readable format dialog Browse and select desired export folder e Click Export readable e Click OK in the Export List Loader in Readable Format dialog to confirm export readable The selected List Loader is now present in a readable format in the selected export folder Delete Delete is
165. eplicate number can be changed compared what was defined during the run design e Include limited CD box is ticked if a partially used limited CD was included when the run was designed Chapter B3 1 2 It will always be the first CD in the Run that is partially used It is possible to remove limited CD or change number of available CD segments The CD and CD segment consumption is calculated based on number of samples and replicates For all samples position on the CD s is automatically randomized and distributed by the software For multiple CD runs If Calibration Controls are used these will be placed on each CD that do not have a corresponding Standard series Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A B3 Design run Step Action 4 Click Loading List Gyrolab Control Loading screen is opened e Gyrolab Control Loading holds microplate loading information and is used when preparing microplates for a run Name concentration volume microplate and well position is included for all sample types An overview of microplates with indication of used wells is also provided e Click Printer button to print the Gyrolab Control Loading TIP Select File Export to export the Loading list in PDF or text format This is useful when printing from another computer is required 5 Close Gyrolab Control Loading 6 Click OK A screen with two tabs Targets and Reports is opened Copyright 2015 G
166. er 1 and for instructions on how to use Gyrolab Evaluator refer to Chapter Cy Available Add ons and plug ins e Gyrolab Viewer is an add on software module to Gyrolab Evaluator used to study the binding profiles in Bioaffy CD columns produced during data evaluation This can be useful during assay optimization to help identify suitable reagents during trouble shooting to investigate outliers and for quality control purposes For instructions on how to use Gyrolab Viewer refer to Chapter D1 Serial Dilution Analysis is a plug in to Gyrolab Evaluator used for automatic evaluation of spike recovery to verify the sample analysis accuracy using dilution series of spiked and unspiked unknown samples For instructions on how to use Gyrolab Viewer refer to Chapter D5 1 2 Gyrolab Evaluator main features 1 2 1 Data analysis Using the Quantification module analyses of selected Runs using certain analysis settings are performed Different analysis settings can be tested to find optimal curve fits Samples are quantified using the selected Analysis settings Subsets of Run results are selected for inclusion in Reports and the resulting analysis report is displayed in the Project view under Analyses Quantification refer to Chapter Cy 1 Different analyses are compared using the Data Comparison module Chapter 4 2 For example is it possible to compare sample data and standard curves from different experiments in the same Run or from diffe
167. er List ccccesceccecestecteceeceeceesentectecees H 12 H2 4 4 Create or edit RUN cccceceecc cece eeeeesceeteectenseeseeenes H 15 H2 5 Prepare Custom RUN ccceeceecceeceeceeeeeceeseeeeeseesees H 19 H2 6 Sample and reagents preparations H 20 H2 6 1 Capture reagent and detection reagent H 20 H2 6 2 Standard series and Calibration Controls H 20 H2 6 3 Unknown Samples and Quality Controls H 21 26 4 MICO DIALS sssamsas sine rzaco in dns eea sandra isa rap E H 21 H2 7 Start Run procedureS essssssssssssessscssessesessseeeseseeessee H 21 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A H2 8 After Run procedures and result ExpOrt cceeeeeeeeeeees H 21 H2 9 Examples of run set up and experiment mapping H 22 H2 9 1 Examples of experiment mapping for 1 CD runs H 22 H2 9 2 Examples of experiment mapping for multi CD Runs H 25 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A H1 H1 Products accessories and consumables Products accessories and consumables H1 1 Gyros products Visit www gyros com for the latest updates on available products and services Product number Pooo4 42h Pooo4180 P0004253 P0020026 P0003313 P0004861 Po0014820 Po0014821 Po0014822 Po0014823 Pooo4994 P0004995 P0004996 P0004997 P0020033 P
168. er to Chapter C4 4 for more information e Click Next Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 33 D2 Gyrolab ADA Software Step Action 2 Click Quantification in the lower left corner The Quantification window opens A 1 Meeting 2 et 2 O nasonanaias se a e mee T ramo rage stream Aami qem Cie e one ass arsye teses 10 Sete to sa temas NEL Da SA 4 a es tment ee e tm rem cometem comem The left panel of the Quantification window displays available experiments in the run and Run information refer to Chapter Cy 1 The right panel of the Quantification window displays collapsable expandable views for Standards described in Chapter 1 1 e Quality Controls described in Chapter 4 1 Calibration Controls described in Chapter C4 1 ADA controls data table with analysis results for ADA controls e Unknowns described in Chapter 4 1 3 Click Curve Intersection and enter a response value to get a concentration value for where response intersects with standard curve KBE v Chart Settings Standard Curve 100 10 1 Response 0 1 Use standard curve to calculate concentration from response Response 0 818 Concentration 100 05 0 01 100 1 0 Concentration ng 2 10 Standard curve fit status Done Curve Intersection 4 View options chart settings chart zooming inclusion exclusion of data point notes and analys
169. er to Product Information Sheets and Instructions For Use A2 4 1 Gyrolab Bioaffy CDs Gyrolab Bioaffy CDs are intended for quantitative determination of analytes using miniaturized immunoassays Bioaffy CDs contain a number of microstructures grouped into segments of 8 individual microstructures Each microstructure has an individual sample inlet and a volume definition chamber that precisely defines the amount of sample and reagents applied to the column For each segment of microstructures there is a common sample inlet enabling the same liquid to be added to all microstructures in that specific segment See Figure 6 for a view of a Bioaffy CD microlaboratory and Figure 7 for details of an individual microstructure Gyrolab CD Segment Microstructure Prepacked Streptavidin morgtaboratary columns bead Figure 6 Gyrolab Bioaffy CD microlaboratory overview h If Volume definition ommon channel for aren 200 nL liquid distribution Hydrophobic barriers stop liquid flow Individual inlet Volume definition chamber 20 200 or 1000 nL Overflow channel for excess liquid Capture column 15 nL Figure 7 Bioaffy CD microlaboratory microstructure showing functional units including the individual sample inlet Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A A 13 A 14 A2 Introduction to the Gyrolab platform There are three different types of Bioaffy CDs availab
170. erform data analysis on a Run refer to Chapter Cy 1 and Chapter Cy 2 2 2 3 Manage menu The Manage menu holds functionality to administrate Projects To search for folders Project Runs and Analyses refer to Chapter 2 2 3 1 e To explore and administrate Folder structure refer to Chapter 2 2 3 2 e To create a new Project refer to Chapter 2 2 3 3 e To edit analysis settings for a Project refer to Chapter 2 2 3 4 Manage C 10 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C2 Log in main menu functions and analysis administration 2 2 3 1 Search for Folders Projects Runs and Analyses Step Action 1 Click Manage in Gyrolab Evaluator start view and click Search in the Manage win dow 2 In the Search section set search criteria for one of the following items e Projects and Folders e Projects with Analysis Projects with Runs A Projects with Runs Ln a e a Name Versions Latest Version Parent Folder Created by Created Matching Content 3 For Projects and Analyses it is possible include identity number in search criteria The identity number is a unique identifier for the Project or Analysis Project identity number is found on Projects that have been printed or been saved to xps format Analysis identity number is found at the bottom of Analysis reports Click Search 5 Results are displayed in the Results section Sort b
171. eriment mapping Evaluation of results of samples of different types Standard series Unknown Calibration Control Quality Control in Gyrolab Evaluator are based on which reagents Reagent combination that are used for the specific sample By using the option of Experiment mapping refer to Chapter H2 5 it is possible to group sample analyses made by identical reagents but with different reagents names by giving them a common Experiment name Gyrolab Evaluator will analyze all samples with a common Experiment name together if it is present If not present the Reagent combination will be used The following chapters provide examples to high light how sample naming and experiment mapping will affect sample grouping during data analysis in Gyrolab Evaluator H2 9 1 Examples of experiment mapping for 1 CD runs Four examples of run set up for 1 CD runs are provided Example 1 One Reagent combination and one standard curve bip Not Applicable oo n doene o e o d d 2 PR f smn O O E O E E RR RE o o E suas Oo RT o cunts S PS DE Rs un PR crags E sane ES canna E snags E sana ES range PS RS sanar Figure 9 One calibration reference and one standard curve in transfer list A Run using this transfer list will generate following in Gyrolab Evaluator One Reagent combination Capture Detection e One standard curve in duplicates
172. essseee B 44 B3 2 5 Macros for creating names for folders and files B 47 B4 Prepare samples and reagents B 49 B4 1 Instructions for Gyrolab XP sssssssssssessssseoseesssssssessso B 49 B4 1 1 Reagents and samples sssssessssssssssessssesssressessesesese B 49 By 2 2 Load microplates cece ecese ee eceecesceeeeeeseeseneeneeees B 53 By 2 Instructions for Gyrolab xPlore cceccesceeceeeeeneeeeees B 52 By 2 1 Reagents and samples e cece ee eeecec eee ececeeeeeeeeeeees B 52 Bi 2 2 Load microplates sacecccivescccsecsesoedeosones vvedecess iiien B 53 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 5 Start Run procedures s api apne eae dads B 55 B5 1 Instructions for Gyrolab XP ccc ecceeceeceeeeeceeneeeees B 55 B5 1 1 Load Gyrolab instrument ce eeeeceeeee ec eeeeeeceeeeeees B 55 BS 122 Load CDS datsccatscsessecsdoastcesecadenescehdodesansieed N E B 56 B5 1 3 Start RUM encsi sennen cesses cnctevecosteses dies edi seas B 60 B5 2 Instructions for Gyrolab xPlore ccecceeceeceeeceeceeeees B 61 B5 2 1 Load Gyrolab instrument e eenn einen B 61 B5 2 22 LOA CDS rsca cia sr asi assis dead sa dim ads vind Cenas Bida ENERE B 65 B5 2 3 Start RUM ass uere aoie o dsta va dE nai vo cdi sandes aa de nada na singles wis B 66 B6 After Run procedures and result export B 67 B6 1 Instructions for Gyro
173. et tere Pur apon Versor 1 22100211 Runt ZLOB 11 38 54 AM Taanon of reageres vermen 1 0200211 Cptrnze 2010 288 21 20 17 40 PM EB Matra ewer 0 201002 Out 2250 FES 13 02 37 47 EM E 2 Matra vengar 0 20100212 Ogumima 2220 FES 13 I2 47 47 PM E 1 Matra vesen 0 2020022 Cent 2020 085 13 03 17 47 PA as e Saeed ire re 5 To display information for a specific analysis set Click the desired analysis set in the Selected Data panel The selected row in the list is highlighted e Click Run Info to display run information such as user and date e Click Standard Curve Info to display information on the analysis settings used when the quantification was performed EZ 1 Quantification 1 Version 0 Assay 1 2009 NOV 10 03 45 55 PM 4 2 Quantification 1 Version 0 Assay 1 2009 NOV 10 03 45 55 PM Run Info A User Administrator Date 2009 11 10 15 45 55 Number of experiments 1 Number of CDs 1 Standard Curve Info A Fit model Five parameter logistic curve Weight Response Blanks included in fit No Model equation v A B 009 8 Fit status Not OK R2 0 001334 Parameters A 57 973 B 57 973 C 3333 D 0 00013446 E 22 084 6 Untick the box of a specific analysis set in the Selected Data panel to remove that analysis set from the Data Comparison panel Tick the box again to display the analysis set in the Data Comparison panel again Copyright 2015 Gyros Gyrolab User Guid
174. etween Low and Medium ranges for CV conc and Average Bias refer to table below Upper limit of Quantification e For Unknown samples the ULOQ defines the highest level of analyte concentration measurable e For Standards Quality Controls and Calibration Controls the ULOQ defines the border between Medium and High ranges for CV conc and Average Bias refer to table below The T test analyzes whether a blank and any single Standard respectively belong to the same data population Coefficient of variation of concentration of replicates of a sam ple sample group or sample subgroup Set acceptance CV conc values for Standards Quality Controls and Calibration Controls samples for e Low concentration values lt LLOQ e Medium concentration values from LLOQ to ULOQ e High concentration values gt ULOQ NOTE For Quality Control samples the average concentration is calculated on a sample Group or sample Subgroup if there is any sample with Group information included in the Experiment Average Bias from included replicates Average Bias is the deviation from the expected value that is Average concentration Nominal concentration Nominal concentration x100 Set acceptance Average Bias values for Standards Quality Controls and Calibration Controls samples for e Low concentration values lt LLOQ e Medium concentration values from LLOQ to ULOQ e High concentration values gt ULOQ
175. f format from a Gyrolab run The report file is copied to the selected file destination The user sets the name and destination for the report folder and name The settings from the last run of the current user will be pre selected Note that Gyrolab reports are always saved in Gyrolab Result Database Import Target Settings Export Target Settings Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D 48 D4 Gyrolab Control Report Step 2 Action Files are saved to the location specified in Gyrolab Report result folder field and with the name specified in Gyrolab Report result file name Settings are preserved from the user s last Run To import default settings for Gyrolab Report result folder and Gyrolab Report result file name Click Import Target Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Default Settings select GyrolabReportTargetSet tings xml and click Import e To customize settings for Gyrolab Report result folder and Gyrolab Report result file name To edit Gyrolab Report result folder click Browse Browse and click Select to set new folder in the Select folder dialog To edit Gyrolab Report result file name click in the field and edit NOTE The maximum number of characters in folder name and file name is 30 including file extension Do not begin the folder name and or file name w
176. f the Experiment results comprises all results using a common standard curve In some Runs a com mon standard curve is used for all CDs generating a single Data set subset per Experiment subset In other Runs one standard curve per CD is used generating a number of Data set subsets per Experiment subset Each Data set subset of samples is detected in Gyrolab using one or more PMT settings Normally each sample is detected using three different PMT settings In Quantification module analysis one or more PMT setting subsets are selected for inclusion in analysis reports Run results analyzed using Quantification module in Gyrolab Evaluator Results of comparison of Quantification Analyses using the Data Comparison module in Gyrolab Evaluator Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A 17 A2 Introduction to the Gyrolab platform Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A A3 Gyrolab immunoassay workflow Gyrolab immunoassay workflow This section provides an introduction to immunoassay workflow run recommendations and assay development on the Gyrolab platform For further information and support on assay development please contact Gyros A3 1 Gyrolab workflow options There are three different workflow options called Design types available for performing immunoassays e Wizard LIMS available as a software add on module e Custom The Design types differ mainly in t
177. face on the computer will however not be able to follow the process in the instrument any longer nor can it be used for unloading once the run has finished This has to be done manually before a new run is started Results from a run will be transferred to Gyrolab Results Database once the instrument gets contact with the computer again Lost contact with the instrument may occur in the following scenarios USB cable removed or communication disturbed e Computer restarted shutdown e Gyrolab Client Shutdown G1 3 Gyrolab xPlore front panel LEDs Problem Action If the Instrument Ready LED to the left on the front does not light up after a couple of minutes the instrument has failed to start This might be resolved by turning off the instrument using the power switch on the rear of the instrument and try to start again If the LED on the Power button to the right on the front do not switch off after a couple of minutes when trying to power down the instrument the instru ment has failed to power down This might be resolved by turning off the instrument using the power switch on the rear of the instrument and try to start again Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A G1 Instrument issues Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A G2 Software issues This section contains information on how to diagnose and possibly solve problems related to software or software
178. factor B Intersect x The known original concentrations y The known responses 4 4 1 5 MMF curve Morgan Mercer Flodin curve a sigmoidal curve with a transition from one response level to another Model equation y AB Cx B x Model parameters A The level of the curve when x approaches zero B The EC50 factor The term half maximal effective concentration EC50 refers to the concentration of a drug antibody or toxicant which induces a response halfway between the baseline and maximum after some specified exposure time It is commonly used as a measure of drug s potency EC50 value represents the x value at which the middle y value is attained and is pi C The level of the curve when x approaches positive infinity D The slope factor D is always positive A and C values determine if y is decreasing as x increases or y is decreasing as x decreases fitted using Levenburg Marquardt algorithm x The known original concentrations y The known responses Note that the MMF curve model equation can also be expressed as y C C A Ex C 44 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C5 Gyrolab Evaluator installation on office computer Gyrolab Evaluator installation on office computer The analysis software Gyrolab Evaluator is included in the standard installation of the Gyrolab system This chapter described how to install Gyrolab Evaluator on an office computer to e
179. fic CD to be used A transfer list can be used for one specific Run There are several templates available for different types of assays For each assay type one template is provided for running 1 CD and another template for running up to 5 CD microlaboratories Step Action 1 2 Open ta suitable Transfer List Template found in C Program Data Gyros Gyrolab Templates Lists From row 3 and below one row represents one inlet on a CD and column from col umn D and further represent transfer operations in the method The columns labelled M are mandatory and the columns labelled O are optional EEE Se E Eee E F G H o A ee E pping lu 0 Gyrolab Bioaffy 1 M Mandator O Optional Applicable I addition RES a FR DO DR a RR PO O MA L Structure inlet 8 Structure inlet Structure inlet 2 Structure inlet 3 Structure inlet Structure inlet Structure inlet Structure inlet Figure H2 3 Transfer List template NOTE Cells with a red mark in the upper right hand corner have a comment attached The comment is a description of the information to be included in the column cell NOTE The number of columns in the template depends on the number of cus tomized transfers in the used Method Fill in transfer information according to Table H2 2 Click File Save As to save the Transfer list in a folder accessible by the Gyrolab com puter NOTE Do not save the file in the c ProgramData Gyros Gyrol
180. fies the exe file and does not include additional parameter G 10 G2 3 Gyrolab Evaluator Problem Installation and or database communi cation problems Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A G2 Software issues Action Go to the folder C Program Files Gyros Gyrolab Evaluator N N N N soft ware version or the folder that was cho sen for the installation and start the application DatabaseConfigTool exe Database Config Tool Click on Test to check that it is possible to connect to the database and that the com munication with the database is working P Test configuration tel est Results B Test to connect to the database Check application settings EB Load settings from configuration file E Connect to database for user information Connect to example using port 1521 Get host by name from DNS Ping computer Connect to database Check version Connect to database for runs EE Connect to database for projects and analysis results est Details est to connect to computer example Failed Ifthe communication is working all text in the dialogue is green e lf there is a database communication problem the text is colored red e To find out more check messages on the innermost red nodes In the example shown above it was not possible to connect to the computer using the specified host name This can be caused by a firewall on the instru
181. files generated by Gyrolab Control Files are available in the Gyrolab database and accessible through Gyrolab Database Explorer Copies of files may be available in other locations as set during run preparations The locations are displayed in the log panel after a Run Processing information 3 7 09 12 46 47 PM CET CD 0001020 001 Analysis of Detect PMT 25 completed Wrote C Gyrolab Results EvaluatorResult_ProteinQuantification 2_2009 03 07_12_42_10 xml Wrote C Gyrolab Results Administrator 2009 03 07 ProteinQuantification 2_12_42_10 GyrolabReport_ProteinQuantificati Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect ba Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect ba Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect ba Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect Ph Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect Ph Moving data from C Gyrolab Results ProteinQuantification 2 2009 03 07 12_42_10 LIFImages 0001020 001 Detect Ph Data moved successfully Files generated Run execution finished Hatch unlocked Run log panel showing location of generated files O Copyright 2015 Gyros Gyrolab User Guide
182. find the most suitable for the specific assay In combination with evaluating standard curves and result data in Gyrolab Evaluator the Viewer images can provide useful insights To achieve acceptable assay performance reagents with appropriate affinity should be selected When the assay is intended to measure low analyte concentrations high affinity reagents are required For assays with a working range at higher analyte concentrations reagents with lower affinity can be selected Binding profiles where capture reagent analyte interaction is weaker normally display a peak that is broader in radial direction i e the signal is more widely distributed along the flow direction in the microstructure column Figure 3 e Binding profiles of where capture reagent analyte interactions are strong display sharp peaks The reagent is more efficient in enriching the analyte in the top of the column compared to a capture reagent with lower affinity Figure 3 ee tasan Figure 3 Example of binding profiles that indicate lower affinity left and higher affinity right between capture reagent and analyte D1 3 3 Using Gyrolab Viewer to investigate outliers When analyzing assay results Gyrolab Viewer may assist in investigating outliers Fluorescent spikes may occur in the low end of the concentration range and affect the performance of the assay in this region When spikes appear in the column profiles this may indicate contamination in samples
183. g list with volume requirements for all types of samples assay reagents and wash buffer Alternatively the Loading list can be created in LIMS The loading list is used when preparing microplates Refer to Chapter Chapter D3 for more detailed information on LIMS workflow NOTE To use the LIMS Run workflow a license from Gyros is required to activate the add on A temporary license can be provided for a limited trial period Please contact Gyros Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A 19 A3 Gyrolab immunoassay workflow Recommended for e Routine analysis for users with a LIMS A3 1 3 Custom Run The Custom Run workflow is designed for maximal flexibility The Custom Run workflow allows the user to customize what samples are quantified towards what reagent set Custom Run can be used when non standard transfer from microplates to CD microlaboratories is required or when a variation of replicates for different samples and standard points for example during assay development is required No Loading List is generated Transfer and Reagent List necessary Refer to Chapter Chapter H2 for more detailed information on Custom workflow Recommended for Assay development and assay optimization experiments with special demands A3 2 Gyrolab methods Gyrolab methods are comparable to assay protocols The assay run is automated within the Gyrolab workflow but is still as flexible as manual assay protocols
184. ge cccceeceeceeeeees F5 3 Non logged system time Changes ceeeeeee eee eeeees Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Fu F1 Fi Gyrolab Control Gyrolab Control NOTE F1 1 F1 1 1 There are two separate instructions one for Gyrolab xP and one for Gyrolab xPlore Instructions for Gyrolab xP Start Gyrolab Control The control software consists of the server and the client The server must be running before starting the client Step 1 Action Start Gyrolab Server e Click Start All Programs Gyros Server e Gyrolab Instrument Log is displayed and Gyrolab server icon appears on the task bar a Start Gyrolab Control software Select Start All Programs Gyros Client The Login dialog box is displayed Enter user name and password in the Login dia log box NOTE User name and password are case sensitive NOTE The software will request the user to log in anew when the system has been inactive for 31 minutes User Name Password Change Password 7 Gyrolab Control GYR j S Version Password must be changed when requested by Gyrolab Control Password may also be changed when desired by a user he Change Password window opens Enter present Password Enter New Password Confirm Password e Click OK Copyright 2015 Gyros Gyrolab User Guide
185. ged Version number is available as a tool tip C 18 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 3 Manage analysis projects 3 2 Add and remove run in Project Click Edit Add Run or the button to add a Run to an open Project A dialog opens Select Runs to Add to Project Bi A O L 2009 02 04 11 54 45 2009 02 04 13 28 51 ha alt ores stevie bay ha rv Laker Select one or more Runs to be analyzed in the Project and click Add e Unselect a Run by clicking on the name again e Use the list in the down left corner to view different subsets of Runs or all available Runs Select a Run in the Runs list and click Edit Remove Selected Run to remove a Run from a Project 3 3 Add remove and export analyses in a Project To add analyses to the project click Quantification L Quantification refer to Chapter Cy 1 or click Data Comparison Z Data Comparison refer to Chapter Cy 2 To remove an existing analysis from a Project select the Analysis in the Analyses list and select Edit Remove Selected Analysis This action requires System Administrator or Project Manager user level privileges To export save to file an existing analysis select the Analysis in the Analyses list and select File Export Selected Analyses To perform this step the Project must be saved All modifications are logged in the Audit Trail NOTE No further traceability of the file and data i
186. get Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Default Settings select GyrolabEvaluatorTargetSet tings xml and click Import e To customize settings for Gyrolab Evaluator result folder and Gyrolab Evaluator result file name e To edit Gyrolab Evaluator result folder click Browse Browse and click Select to set new folder in the Select folder dialog To edit Gyrolab Evaluator result file name click in the field and edit TIP Macros can be used to construct file names and locations refer to Chap ter B3 1 5 for a list of available macros TIP The settings in the Targets tab can be exported and imported which enables settings to be shared between users instruments and projects 8 The Targets tab Gyrolab Report section contains settings specific for the software module Gyrolab Control Report and is only available if a licence for Gyrolab Control Report has been acquired Refer to Chapter D4 2 for more information B 30 Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Step 9 10 B3 1 5 By using B3 Design run Action Open Reports tab Targets Reports tylesheet Destination YProgramDatalGyrosiGyrolabyTemplatesiStylesheC ProgramDatalGyrosiGyrolabiResults user d J il I DE ii I D gt Add Ei Remove Import Output Settings Export Output Settings
187. ght 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D2 Gyrolab ADA Software 000 eee eee D 13 D2 1 Introduction to Gyrolab ADA Software workflow D 13 D22 RUMISCESUD cspeniaas menta eee ada a io eai ipa mig ipa D 13 D2 2 1 Design Method nacese ii iei i eaae anan D 13 D2 2 2 Design RUMiscvescsvercs anane n a a a nasais ea D 15 D2 3 Prepare RUM assess corsanesan ease seios Ersa D 21 D2 4 Data CValU ATOM ess ssess names do se signlenndeesdinieslsin so do tienen as Es peas D 24 D221 SCKOOMING s asicctuscisdiesweanestassesescnes desde da capita adiu sociales D 24 D2 4 2 CONFIPMATION cc cece eecceeeecceeeeceeeeceseucceeeeceeeeees D 29 D243 QUANTIFICATION viccevisisccwerevdeonesvecsenes SevsasSecatecssaestwseces D 33 D2 4 4 Data export and report generation D 35 D2 5 Installation of Gyrolab ADA Software ccceeceeeeeeees D 35 Gyrolab LIMS Interface ee ee ee ee ee D 37 D3 1 Introduction to Gyrolab LIMS Interface workflow D 37 D3 2 Create or edit a LIMS RUN ccc ccc ce ecee cee eeeeeceeeeeeeees D 38 D3 3 LIMS worklist generation cccccceeccescesceeceeeeeeceesees D 41 D3 4 Prepare LIMS RUN ccccsceesccecsceeseccesscessseesaceeseeees D 42 D3 5 Gyrolab LIMS Interface data output cee eceec eee eeeees D 46 D3 6 Data evaluation ccccccecceesceeccceeseeeesseecteesseeesseees D 46 D3 7 Installation
188. h unlocked Figure 1 Run log panel showing location of generated files B 70 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B6 After Run procedures and result export B6 2 Instructions for Gyrolab xPlore B6 2 1 Finish Run When the Run is completed microplates and CD must be unloaded from the instrument Unloading is carried out in the same way as the system is loaded that is by following the instructions on the screen After each step has been completed a green LED is lit on the left side of each section Step Action 1 The system stops automatically when the run is completed Click Finish The Exe cute Run screen a checklist for unloading appears with a dialog Run Protein Quantification 2 CD type Gyrolab Bioaffy 200 Execution name Protein Quantification 2 o Samples Loaded No of EM O em Name Available Unioael o Please remove the CD and all of the Microplates and confirm Please remove the CD and al of the Microplates and confirm e Remove all of the Microplates Remove CD e Click Confirm Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A B 72 B6 After Run procedures and result export Step 3 B6 2 2 Action Click Finish NOTE Finish cannot be activated until all LEDs are lit in the screen to indicate that unloading is complete The Standby dialog open
189. have Unknown samples on the Sample Microplate and place all other sample types on a Reagent Microplate delete all samples but unknowns from the generated Sample List The software will automatically place deleted samples on a Reagent Microplate during Loading List generation refer to Chapter B3 1 4 When evaluating results in Gyrolab Evaluator refer to Chapter C samples are sorted based on sample identity group and subgroup refer to Table B3 2 on page 27 for details Statistics such as average standard deviation and CV are available for these groups NOTE Only edit rows 8 and below Edits in other parts of the Sample list may cause the list to be incompatible with the run Save the edited Sample List Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 25 B3 Design run Sample List item and column Index Column A Sample type Column B Sample Iden tity Column C Sample Group Column D Sample Subgroup Column E Dilution Factor Column F MP Identity Column G Well Column H Table B3 1 Details for Sample List items Mandatory Optional Mandatory for Unknown samples not used for other sample types Mandatory Mandatory Optional Optional Optional for Unknown samples not used for other sample types Mandatory Mandatory Information The index is an identifier for Unknown samples UNK The form of the entry is predefined and the entries must be c
190. he Gyrolab Evaluator 1 2 4 Traceability of analyses To ensure data integrity and traceability to comply with GxP requirements all data modifications are recorded in an Audit Trail Chapter 2 3 and Chapter 3 10 To further increase traceability it is possible to require users to enter change descriptions for Analyses and Projects 1 2 5 Export of reports Analysis reports and Audit trail reports can be exported in different formats refer to Chapter 2 3 and Chapter 3 11 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C2 C2 Log in main menu functions and analysis administration Log in main menu functions and analysis administration This chapter describes log in procedure and available functions in the main menu of Gyrolab Evaluator For instructions on how to install Gyrolab Evaluator on a office computer refer to Chapter C5 C2 1 Start and log in Step Action 1 Start Gyrolab Evaluator Select Start All Programs Gyros Gyrolab Evaluator 2 Enter user name and password in the Login dialog box and click OK The user name and password is the same for all Gyrolab software For further infor mation on user and password administration refer to Chapter F2 2 6 Password must be changed if requested by the software for example when a new user logs in or if 90 days have passed since last password change Password may also be changed when desired by the user To change password e Mark the ch
191. he way that runs are set up and what output is generated A3 1 1 Wizard Run The Wizard Run workflow is designed for a flexible but also easy entering of various experimental parameters One or more analytes and sets of reagents can be used Gyrolab Control generates a Loading list with volume requirements for all types of samples assay reagents and wash buffer Alternatively the Loading list can be created in LIMS The loading list is used when preparing microplates A Sample List is automatically generated by the software or it can be created in Microsoft Excel All Unknown samples are quantified against all combination of reagents Refer to Chapter B for more detailed information on Wizard workflow Recommended for e Assay development and assay optimization e Routine analysis e Validation experiments A3 1 2 LIMS Run The LIMS Run workflow allows integration of Gyrolab quantification analyses with LIMS Contact Gyros for compatibility questions The LIMS Run workflow is designed for immunoassay work in combination with a LIMS The LIMS Run workflow ensures traceability and efficient communication with LIMS by import of LIMS worklists and generation of output files for LIMS The LIMS Run workflow is GxP compliant One assay and one set of reagents is used per Run The LIMS Run workflow is not designed for assay optimization studies Assay optimization is performed using the Wizard Run workflow Gyrolab Control generates a Loadin
192. ht 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A B 67 B 68 B6 After Run procedures and result export Step Action 2 In Samples section click Unload The Unload Microplate dialog opens F Unload Microplate Please remove MP1 from instrument and confirm or use MP button in instrument to confirm e Remove plate e Click Confirm e Repeat for all microplates 3 In CD Data section click Unload The Unload CD dialog opens unloadcD Remove CD 0001020 001 from instrument and confirm or use CD button in instrument to confirm Remove CD e Click Confirm e Repeat for all CDs 4 In Reagents section click Unload The Unload Microplate dialog opens F Unload Microplate Remove R MP1 from instrument and confirm or use MP button in instrument to confirm e Remove plate e Click Confirm e Repeat for all Reagent Microplates Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B6 After Run procedures and result export Step Action 5 Click Finish NOTE Finish cannot be activated until all LEDs are lit in the screen to indicate that unloading is complete The Standby dialog opens d Gyrolab Control x Would you like to set the system in standby mode e If another Run is scheduled later during the day click No and start the new run e If itis the last Run of the day click Yes The Ensure enough standby solution is available
193. icates multi plied by the dilution factor The average concentration of the spiked sample The concentra tion used is multiplied with the Dilution Factor Dilution Factor is multiplied with calculated concentration Dilution Factor is defined in sample list If no Dilution Factor has been given the value will automatically be 1 The average concentration of analyte in unspiked sample repli cates without multiplying by the dilution factor The concentration from the Unspiked Result column checked against LOD value the Lower Limit of Quantitation and the Upper Limit of Quantitation The reported value will be lt LOD lt LLOQ or gt ULOQ if the value falls outside of the acceptance cri teria The average concentration of analyte in spiked sample repli cates without multiplying by the dilution factor The Spiked Result divided by the Spike analyte concentration multiplied by 100 The Spike recovery percentage checked against the values for lowest and highest acceptable spike recovery Value is either Bad Spike or Pass Either the calculated mean analyte concentration among repli cates or the disposition of the sample based on user input sam ple analysis parameters i e NA for Bad Spike lt LLOQ lt LOD or gt ULOQ The standard deviation of Dilution adjusted unspiked value between the serial dilutions Values are only used if they fall between the LLOQ and ULOQ and have passing spike recoveries The average of D
194. ilution adjusted unspiked value between the serial dilutions Values are only used if they fall between the LLOQ and ULOQ and have passing spike recoveries The coefficient of variation of Dilution adjusted unspiked value between the serial dilutions Values are only used if they fall between the LLOQ and ULOQ and have passing spike recoveries Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D 55 D5 Gyrolab Serial Dilution Analysis Column heading Description Reported Results The main result column The average analyte concentration over all passing dilutions of a sample Results are only reported if they meet CV requirements and if the number of passing dilu tions exceeds the user input number If no reportable numerical results exist the value will be either lt LLOQ lt LOD gt ULOQ or Retest i Comment Space to input any necessary comments about samples D 56 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D5 Gyrolab Serial Dilution Analysis Ds 5 Analysis settings for Gyrolab Serial Dilution Analysis The table below describes available analysis settings for Projects and analyses when analyzing with Gyrolab Serial Dilution Analysis Parameter LLOQ ULOQ Upper spike pass Lower spike pass Acceptable CV Spike concentration Spike subgroup prefix Unspiked subgroup prefix Requested PMT Name Comment The lower limit for the assay that is the LLOQ value The value
195. ing does not affect the physical ability of the Gyrolab instrument but may have an impact on the results Yes This alarm indicates an error in the physical operation of the Gyrolab instrument The instrument will either complete a specific operation or pause immediately It should be possible to resolve the problem and con tinue with the system in operating mode Yes This alarm indicates an error in the physical operation of the Gyrolab instrument The instrument will either complete a specific operation or pause immediately The problem must be resolved and the system must be re initialized View information on individual alarms To display information on current active alarms click View Alarm on the main menu e To view detailed information for a specific alarm select the alarm in the list The additional information is displayed in the box below the list Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Fi Gyrolab Control EC PDC SYSTEM L Alarm information Figure 7 View alarm information When an alarm occurs a dialog box is displayed in which the alarm can be confirmed and the View Alarm dialog can be accessed NOTE All Normal red and Critical red flashing alarms must be confirmed Address the issue displayed in the View Alarm dialog and click Resolve F1 1 3 13 Instrument access Instrument access status is indicated by a green LED below the func
196. inistrator Project Manager Description System Administrators have unlimited user privileges They can per form all actions of all other user levels as well as some actions unique to System Administrators such as creating and editing other users Complete user level privileges are indicated by ticked boxes S Rc d F Oo Foe F F Edt a Pis r F vev A E BF tretirment RE bein E vs Ri E territ Mar F este F Mo Ry Ros F Deer F ime Res F WF aretan Midt Pe Pes dede F oper FE Dolto R FO E mens F oa Sy Fi Bee ww o Ros Ros F manage Feu Fe Re x Fo F g tado 7 Rh F o We Ro E re Res Re F Doista arg tm Ros Em Wa F opor voa Rim E F R eva Fe Fe We BR eval Pe A Res Re F Fe Re Re F Re Re H Ro Be Re Fe Fine Fe Row User Name and Password for Gyrolab Software for one System Administrator user is provided by Gyros during customer training It is the customers responsibility to change User Name and Password for this user to prevent unauthorized use of Gyrolab software A Project Manager can perform administrative tasks such as create folders import and export objects in Administration Tool and approve projects in Gyrolab Evaluator In addition a Project Manager can perform all actions of Operators and Method Developers Com plete user level privileges are indicated by ticked boxes below Er asnannanannanannananam anmaunnaannnnanannanamnanas TEE EES q E ER g 3 r e ni 9 asnnn
197. installation If you cannot identify the problem or if the problem remains please contact Gyros for support G2 1 Problem Sample list error message during Execute Run in Gyrolab Control Not possible to create a status report or result report of type gyr Results are not visible in Gyrolab Result Database G2 2 Problem Back up of the Gyrolab Database using Gyrolab Database Backup Manager is scheduled in Windows The Gyrolab Result Database Manager software opens but does not automati cally start the data back up It waits fora confirmation and someone has to physi cally press the button Gyrolab Control Possible cause e Required information missing in the Sample List e Information missing in Transfer and or Reagent Lists Custom Run only Incorrect computer disc location The run has not completed the results yet If a prob lem has occurred it might require manual action to get the results transferred Action Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A G2 Software issues Action e Open Sample List and add any missing infor mation e Open list s and add any missing information The gyr file must be saved on the local computer disc usually the C disc Restart the instrument and computer Gyrolab Result Database Backup Manager Ensure that the path to Gyrolab Result Data base Backup Manager as used in the Windows scheduled task speci
198. into Gyrolab and confirm or use MP button in instrument to confirm Either scan the barcode ID or click Enter ID Manually and enter microplate ID as stated in the Loading List Insert sample microplate in loading position Chapter A2 2 1 e Click Confirm The microplate ID will appear in the list on screen 4 Repeat for each reagent microplate until all reagent microplates are loaded Ensure the BCR is configured so that Enter or Carriage Return is not added when scanning the identity of a MP Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B 59 B 60 B5 Start Run procedures B5 1 3 Start Run When loading is completed as confirmed by all green LEDs being lit on screen the Run can be started Step Action 1 Close the instrument hatch 2 Click Start An event log is displayed where all steps of the Run are registered along with event time Run ProteinQuantification 2 CD type Gyrolab Bioaffy 200 Execution name ProteinQuantification 2 r CD information Ff Yoon REE Oe r Operation list Particle wash 2 common Particle wash spin 2 apture reagent addition apture reagent spin apture reagent wash 1 apture reagent wash spin 1 apture reagent wash 2 apture reagent wash spin 2 Analyte addition Analyte wash spin 1 Analyte wash 2 Analyte wash spin 2 D alianment 1 r Processing information
199. ion 1 Preparation of capture reagent Refer to supplier provided instructions for the biotinylation reagent The protocol in this chapter is based on instructions for EZ Link Sulpho NHS LC Biotin Thermo Scientific Use 100 ul of 1 mg ml capture reagent antibody or other suitable capture reagent for biotinylation labeling The capture reagent to be biotinylated must be in a buf fer free from stabilizing proteins for example BSA ammonium ions primary amines and sodium azide to obtain the best possible degree of labeling e Ifthe concentration of sodium azide in capture reagent solution is gt 3 mM 0 02 remove the sodium azide refer to Chapter B1 3 e Ifthe capture reagent solution is in an amine containing buffer exchange buf fer to PBS pH 7 2 8 0 refer to Chapter B1 3 e If concentration of capture reagent solution is lt 1 mg ml concentrate capture reagent solution refer to Chapter B1 3 e If concentration of capture reagent solution is gt 1 mg ml dilute with PBS e Ifthe capture reagent t is a powder lyophilized from an appropriate buffer it is reconstituted in PBS Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 5 B1 Labelling of capture and detection reagents Step 2 Action Preparation of Biotinylation reagent Allow biotinylation reagent EZ Link Sulfo NHS LC Biotin to reach room tem perature e Dissolve 0 5 1 mg of the biotinylation reagent in ice cold deionized
200. ion Cut and Cut and Paste are used to move a Maintenance method within the folder Paste structure Browse the folder structure to the left in the Maintenance screen to locate the folder that holds the Maintenance method to be cut Select folder e Select Maintenance method to be cut in the list to the right in the Methods screen e Click Cut Browse the folder structure to the left in the Maintenance screen to locate a new folder for the run e Click Paste The Maintenance method is now located in the new folder NOTE To paste a Maintenance method into a folder the folder must have status Allow Maintenance method refer to Chap ter F2 2 2 Delete Delete is used for to delete a Maintenance method Browse the folder structure to the left in the Maintenance screen to locate the folder that holds the Maintenance method to be deleted Select folder e Select the Maintenance method to be deleted in the Maintenance method list to the right in the Maintenance screen e Click Delete e Click OK in the Delete Maintenance dialog to confirm deletion The selected Maintenance method is now deleted from the Maintenance method list Import Import is used to import Maintenance methods into Administration Tool to make them available for use in Gyrolab Control Browse the folder structure to the left in the Maintenance screen to locate the folder into which the Maintenance method is to be imported Select folder Cli
201. ion list may change Click Settings again to close the Settings view 8 Optional To copy data from Gyrolab Serial Dilution Analysis in text format txt click Copy Data To File button and browse for desired location and click Save 9 Click Create Report 10 Set Analysis Name and click OK 11 The analysis is now saved under Analyses Quantification in Gyrolab Evaluator Proj ect view Expand the structure under the Quantification Report to access the Serial Dilution Report The functionality for exporting analysis reports in xps format is not available for the Serial Dilution Report D 54 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D5 Gyrolab Serial Dilution Analysis D5 4 Gyrolab Serial Dilution Analysis data table description Description of result data displayed by Gyrolab Serial Dilution Analysis is available in the table below Number of columns displayed may differ depending on available sample results and type of sample Column heading Sample ID CD ID Dilution adjusted unspiked value Dilution adjusted spiked value Dilution Factor Unspiked Results Checked Unspiked Results Spiked Results Spiked Recovery Per centage Spike Recovery Check Result Std Dev Average CV Description The sample ID common for a number of sample dilutions Identity of Gyrolab CD microlaboratory used to process the sam ples Average concentration of unspiked spiked repl
202. ired Folder in which the new Project will be placed and click to highlight that Folder Enter desired Project name in the Name text box and click Save The Save Description window opens Save Description Describe the reasons for your changes in the text box below before saving New assay development project Change list Enter a comment in the text box to describe the Project rationale The comment is saved in the Audit trail 2 2 3 4 Edit analysis settings for Project Step 1 2 Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A Action Click Manage in Gyrolab Evaluator start view and click Edit Analysis Settings in the Manage window Refer to Chapter 3 8 for further instructions C 15 C2 Log in main menu functions and analysis administration 2 2 4 Recent Runs menu Step Action 1 Click on one of the run names displayed below the Recent Runs headline in Gyrolab Evaluator start view 2 The Project view opens where the chosen Run has been added to a new Project For more information on the Project view and how to manage and save the new Project refer to Chapter 3 To perform data analysis on a Run refer to Chapter Cy 1 and Chapter Cy 2 To discard the project click File Close or the or click Close button K to close the Project C2 3 Gyrolab Evaluator Audit trail All system and Projects modifications are logged together wi
203. ired Only data from PMTs with names that match the requested PMT name will be included in the analysis Ds 2 Create Run Create the Run using the Wizard workflow Chapter B3 1 2 Gyrolab xP or Chapter B3 2 2 Gyrolab xPlore or the Custom workflow Chapter H2 To enable analysis with Gyrolab Serial Dilution Analysis certain conditions apply to the Sample List Sample Identity must be the same for all dilutions of the same sample Sample Subgroup is mandatory and used to pair spiked and unspiked samples of the same dilution factor The Subgroup shall be set to Unspiked_1 and Spiked_1 for the first dilution pair within a sample Unspiked_2 and Spiked 2 for the second dilution pair within the same sample and so on An example is given in Figure 1 Dilution factor is mandatory to enable calculations For information on the other Sample List fields refer to Chapter B3 1 3 Gyrolab xP or Chapter B3 2 3 Gyrolab xPlore M Mandatory Type M PCR O Optional Name 0 Result File N A Not Applicable Path 0 Sample Sample Sample Dilution RE Er era rou Nr Index M N A Type M M 0 1 2 UNK UNK x Unspiked_1 MP1 Al x Unspiked_2 4 MP1 A2 3 UNK X Unspiked_3 8 MP1 A3 4 UNK X Unspiked_4 16 MP1 A4 5 UNK x Spiked_1 2 MP1 A5 6 UNK x Spiked_2 4 MP1 A6 7 UNK xX Spiked_3 8 MP1 A7 8 UNK X Spiked_4 16 MP1 A8 9 UNK Y Unspiked 1 5 MP1 B1 10 UNK Y Unspiked_2 10 MP1 B2 11 UNK Y Spiked_1 5 MP1
204. is expired Do not use the CD if the CD is expired L Remove the CD from the Gyrolab instrument 5 Click Close to close the CD information screen F1 1 3 9 Logout Logout is used for shut down log off or restart of Gyrolab Control Step Action 1 Click Logout The Logout dialog opens Administrator is currently logged on to the Cancel system What would you like to do 2 Select desired function Shut down Log off or Restart and click OK 3 Gyrolab Control performs desired function Additional windows may open Select desired function and click OK to complete Shut down Log off or Restart F1 1 3 10 Help To access the help section a pdf version of Gyrolab User Guide click Help on the main menu and browse for needed Gyrolab User Guide chapter F1 1 3 11 About Click About to get information about the software versions and licences for Gyrolab Control F1 1 3 12 View Alarm Gyrolab Control has a built in warning system A traffic light icon in the bottom left hand side of the main menu indicates alarm state e o o FEAR eram Figure 6 Alarm LEDs F 14 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Alarms LED Green Yellow Red Red flashing Level No active alarm Warning alarm Normal alarm Critical alarm Fi Gyrolab Control Requires action No Optional A warning means that the system cannot operate according to configuration set up A warn
205. is settings are explained in detail in Chapter C4 1 and descriptions for data tables are found in Chapter Cy 3 5 To export data or generate analysis report continue to Chapter D2 4 4 D 34 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software D2 4 4 Data export and report generation Step Action 1 Optional To export data to tab separated text format txt or to Excel XML spread sheet format xIs click Copy Data To File button browse for desired location and click Save This functionality is useful when further data analysis e g cut point determination calculations are needed NOTE No traceability of results is achieved using Copy Data To File A copy of a Result file is created but this can be done for example before an analysis is saved and it is NOT logged in the Audit Trail To fulfil the requirements of 21 CFR part 11 data must be exported from a saved Project refer to Chapter 3 5 2 Click Create Report to save analysis All results from chosen included experiments and analysis functionalities Screening Confirmation Quantification will be included in the report 3 Set Analysis Name and click OK D2 5 Installation of Gyrolab ADA Software The Gyrolab ADA Software module is available for Gyrolab Control version 5 4 or higher and Gyrolab Evaluator version 3 3 and is activated by the user with a licence key Licences are instrument specific Contact Gyros to purchase Gyrolab
206. ith a number TIP Macros can be used to construct file names and locations refer to Chap ter B3 1 5 Gyrolab xP or to Chapter B3 1 5 Gyrolab xPlore for a list of available macros TIP The settings in the Targets tab can be exported and imported which enables settings to be shared between users instruments and projects Continue with target settings for other modules as described in step 7 in Chap ter B3 1 4 Gyrolab xP or to Chapter B3 2 4 Gyrolab xPlore and with run prepara tions start and finish as described throughout Section B in Gyrolab User Guide When the run has finished Gyrolab Control will generate an output report file in pdf format including specific information about the run Dy 3 Gyrolab Control Report output The report file is automatically placed in the Gyrolab Result Database A copy of the report is if requested by the user placed at the location specified by in the target setting refer to Chapter Dy 2 rs Gyrolab Report GYROS Run Run information Ome ae em 2010 06 18 122908 Aun by Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A The following run experiment and sample information is included Run information Date and Time Run by Method Design type Experiments Sample reagent transfer list file nameis Detect operations Instrument name Database name Gyrolab Control version Experiment information Sample identity Replicate number Sample
207. l Calc Yes Analyte concentration calculated from a single sample response Conc read from a standard curve Average Yes The average calculated analyte concentration of replicates of a conc sample CV Conc Yes Coefficient of variation of analyte concentration of a replicate series of a sample Bias Yes Deviation from the expected value e For Calibration Controls Bias 100 x Calculated Concentration Average calcu lated concentration for the standard sample s Average calculated concentration for the standard sample s For other samples not Unknown Samples Bias 100 x Calculated Concentration Expected Con centration Expected Concentration Average Bias Yes Average Bias for a set of sample replicates Average Yes Average of response values for replicates of a sample sample Response group or sample subgroup CV Response Yes Coefficient of variation of response of replicates of a sample Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Cy Analyze data Column Original Description heading view Dilution Yes The dilution Factor for Unknown samples and Quality Control samples Dilution factor for Unknown samples is added in the sample list For Quality Control samples the dilution factor is entered when setting up a Run using Design Run refer to Chapter B3 1 3 The experimentally determined concentration is multiplied with the Dilution Factor to obtain the cal
208. l version 5 3 and Gyrolab Evaluator version 3 2 or higher converts on column fluorescence data into a binding profile revealing the interaction taking place on the column within each CD microstructure The binding profiles are accessed through Gyrolab Evaluator Gyrolab Viewer is used during assay development for relative ranking of binding affinity and to aid in the selection of optimal reagent pair It is also used during quality control and assay troubleshooting to investigate outliers Refer to Chapter D1 for details Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A 15 A2 Introduction to the Gyrolab platform e Gyrolab ADA Software The Gyrolab ADA Software module for Gyrolab Control version 5 4 and Gyrolab Evaluator version 3 3 or higher is designed to analyze anti drug antibodies ADA assays run on Gyrolab Mixing CD During ADA analysis clinical samples are screened for ADA positives in a screening assay Confirmation assays are then performed to investigate whether positive samples from screening are true positives Evaluation functionalities are available in Gyrolab ADA Software to support these analyses Refer to Chapter D2 for details e Gyrolab LIMS Interface The Gyrolab LIMS Interface module for Gyrolab Control version 5 2 or higher is compatible with the generic raw data file for Watson LIMS 6 4 The software module is designed to support users that carry out experiment set up and data analysis within a LIMS syst
209. lab XP eee ce eee ee eee e eee eeee ones B 67 B6 1 1 Finish RUN sasesescassasasmarcesasaisomeiesosasda vanes eines etecnoceees B 67 B6 1 2 How to turn Gyrolab Off ee eee ce cece eeeeeeeeeeeeeeees B 69 B6 1 3 Generated Gyrolab Control files cece cece ee ee ee eee ees B 70 B6 2 Instructions for Gyrolab xPlore ccecceeceeeeeeeeeceeeeees B 71 B6 24 Finish RUM secs eceasesesdessicenesccetedvew ed ceuicieosvurseescaseessorees B 71 B6 2 2 How to turn Gyrolab Off ee eee ee cece e ee eeeeeeeeeeeees B 72 B6 2 3 Generated Gyrolab Control files eee ee ee ee eee ee eee B 73 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B1 B1 Labelling of capture and detection reagents Labelling of capture and detection reagents This chapter contains protocols for e Biotinylation of capture reagent Chapter B1 1 e Fluorophore labeling of detection reagent Chapter B1 2 Buffer exchange protein concentration Chapter B1 3 For recipes refer to Chapter E1 B1 1 Biotinylation of capture reagent The following solutions and consumables are required e Biotinylation reagent e Capture reagent Milli Q water PBS Protein Desalting Spin Column Thermo Scientific cutoff 7K For larger proteins consider using Nanosep 30K Pall Life Sciences 1 5 2 0 ml microcentrifuge collection tube Step Act
210. laced on the CD and in which operation NOTE Methods and transfer lists are connected through the Run The order of operations in the transfer list must follow the same order as the operations in the method For each customized transfer operation in the method one column is needed in the Transfer list Contact Gyros for more details on method design Second operation in the method The name must be written as Op_ lt your customized transfer name from method gt for example Op_Analyte addition Naming is case sensitive The entries are the reagent or sample name from the Reagent list or Sample list This specifies where the reagent or sample will be placed on the CD and in which operation it will be used NOTE Itis crucial that all replicates of the same Standard series Unknown Calibration Control Quality Control sample are placed on the same CD Third operation in the method to be performed The name must be written as Op lt your customized transfer name from method gt for example Op Detection reagent addition Naming is case sensitive The entries are the reagent or sample name from the Reagent list or Sample list This specifies where the reagent or sample will be placed on the CD and in which operation it will be used Forth operation in the method to be performed The name must be written as Op lt your customized transfer name from method gt for example Op Detection reagent addition Naming is case sensitive The
211. le Bioaffy 20 HC Bioaffy 200 and Bioaffy 1000 The main difference between the three CDs is the sample volume applied over the column Gyrolab Bioaffy 20 HC 8 microstructures x 14 segments gt 112 microstructures generates 20 nL sample volumes making it ideal for quantification in the mg L range This reduces the need for pre analytical sample dilutions Bioaffy 20 HC is suitable for quantification of drug product or contaminants for example host cell proteins in crude cell supernatants Gyrolab Bioaffy 200 8 microstructures x 14 segments gt 112 microstructures generates 200 nL sample volumes making it suitable for assays requiring a modest to low detection limit This is useful for example for quantification of contaminating proteins requiring an assay working range at a modest analyte concentration Gyrolab Bioaffy 1000 8 microstructures x 12 segments gt 96 microstructures generates 1000 nL sample volumes making it suitable for assays requiring a low detection limit The detection limit is lowered compared to Bioaffy 200 in assays requiring an assay working range at very low analyte concentrations A2 4 2 Gyrolab Mixing CD The detection of ADAs is a prime example of integrating sample pretreatment into the nanoliter scale immunoassay workflow of Gyrolab Mixing CD Addition of a mixing chamber allows for greater flexibility in assay workflows requiring additional incubations for equilibration acid treatment or enzymatic reac
212. les In Custom Run panel e Click View button to view the contents of the imported Reagent List file Click Close after viewing e Click Remove button to delete the imported Reagent list H 16 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A H2 Custom Run workflow Step Action 6 Click Import under Transfer List the Import Transfer List dialog appears Browse to locate the desired Transfer list file prepared in Chapter H2 4 3 and click Import Import Transfer List E Gyrolab CustamRunLists E B Reagents_list_ProteinQuantification_3 xls E Reagent_list_ xls a Reagent list Protein Quantification 4 xls a Sample list Protein Quantification 4 xls H Sample list ProteinQuantification 3 xl5 E Transfer _list_Protein Quantification 4 xls Transfer_list_ProteinQuantification_3 xls File name Transfer_list_Protein Quantification 4 xls Files of type In Custom Run panel e Click View button to view the contents of the imported Transfer List file Click Close after viewing e Click Remove button to delete the imported Transfer list Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A H 17 H2 Custom Run workflow Step Action T NOTE After selecting Method Reagent list and Transfer list the Experiment mapping sec tion lists information on Reagent combinations Run name Proteinquantification 4 al Design type as tom Sel
213. les are included in Audit Trail reports Two alternatives are available compressed gyr format and readable XML format F3 5 1 Compressed Audit Trail report Status Report A compressed Audit Trail report is called a Status Report Output format is gyr which is a compressed format suitable to e mail to Gyros support function Since this report does not contain any run data it can be used for support matters where data can not be shared for some reason Step Action 1 To open Gyrolab Result Database Explorer e Open Windows Explorer e lick on Gyrolab Result Database Explorer 2 Gyrolab Result Database Explorer window opens Click Folders B Desktop Main View 3 My Computer E My Network Places g E 3 Right click Main View and select Generate Status Report 4 Set Start date and End date for the status report Default setting is 10 days from current date Generate Status Report 2007 10 21 2007 10 31 x ca Click OK 5 In the Save As dialog name the status report file and browse for desired location The location must be at the local disc usually the C disc Click Save 6 The exported status report is now found at its specified location The file contains the instrument audit trail system log and is compressed to gyr format O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 63 F3 Gyrolab Result Database Explorer F3
214. licates for the same needle can be used in a Gyrolab Bio affy 1000 CD Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Step 11 12 B3 Design run Action Select Quality Control This step is optional Quality Controls are samples with known concentration Quality Controls may be used for quality control or when comparing results from different Runs and experi ments Standard series Replicates 2 v Quality control name Concentration Dilution Add Joc 1 20 0 10 0 Joc 2 40 0 10 0 Delete joc3 80 0 10 0 jec4 160 0 10 0 Concentration unit pM e Set number of replicates in the Replicates list Highest number of replicates is 8 e Specify Quality control name Concentration and Dilution for each Quality Control sample The concentration value corresponds to Quality Control sample concen tration before dilution The dilution value corresponds to the dilution of the Quality Control sample A value of 1 corresponds to an undiluted sample Dilu tion values must be 1 or larger e Specify the unit in the Concentration unit text box NOTE Note that the same unit must be used as used for the Standard series refer to step 7 e Click Add for adding an additional Quality Control sample e Highlight Quality control sample and click Delete to remove e Add additional Analytes by clicking E in the Analytes bar e Delete Analytes by clicki
215. lick Next Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 25 D2 Gyrolab ADA Software Step Action 2 Click Screening in the lower left corner The Screening window opens ADA 1 Floating cut pomt 2011 gt P MAYO 08300 PM rex Ongnai F wab vececates hds negates uninonni andei lowes a fxpermert 1 raras Setengs Ca port 006 a Detect 1 7 Se Chet Detect 5 ia 1 jos pos 0 9 2 e gt e r E E x x k z 4 H i g amp at Comrois Identity 1D CD Struct H 8 0538 6 0252 n PE 0 0388 oa e E gal a E nos 00123 coca L or L k tele i ei sa E sioen Quantita ston Sna Cem aer dom rop The left panel of the Screening window displays available experiments in the Run and Run information refer to Chapter C4 1 The right panel of the Screening window displays collapsable expandable views for e Bar Chart Visualizes average response results for ADA controls and unknown samples compared to the screening cut point Standard deviations are indicated with error bars Samples above cut point are indicated with orange bar color Samples below cut point are indicated with blue bar color ADA controls Data table with analysis results for ADA controls ADA controls with results that fall outside of acceptance criteria as set up in step 1 are high lighted Negative controls with response above screening cut point and positiv
216. lity controls list e For multi CD runs Tick Use on all CDs to place Quality Controls on all CDs included in the Run e If Use on all CDs is selected the Quality Controls samples will be applied on all CDs included in the Run e If Use on all CDs is not selected the Quality Controls samples will be applied on one CD even if the experiment is included on several CDs Select Quality Controls in the Quality control name list s Only Quality Controls specified in step 8 are available The Number of ADA controls field is specific for and only used with the software module Gyrolab ADA Software Refer to Chapter D2 2 for more information Name Analyte 1 Name Experiment 1 Capture reagent addition Cap v Detection reagent addition Det v Number of Standard series 1___ use on all CDs Standard series name Standard A v Number of Quality controls 4 v v Use on all CDs Quality control name QC 1 ly Quality control name QC 2 v Quality control name QC 3 v Quality control name QC 4 v Number of ADA controls O wv Y Use on all CDs Only used in multi CD runs B 38 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B3 Design run Step Action 12 jade e Add additional Analytes by clicking in the Analytes bar Delete Analytes by clicking x in
217. low it to set tle NOTE The purification resin is a 30 000 Mw size exclusion resin Do not use for proteins lt 30 kDa e Add additional purification resin until the bed volume is approximately 1 5 ml Allow the column buffer to drain from the column by gravity e Place column in provided collection tube Centrifuge at 1100 x g for 3 minutes Purification of fluorophore labeled detection reagent e Load 100 ul of the labeled reagent onto the purification column e Place column in an empty collection tube e Centrifuge 1100 x g for 5 minutes Transfer the labeled reagent in the collection tube to a dark vial Determination of concentration and labeling efficiency e Measure absorbance of the purified fluorophore labeled detection reagent at A280 and Asso Dilute an aliquot of the fluorophore reagent 1 10 in PBS for absor bance measurement e Calculate detection reagent concentration Concentration M A so Agso 0 03 x dilution factor e e 203000 cm M NOTE The extinction coefficient z for IgG at A so 203000 cm M other values may be valid for other reagents e Calculate degree of labeling moles fluorophore per mole of detection reagent Labeling degree Asso dilution factor e x Concentration M e 239000 cm M of fluorophore at Asso NOTE For antibodies a degree of labeling of 3 7 moles of fluorophore dye per mole of antibody is recommended Dilution and storage of fluo
218. ls are described in more detail in Chapter Cy 1 5 Click Next 6 The Serial Dilution window opens This window holds the analysis results that are specific to Gyrolab Serial Dilution Analysis Serial Dilution EEE ao 735 79 06 on ngs ineo a a ami me spp Jur 1 808 003 1 80E 003 me a ii dl ee ee ee re E laas a a 8778 005 188E 004 200 439f 439 ssa on9 PASS 877003 1 5855003 8 896 003 9 89E 003 enoo oeno ug ml ml sai otros Lungstoy oq SB e In the Serial Dilution list Unknown samples and analysis result are listed Val ues that fall outside of acceptance criteria set in step 3 are indicated by red cell background color e For data columns definitions refer to Chapter D5 4 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 53 D5 Gyrolab Serial Dilution Analysis Step Action 7 Click Settings to view and or edit settings for Gyrolab Serial Dilution Analysis Refer to Chapter D5 5 for information on the different parameters Serial Dilution AN 4 Analysis Settings Log E m Cg Upper spike pass 126 0 is Lower spike pass a Acceptable CV a Number of passed dilutions for sample to pass 2 ig Spike concentration a Spiked subgroup prefix Spiked Unspiked subgroup prefix Unspiked Requested PMT Name Detect PMT 5 e By changing parameters settings the approved unapproved status for the Unknown samples listed in the Serial Dilut
219. luator Version number of the analysis module An Analysis report contains e Analysis name e Processed data analyzed data such as Standard curve quantification data sample results e User created analysis e Version number of the Gyrolab Evaluator Version number of the analysis module 3 11 2 View print and export report data Step Action 1 Select desired Run available Runs are shown under Runs or desired analysis available analyses are shown under Analyses 2 To include all available sample information in the report select Report ViewTables Run report only 3 The selected Run Analysis report is shown in the right part of Gyrolab Evaluator Project view ariana ae s GYROS Run Assay 1 2009 NOV 10 03 45 55 PM Ris inlor Date and see 2009 11 10 164555 erra O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C 27 3 Manage analysis projects Step 4 Action Use the following buttons to view the report gt Zoom in D 7 Zoom out View Report in actual size View Report in maximal width E im View one page of the report at the time Ed View two pages of the report at the time Use the search field to find specific parts of the report Several search options are available by clicking the black arrow Type text to find lt gt Select File Print Selected Report or click button to print the report Select File Save report as Xps
220. lyze data 4 3 Result data table descriptions Data table content is the same for both Quantification and Data Comparison modules In the Quantification module it is possible to choose between Original and Extended view and to view values with or without replicates If Original view is selected the number of columns displayed may differ depending on available sample results and type of sample In Data comparison module replicates are always shown and it is possible to select which columns to view however Identity and Expected conc are always shown Columns displayed in the Quantification and Data Comparison modules will be included in reports generated If Original view is selected only columns indicated with a Yes below will be displayed If Extended view is selected all available columns are shown NOTE Ifa cell ina column is empty a value could not or should not be calculated for that cell Examples of this is CV calculation when only one replicate is available and for calculated concentration for a blank sample Column Original Description heading view Identity Yes Sample identity Expected Yes Given for samples with known concentrations such as Standard conc Samples Quality Controls and Calibration Controls Response Yes Integrated volume of the fluorescent binding surface of a reac tion in a microstructure SIB Yes Signal to background The ratio between the signal and the absolute value of mean of the blanks signa
221. m Its intended use is to degas the buffers for the Syringe Pumps For more information refer to Instructions for GL Degasser The normal status for GL Degasser is The green LED for Vacuum is lit e The yellow LED for Status is off NOTE Always leave the GL Degasser on as long as the instrument is on Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A A 5 A2 Introduction to the Gyrolab platform A2 2 A2 2 1 Gyrolab instrument front view Gyrolab xP Figure 1 Gyrolab xP instrument front view No FUN Part Microplate carousel where the microplates are loaded Microplate loading position Wash stations CD spinning unit with protective casing A 6 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 1h 15 16 A2 Introduction to the Gyrolab platform Part CD vacuum arm CD loading position Liquid transfer device Syringe pumps for the needles Peristaltic pumps for wash stations and waste Hatch Connecting panel for external tubing Fluorescence detector Instrument buttons MP Microplate button Fluorescence button present on some instruments CD button Instrument Power LED Green light indicates that the instrument is on Instrument Run LED Green light indicates that the instrument is performing a Run Instrument Alarm LED Red light indicates that the instrument is in alarm state Copyright 2015 Gyros Gyrolab User Guide Poooy
222. m the microstructure column is amplified by a photo multiplier tube PMT when the signal reaches the detector The degree of amplification needed to obtain a sufficient response value depends on the signal intensity of the measured sample The signal amplification is controlled by the PMT setting in a Gyrolab method Since the response signal is dependent on the analyte concentration of the sample as well as the PMT setting combining a high analyte concentration and high PMT setting may saturate the detector An example of a saturated signal is given in Figure 2 To ensure proper quantification of response signal when analyzing run results use data produced with a PMT setting that does not saturate the detector If such results are not available within the run rerun the assay using a lower PMT setting in the Gyrolab method Figure 2 Example of binding profile that indicates saturated detector signal If the calculated concentration for a sample is very low and Viewer images display low intensity binding profiles even for samples with highest expected concentration use data produced with a higher PMT setting If such results are not available within the run rerun the assay using a higher PMT setting in the Gyrolab method D 10 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Di Gyrolab Viewer D1 3 2 Using Gyrolab Viewer to characterize binding properties During assay development different reagents are evaluated to
223. mbination 2 Capture 2 Detection 2 Samples 3 and 4 will be quantified against curve 1 Reagent combination Capture 1 Detection 1 Samples 5 and 6 will be quantified against curve 2 Reagent combination Capture 2 Detection 2 O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H 23 H2 Custom Run workflow Example 3 Two different Standard series and one Reagent combination M Mandator Curvel Blank r Pe RR RR Dc Iommi omismimo O DO demene mem e Pe RR RT a Semene caer sundae e Seene ESP rs ee eee e RR RR RT r Re caveat Ls anene comer stds Figure 11 Two different Standard series with for example different standard preparations dilutions but only one Reagent combination will generate one standard curve A Run using this transfer list will generate following in Gyrolab Evaluator One Reagent combination Capture Detection e One standard curve in 4 replicates NOTE Even though the Standard series have been given different names in the transfer list see figure for current example they will be analyzed against the same Reagent combination and thus they will be evaluated as replicates of the same curve In order to generate two different standard curves for example with different standard preparations dilutions two different Reagent combination are needed see figure for example 4 O Copyright 2015 Gyros Gyrolab User Guide Pooo4
224. ment computer or on the network where the office computer and the instrument com puter is placed G3 Application issues Application issues This section contains information on how to diagnose and possibly solve problems related to immunoassay performance and results If you cannot identify the problem or if the problem remains please contact Gyros for assistance G3 1 No response values are generated G3 2 G3 2 1 Possible cause Was the CD positioned upside down Was the LIF button in pressed down position Only valid for Gyrolab instruments with a LIF button refer to Chapter A2 2 1 Were all samples reagents and solutions placed in microplates according to Load ing list Was the microplate foil applied on microplate according to recommenda tions Were all microplates correctly loaded in the microplate carousel Possible cause Were correct volumes of reagents and samples loaded in microplate wells Were there air bubbles in microplate wells Action Make sure the text on CD is readable after loading CD in Gyrolab instrument Press LIF button Initialize Gyrolab instrument 30 min before starting experiment Check instructions in Chapter B2 1 Check instructions in Chapter By 1 2 Gyrolab xP or Chapter By 2 2 Gyrolab xPlore Check that microplate foil is applied according to Microplate foil adapter instructions sup plied with the microplate foil Check instructions in Chapter B5
225. mple sample Response group or sample subgroup SD Response Yes The standard deviation of responses of sample replicates CV Response Yes Coefficient of variation of response of replicates of a sample Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D 27 D 28 D2 Gyrolab ADA Software Column heading Dilution CD ID CD Structure Average Cut Point Cut Point Log of Response Log of Aver age Response MP Identity MP Well Detect Result Sample Type Needle ID Notes Original view Yes Yes Yes Yes Yes Description Dilution factor for Unknown samples is entered in the Sample List For ADA control samples the dilution factor is entered entered during Run set up refer to Chapter D2 2 If no Dilution Factor value has been assigned a factor of 1 will automatically be used Identity of Gyrolab CD microlaboratory used to process the sam ples Identity of structure on Gyrolab CD microlaboratory where the sample was processed Describes whether average sample response for replicates of a sample sample group or sample subgroup are above or below cut point Negative or positive Describes whether sample response is above or below cut point Negative or positive The logarithm of Response value The logarithm of Average Response value Identity of the microplate where the sample was placed Well position on the microplate where the sample or standar
226. n a name browse to select folder and click Save If Save is clicked the original Run will be lost If changes are made to the transfer and or reagent lists they must be re imported to the Run to be performed O Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H Doo23573 A H2 5 Prepare Custom Run Step Action 1 Click Execute Run on the Main menu 2 Browse and select desired Run from the list and click OK Run Protein Quantification_3 Number of samples O sample list not loaded Click Sample List File 3 Browse and select desired Sample List and click Select Select Source Data File EAGyrolab CustomRunLists e i uid Reagents_list_ProteinQuantification_3 xls E Reagent_list_ xls Reagent list ProteinQuantification 4 xls B Sample list ProteinQuantification 4 xls Bs sample _list_ProteinQuantification_3 xls Transfer list ProteinQuantification 4 xls E Transfer list ProteinQuantification 3 xs File name Sample _ist_ProteinQuantification_3 xs hee Sample list not loaded List Loader SampleListLoader H2 Custom Run workflow Files of type Excel Files xls L Number of samples is displayed and the Sample List status is set to Loaded Click OK 5 A screen with Targets tab and Reports tab is opened Refer to Chapter B3 1 4 for settings 6 Click OK Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A H 19 H2 Custom Run workflow H2
227. n cut point e ADA controls Data table with analysis results for ADA controls ADA control with results that fall outside of acceptance criteria set in step 1 are highlighted Neg ative controls with response above confirmation cut point and positive controls with response below confirmation cut point are highlighted Refer to Chap ter D2 4 2 1 for detailed information on column data e Unknowns Data table with analysis results for unknown samples Samples with results that fall outside of acceptance criteria set in step 1 are highlighted Refer to Chapter D2 4 2 1 for detailed information on column data 3 Click Analysis settings to change settings for the confirmation view 4 To simplify bar chart view and facilitate data evaluation it is possible to hide unknown samples with response values below the cut point e Mark check box Hide negative unknowns D 30 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D2 Gyrolab ADA Software Step Action 5 General commands for data tables In the View list select display option for data tables Original A selected number of data columns default e Extended All available data column If the With replicates box is ticked default all replicates for samples are shown Untick the box to display average values for samples It is possible to include or exclude data points e To exclude a data point right click on the sample and select Exclude To perform this Wi
228. n cut point determination refer to Gyrolab ADA assay protocol NOTE The confirmation functionality calculates the percent inhibition for samples This serves as a base to determine the confirmation cut point e Inthe Evaluation section mark check boxes to indicate what sample subgroups that have been spiked and which are unspiked Inthe Acceptance Criteria section add acceptance criteria for Unknown samples in the field CV unknown samples e Click Next Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D2 Gyrolab ADA Software Step Action gt Click Confirmation in the lower left corner The Confirmation window opens pia ew SI Cl wen ER a Expement3 mem 44 inays Serdogs Ct pont W Detect 1 4 Detect 5 A Sethe 73 28 E s 210 ss 0 7 i 3 gt pd YY we E eS fe 4 E pi s A z z z E emu to mm Conte tepon _ Cacai The left panel of the Confirmation window displays available experiments in the Run and Run information refer to Chapter Cy 1 The right panel of the Confirmation window displays collapsable expandable views for e Bar Chart Visualizes inhibition value for ADA controls and unknown samples compared to the confirmation cut point Standard deviations are indicated with error bars Values above cut point are indicated with orange bar color Values below cut point are indicated with blue bar color A true positive should be above confirmatio
229. n of how to create or edit Wizard Runs refer to Chapter B3 1 2 Gyrolab xP or Chapter B3 2 2 Gyrolab xPlore e Fora detailed description of how to create or edit LIMS Runs refer to Chapter B3 1 5 Gyrolab xP or Chapter B3 2 5 Gyrolab xPlore F1 1 3 3 Execute Run Runs are prepared loaded executed unloaded and finished in the Execute Run function The run design is completed with sample information Sample List and settings for result and report files Input data and settings differs depending on which design type which type of Run is used Fora detailed description of how to prepare and execute Wizard Runs refer to Chapter B3 1 4 Gyrolab xP or Chapter B3 2 4 Gyrolab xPlore e Fora detailed description of how to prepare and execute LIMS Runs refer to Chapter D3 e Fora detailed description of how to prepare and execute Custom Runs refer to Chapter B3 1 4 Gyrolab xP or Chapter B3 2 4 Gyrolab xPlore Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 7 Fi Gyrolab Control F1 1 3 4 Prime Instrument priming is performed through this function Refer to Gyrolab Instrument Guide F1 1 3 5 Maintenance Maintenance function is used for system maintenance Refer to Gyrolab Instrument Guide for information about specific methods and procedures F1 1 3 6 Initialize System Hardware tests of the components are performed during initialization for example robot arm movements carousel rotation
230. n samples four on each CD Sample List not shown The figures included in this example demonstrates Reagent and Transfer lists for a two CD Run using two Standard series on separate CDs Unknown samples are present on both CDs In spite of the use of a common Experiment name using this strategy Unknown sample 1 4 will be quantified against the Standard series on CD 1 and Unknown sample 5 8 will be quantified against the Standard series on CD 2 Curve CD 1 Blank Curve CD 1 Standard 1 Curve CD 1 Standard 2 Curve CD 1 Standard 3 Curve CD 2 Blank Curve CD 2 Standard 1 Curve CD 2 Standard 2 Curve CD 2 Standard 3 Curve CD 1 Blank Curve CD 1 Standard 1 Curve CD 2 Blank Curve CD 2 Standard Curve CD 2 Standard 2 A two CD Run using current lists will generate following in Gyrolab Evalua tor e Two Standard series e Unknown sample 1 4 will be quantified against the Standard series on CD 1 Unknown sample 5 8 will be quantified against the Standard series on CD 2 O Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Po004354 H D0023573 A Corporate headquarters Gyros AB Uppsala Science Park SE 751 83 Uppsala Sweden Visiting address Dag Hammarskjolds vag 52A Tel 46 0 18 56 63 00 Fax 46 0 18 56 63 50 www gyros com Regional sales office Gyros Inc 30 Technology Drive Ste 1F Warren NJ 07059 USA Tel 1 908 755 0011 Fax 1 908 755 0001 GYRES
231. n the folder structure in the left panel of the Fold ers screen e Click Edit folder Inthe Edit folder window change folder name and or change status for allow or deny Folders Runs Draft Methods and Approved Methods in the folder e Click OK The folder settings are now updated Click on Close in the top right hand corner of the Folders screen to exit Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2 Gyrolab Administration Tool F2 2 3 Runs Click on Runs on the main menu to access the Runs screen Select a folder in the folder structure to display its content Runs System versions supported 1 2 E Root E gt Bioaffy amp Root Bioaffy Runs Custom methods ot Runs 2 Runs allowed Yes B A Wizard methods Service ProteinQuantification 2 Pe me Export Readable It is possible to perform six different administration tasks Cut Paste Delete Import Export and Export Readable NOTE Select a run in the list to activate unavailable task buttons Button Action Cut and Cut and Paste are used to move a Run within the folder structure Paste Browse the folder structure to the left in the Runs screen to locate the folder that holds the Run to be cut Select folder Select Run to be cut in the list to the right in the Runs screen e Click Cut Browse the folder structure to the left in the Runs screen to locate a new folder
232. nable remote evaluation of run result eliminating the need to use the instrument computer for data analysis 5 1 Gyrolab Evaluator installation package Gyrolab Evaluator installation package contains the following software e Gyrolab Evaluator e Microsoft Net Framework 4 e Gyrolab User Guide Software installation instructions Adobe Reader enables access to Gyrolab User Guide and Software installation instructions 5 2 Computer requirements Gyrolab Analysis Software Package should be installed on a computer with access to desired Gyrolab instrument Preferred computer system specifications are 3 GHz processor and 1 Gb RAM memory e Operative system requirement is Windows 7 32 or 64 bit Minimum monitor 1024x768 resolution medium color quality 16 bit 5 3 User level requirements Installation of Gyrolab Analysis Software Package requires administrator privileges on the computer To be able to use the Gyrolab software a user name and password is required Contact the local Gyrolab system administrator to receive login details for Gyrolab Software Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C 45 C5 Gyrolab Evaluator installation on office computer 5 4 Installation Before installation start make sure that the operating system is updated with the latest patches from Microsoft This can be done from the web site http update microsoft com Step Action 1 Insert Gyrolab A
233. nager and Operator Role privileges user privileges are displayed in the Role privileges section Refer to Chapter F2 2 6 1 for more details New Password Enter the new user s password Eight characters of which at least two must be numbers and at least two must be let ters This password is temporary user is required to change pass word at the user s next login Confirm New Password Enter the new user s password again e Click OK in the Create New User dialog The new user is now present in the user list in the Users screen User name Name and Role are displayed Edit User is used for change users privileges This action requires System Administrator user level e Click Edit User OK User name mial Your current password La Name micke New password Ceres Role Operator hd Confirm new password Role privileges E open io E create New Method Gv M Frit Method Er em WZ Fxoriito Ruin FZ vi e Inthe Edit User dialog edit settings edit User Name Name Role user level New Password and Confirm New Password as described in the previous Create User section Enter your own password in the Your current password field e g if you are logged in as administrator use the administrator password as Your current password e Click OK in the Edit User dialog The edited user is now updated User name Name and Role are displayed Click Export User List button The Export User List dialog will open
234. nalysis Software Package CD in the CD drive 2 Gyrolab Evaluator installation screen opens If the installation start screen does not appear automatically browse for the CD folder in Windows Explorer and double click on the file splash autorun exe Select Installation Guide to view installation instructions Select User Manual to access Gyrolab User Guide Select Exit to exit installation procedures Select Install Acrobat Reader and follow the instructions to install Acrobat Reader This is needed only if your system does not have a pdf reader already Select Release Notes to view information on this software release 4 Select Install Gyrolab Evaluator to start installation If the installation software can not determine whether your operating system is of version 32 or 64 bit you will be instructed on how to manually start the correct installation file If NET Framework is unavailable or of inadequate version the installation software will also install required NET Framework C 46 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C5 Gyrolab Evaluator installation on office computer Step Action 5 A Gyrolab Evaluator dialog opens Click Next gt NOTE During the installation procedure it is possible to cancel installation by clicking Cancel and to return to previous step by clicking lt Back 6 A Gyrolab Evaluator dialog opens Click Next gt Welcome to the Gyrolab Evaluator 3 3
235. nding profile display click Chart Settings Select scale for the intensity axis Choose between Autoscale or a fixed Max intensity For fixed intensity axis choose between default values or set a custom value Click Update for the custom value change to take effect Avail able intensity axis value range is 0 001 to 1 Mark check box Integration area to display the integration area on top of the binding profile The integration area illustrates what part of the signal that is included in the calculation of the sample response value Mark check box Autocolor to obtain binding profile coloring where colors range from dark blue to dark red corresponding to lowest and highest signal intensity within each specific image Mark check box Show 3D info to display a text box with sample CD structure and run information This text box is included in the binding profile image when copied or saved to another location Click Chart Settings again to close the settings window Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D1 Gyrolab Viewer Step Action 4 To copy or save the 3D image to file right click in the image and select Save As to save the 3D image to disc In the Save As dialog enter desired file name and choose between available file formats svg jpg ml xaml gif png tiff bmp Click Save e Copy to place a copy of the image on the clipboard E Some CD ieee a Mame Ger werne Test_
236. nformation is displayed bm G neroa 200 3W 001 A select Method information Name Root Bioaffy Wizard methods Bioaffy 200 wiz 200 3W 001 A CD Gyrolab Bioaffy 200 Description Bioaffy 200 CD 3 step capture analyte detection Wizard run One Wash solution used for all needle washes Initial needle wash 2 column washes elect Setup Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B3 Design run Step Action 9 Select Reagents NOTE The software will automatically add reagents to the design depending on selected method 1 step 2 step 3 step or 4 step This can be edited by the user Reagent name Condition Add ap t Delete Specify Name for capture Cap and detect Det reagents The Condition field is optional and can be used for additional information such as concentration value or matrix Click Add to add more capture and detect reagents Add and name one reagent in the software for each different reagent required for the design Highlight reagent and click Delete to remove reagent Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A B 21 B3 Design run Step Action 10 Select Standard series Reagents Add Number Replicates Blank 2 v Standard points 7
237. ng off the Gyrolab instrument Critical alarms User selects Initial ize System and follows the direc tions on the screen Successful initial ization Starting a Run Priming the system Operator selects Standby and follows the directions on the screen F 17 Fi Gyrolab Control Fi 2 Instructions for Gyrolab xPlore F1 2 1 Start Gyrolab Control The control software consists of the server and the client The server must be running before starting the client Step Action 1 Start Gyrolab Server e Click Start All Programs Gyros Server e Gyrolab Instrument Log is displayed and Gyrolab server icon appears on the task bar a 2 Start Gyrolab Control software Select Start All Programs Gyros Client 3 The Login dialog box is displayed Enter user name and password in the Login dia log box NOTE User name and password are case sensitive NOTE The software will request the user to log in anew when the system has been inactive for 31 minutes User name Password Change password Gyrolab Control 4 Password must be changed when requested by Gyrolab Control Password may also be changed when desired by a user he Change Password window opens Enter present Password Enter New Password Confirm Password e Click OK 5 Click OK to log in or Exit to close the dialog box without logging in Once logged in the main menu will appear F
238. ng x in the Analyte bar e Add additional Experiments to an Analyte by clicking ca in the Analyte bar e Delete Experiment by clicking x in the Experiment bar Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B3 Design run Step Action 13 Select Generate Sample List template Number of unknowns Same value must be used when executing run Unknown replicates 2 Tv Same value must be used when executing run Include limited CD Number of free segments F Number of unknowns is doubled and subgroup set to Use spked unspked L spiked unspiked in sample list Generate Template e Save the Run e To save a new Wizard Run click Save Browse to select folder and click Save To save an edited Wizard Run click Save as Name the Run browse to select folder and click Save If Save is clicked the information on the original Run will be replaced with the edited information e Ifany information added to the Wizard Run is incomplete or erratic an error message will be presented The specified issues must be addressed before it is possible to save Specify number of samples to be analyzed Unknown samples in the Number of unknowns list Specify number of sample replicates in the Unknown replicates list Highest number of replicates are 8 e If itis desired to use a CD that previously has been partially used check Include limited CD and define number of available segments in
239. nk BL Calibration Control CC and Quality Control QC Not applicable for Reagent regular RR and Reagent biomolecule RB reagents Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Reagent List Mandatory item Optional Dilution Optional Column E MP Name Mandatory Column F Well Mandatory Column G Table H2 1 Specification for Reagent list H2 Custom Run workflow Information Enter the dilution factor for Quality Control QC sam ples Undiluted samples have dilution factor 1 Dilu tion values must be 1 or higher If nothing is entered the default value is 1 Identity of microplate where the reagent or standard solutions is located Enter the positions of reagents and standard solutions in the microplate for example A1 A2 For optimal liq uid transfer use the same liquid in rows with the same letter 8 well rows e Ifthe MP Type is given and the MP Name and Well columns are completed this information will appear in the Execute Run screens for loading Gyrolab instrument TIP Print the Reagent List and use when preparing reagent microplates Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A H 11 H2 Custom Run workflow H2 4 3 Create Transfer List A Transfer List is required for Custom Run and describes how samples and reagents are transferred to defined microstructures in the CD microlaboratory The Transfer List template must be edited to match the speci
240. nment of Needle 10 completed New X coordinate value 0 0 New Y coordinate value 40 5 Alignment of Needles finished Hatch unlocked 2 Click Finish If the alignment process fails repeatedly please contact your local Gyros office refer to www gyros com for contact details F 12 Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A Fi Gyrolab Control Configure CD stations The CD stations tab displays how each of the CD stations is configured These settings cannot be changed Syringe Pumps Wash Stations Needles CD Stations CD station 1 GENERIC CD station 2 GENERIC CD station 3 JIC CD station 4 TRANSFER CD station 5 GENERIC CD station 6 GENERIC Figure 5 CD stations tab Fi 1 3 8 CD information CD Information is used to read the information stored in the CD tag Step Action 1 Click CD information The CD information screen opens 1 Place CD on loading postion in Gyrolab 2 Read cD 3 CD information Type Identity Number of free segments CD is expired 2 Place CD of interest in the instrument CD loading position refer to Chapter A2 2 1 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 13 Fi Gyrolab Control Step Action 3 Click Read CD The following information of the CD is given Type type of CD e Identity identification number of CD Number of free segments number of unused segments on the CD e CD
241. ns and the allowed deviation ranges NOTE The nominal positions and allowed deviation ranges are set by the manufacturer and cannot be altered Syringe Pumps Wash Stations Needles Needle configuration Position X Coordinate Y Coordinate Max Deviation Deviation Approved 1 2 217 1 5803 v 2 6 7038 1 6102 0 4 a v 3 711 2785 1 6048 0 4 0 075 v 4 15 7017 1 6365 0 4 0 026 v 5 20 2793 1 623 0 4 0 076 wj 6 24 6525 1 5767 0 4 0 061 v 7 29 2925 1 6572 0 4 0 1 v 8 33 8408 1 7183 0 4 0 174 v 9 38 2507 1 6816 0 4 0 085 v 10 42 6189 1 4832 0 4 0 153 v Figure 11 Needles tab Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Fi Gyrolab Control Step Action 1 Click Align The Aligning Needles dialog box is displayed f l Needle Alignment E Alignment of Needle 5 started 7 lignment of Needle 5 completed hen X coordinate value 0 0 lew Y coordinate value 18 0 Alignment of Needle 6 started lignment of Needle 6 completed hew X coordinate value 0 0 lew Y coordinate value 22 5 Alignment of Needle 7 started lignment of Needle 7 completed hew X coordinate value 0 0 lew Y coordinate value 27 0 LJ Alignment of Needle 8 started lignment of Needle 8 completed hen X coordinate value 0
242. ntOL seii aace s dE e a Gh do A F 5 Fi 1 Instructions for Gyrolab XP sssssssessssssesssssssssssessesssessee F 5 F1 1 1 Start Gyrolab CONtrOL cece eeeeeeeeeeeeceeneeeneeseseeeeaeeees F 5 F1 1 2 Gyrolab Control main MENU ceeeeeeeeeeeeeeeeeeee enone F 6 F1 1 3 Main menu fUNCtIONS cccecceceececeeceeceeceeceeseesentens F 6 Fi 2 Instructions for Gyrolab xPlore ccecceeceeceeeeeeseeeeees F 18 F1 2 1 Start Gyrolab Control esesisi sis ires er ererererena F 18 F1 2 2 Gyrolab Control main MeNU eee eee eee eeeeeeeee teens F 19 F1 2 3 Main menu FUNCTIONS ccceccesceesteeceeecteeceenceesseees F 19 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F2 Gyrolab Administration Tool F 29 F2 1 Login procedure ee ee ee ees F 29 F2 2 Gyrolab Administration Tool main menu F 30 F220 Design TYPOS erkens cawetiwatacorsseone ews F 31 F222 FOILS ica sic cateccasiowsagenesecinsadatienoieadadees swe naeete EOR F 33 29 30 RUINS esa sass cegas E aces gras danada aus aguas iss da sus ss seda sta tassedasa F 35 22 Methods ss sessao sas dido nddais dede aigiacreradiave DES Ora do Ses da GSE San F 37 F2 2 5 MA iNteENaNne ccccccccceeccccceccceeecuseeccceseuecseeuceseneess F 39 22276 SOIS iciessusictascaase ias amas Dacia abr ET cons So nbr sa atas nan F 42 25227 ODS siscceuccssavecscvesssnsrivines caasanp iso a iad sad
243. ntification 2 CD information Operation list RS 0001020 007 Customized Transfer fo apture reagent spin apture reagent wash 1 apture reagent wash spin 1 apture reagent wash 2 apture reagent wash spin2 _ inalyte addition nalyte spin nalyte wash 1 inalyte wash spin 1 nalyte wash 2 inalyte wash spin 2 D alignment 1 _ etect background PMT 1 w Processing information Run execution started 2 11 11 14 8 01 59 AM CET CD 0001020 007 Initial needle wash started 11 11 14 8 01 59 AM CET CD 0001020 007 Initial needle wash completed 11 11 14 8 02 04 AM CET CD 0001020 007 Particle wash 1 started 11 11 14 8 02 19 AM CET CD 0001020 007 Particle wash 1 completed 11 11 14 8 02 19 AM CET CD 0001020 007 Particle wash spin 1 started 11 11 14 8 02 20 AM CET CD 0001020 007 Particle wash spin 1 completed 11 11 14 8 02 25 AM CET CD 0001020 007 Particle wash 2 structure started 11 11 14 8 04 10 AM CET CD 0001020 007 Particle wash 2 structure completed 11 11 14 8 04 11 AM CET CD 0001020 007 Particle wash 2 common started 11 11 14 8 04 28 AM CET CD 0001020 007 Particle wash 2 common completed 11 11 14 8 04 28 AM CET CD 0001020 007 Particle wash spin 2 started 11 11 14 8 04 29 AM CET CD 0001020 007 Particle wash spin 2 completed 11 11 14 8 04 34 AM CET CD 0001020 007 Capture reagent addition started 3 It is possible to pause or abort an ongoing run e To st
244. o be exported in the Run list to the right in the Runs screen e Click Export to open Export Run dialog Browse and select desired export folder e Click Export e Click OK in the Export Run dialog to confirm export The exported Run is now present in the selected export folder Export Export Readable is used to export a readable copy of a Run This copy can readable not be used in Gyrolab Control but can be useful for example when con tacting Gyros for support e Browse the folder structure to the left in the Runs screen to locate the folder that holds the Run to be exported readable Select folder Select Run to be exported in the Run list to the right in the Runs screen Click Export Readable to open Export Runs in readable format dialog e Browse and select desired export readable folder e Click OK in the Export Readable Runs dialog to confirm export readable The selected Run is now present in a readable format in the selected export folder Click on Close in the top right hand corner of the Runs screen to exit F 36 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F2 Gyrolab Administration Tool F2 2 4 Methods Click on Methods on the main menu to access the Methods screen Select a folder in the folder structure to display its content Methods System versions supported 1 9 Root Bioaffy Wizard methods Bioaffy 1000 wiz Bioaffy 1 Modified by Gyros AB A
245. oes not affect the physical ability of the Gyrolab instrument but may have an impact on the results Red Normal alarm Yes This alarm indicates an error in the physical operation of the Gyrolab instrument The instrument will either complete a specific operation or pause immediately It should be possible to resolve the problem and con tinue with the system in operating mode Red flashing Critical alarm Yes This alarm indicates an error in the physical operation of the Gyrolab instrument The instrument will either complete a specific operation or pause immediately The problem must be resolved and the system must be re initialized View information on individual alarms e To display information on current active alarms click View Alarm on the main menu To view detailed information for a specific alarm select the alarm in the list The additional information is displayed in the box below the list Alarm Ex Resolve Date Type Code Id Resolved Close Alarm information escription n error occurred which caused the instrument software to stop ction estart the instrument Figure 13 View alarm information When an alarm occurs a dialog box is displayed in which the alarm can be confirmed and the View Alarm dialog can be accessed NOTE All Normal red and Critical red flashing alarms must be confirmed Address the issue displayed in the View Alarm
246. of 4 e Gyrolab Control Loading holds microplate loading information and is used when preparing microplates for a run Name concentration volume microplate and well position is included for all sample types An overview of microplates with indication of used wells is also provided e Click Printer button to print the Gyrolab Control Loading TIP Select File Export to export the Loading list in PDF or text format This is useful when printing from another computer is required Close Gyrolab Control Loading 5 Click OK A screen with two tabs Targets and Reports is opened Refer to step 7 and step 8 in Chapter B3 1 4 for information on target and report settings 6 Click OK and prepare samples and reagents as described in the Assay protocol for ADA 7 Load instrument and start the Run as described in Chapter B5 When the Run is completed unload instrument and finish Run as described in Chapter B6 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 23 D2 Gyrolab ADA Software D2 4 Data evaluation This chapter describes how to evaluate run data from an ADA Run The data analysis is performed in Gyrolab Evaluator using the software module Gyrolab ADA Software Step Action 41 In Gyrolab Evaluator Project view Chapter 3 1 select an ADA run and click the ADA Analysis button iini ADA Analysis 2 The ADA Analysis window opens WADA Analysis Functional ties to Use Runs Select run to perfo
247. of Gyrolab LIMS Interface ceeceeeeeees D 46 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Gyrolab Control Report 2 4 D 47 Dy 1 Introduction to Gyrolab Control Report D 47 Dy 2 Perform run using Gyrolab Control Report D u7 D4 3 Gyrolab Control Report OUtPUT c cece eee eeceee eee eeeees D 48 Du y Installation of Gyrolab Control Report D 4 9 Gyrolab Serial Dilution Analysis D 51 D5 1 Introduction cessit do sadisro sa snide tasas ie ama a dama a caia sa adaga D 51 D5 2 Create RUM sca tonessvancdacsons eita nesavseenssneeavewadeaauses eae news D 51 D5 3 Perform serial dilution analysis e sce eceeeeeeceeceeeees D 52 D5 4 Gyrolab Serial Dilution Analysis data table description D 55 D5 5 Analysis settings for Gyrolab Serial Dilution Analysis D 57 D5 6 Installation of Gyrolab Serial Dilution Analysis D 58 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D 4 D1 Di Gyrolab Viewer Gyrolab Viewer Visit www gyros com for the latest updates on available software modules D1 1 Gyrolab Viewer introduction Gyrolab Viewer is a software add on module for Gyrolab Control version 5 3 and Gyrolab Evaluator version 3 2 or higher The module converts on column flu
248. olab Result Database Explorer window opens Click Folders File Edit View Favorites Tools Help J Gra OD D sen ip rats Address WD Gyrolab Result Database Explorer Bs Folders x B Desktop Emain view My Documents T My Computer 3 my Network Places g Recycle Bin G sult Database Explorer Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 57 F 58 F3 Gyrolab Result Database Explorer Step 3 Action Click Main View The folders Results and System log appear EZS Result Database Explorer B Desktop Main View My Documents E My Computer E My Network Places g Recycle Bin SR Gyrolab Result Databas e Explorer us Results us System Log NOTE Itis possible to create customized database views in Gyrolab Result Database Explorer to facilitate finding specific database files refer to Chapter F3 3 Click Results for a list of Runs stored in the database Click on the icon for the Run of interest 9 Gyrolab Result Database Explorer Main View Results AA 2009 01 29010 19 42 re G D 45 9 seann F rolders 6 Gyrolab Result Database Explorer Main View Results AA 2009 01 29010 19 42 E me Tone Tonto Toon My Documents af C 0001290 046 Thursday Janu 0 37 04 Yes I My Computer 2 MainResult xml E Thursday Janu 1073 KB At ic My Network Places tg Gyrolab Evaluation 2009
249. olution 3 sodium hypochlorite Purpose To be used for sanitizing needles Composition 3 sodium hypochlorite To prepare 10 ml Mix sodium hypochlorite with deionized distilled water The amount depends upon the concentration of the stock solution E1 2 6 Wash Station Sanitize Solution 3 sodium hypochlorite Purpose To be used for sanitizing Wash Station 1 and 2 Composition 3 sodium hypochlorite To prepare 600 ml Mix sodium hypochlorite with deionized distilled water The amount depends upon the concentration of the stock solution Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A E 7 E Recipes E1 2 7 Needle Desorb Solution Gyrolab Wash Buffer pH 11 Purpose To be used for Needle desorb Composition Gyrolab Wash Buffer pH 11 To prepare 1000 ml Dissolve one pack 10 g of Gyrolab Wash buffer pH 11 powder in 1000 ml deionized destilled water Filter through a 0 22 um filter 0 5 Dodecylsulfate sodium salt SDS Purpose To be used for Needle desorb Composition 0 5 SDS To prepare 100 ml Dissolve 0 5 g SDS in 99 5 g deionized distilled water 50 mM glycine pH 9 5 Purpose To be used for Needle desorb Composition 50 mM glycine pH 9 5 Dissolve 375 mg glycine Mw 75 07 g mol in 100 ml deionized dis tilled water Adjust to pH 9 5 with sodium hydroxide To prepare 100 ml 1 5 M NaCl in 20 ethanol Purpose To be used for Needle desorb Composition 1 5 M NaCl in 20 eth
250. on 1 Enter the Prime Volume in ul for Wash Stations 1 and 2 The Prime Volume is the volume used to rinse the tubing between the wash station bottle and the Wash Station during priming O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F 24 Fi Gyrolab Control Step 5 Align n An alignment procedure can be performed to ensure that the needles are correctly aligned i e on target for the wells of a microplate This procedure is normally only performed by Action Click Standby Solution at the bottom of the tab The standby liquid is the solution used to put the system in Standby mode The Wash Station Solution dialog is displayed containing a list of available standby solutions New Wash Station Solution Delete Wash Station Solution Select the Standby Solution to be added by clicking its name in the list To add new liquids to the list click New Wash Station Solution Type a new name and click OK To remove a standby liquid from the list select a name in the list and click Delete Wash Station Solution e Click OK to confirm deletion Click Set The Standby Solution appears on the tab Click Save to save wash station settings eedles Gyros Service staff when needles have been replaced The alignment procedure is controlled from the Needles tab on the Configure System screen The tab holds a list of the needles along with their nominal positio
251. on 2 EE Sample List File 2 ProgramData Gyros Gyrolab Templates Lists Sample_list_Protein Quantification 2 8 UNK xis cancel List Loader SampleListLoader iv Number of samples 8 Sample replicates 2 Use spiked unspiked C Only for unknowns Include limited CD 4 Number of free segments 9 w Number of CDs 1 Loading List Segments Used Comment D To load a Sample List click Sample List file browse and select desired Sample List e List Loader file sets rules for how to import Sample list Choose the SampleList Loader option in the drop down menu Number of Unknown samples will be displayed in the Number of samples field when the desired Sample List is loaded The number of Unknown sample replicates was defined during run design Chapter B3 2 2 and is displayed in the Sample replicates list Sample replicate number can be changed compared what was defined during the run design Include limited CD box is ticked if a partially used limited CD was included when the run was designed Chapter B3 2 2 It will always be the first CD in the Run that is partially used It is possible to remove limited CD or change number of available CD segments The CD and CD segment consumption is calculated based on number of samples and replicates For all samples position on the CD s is automatically randomized and distributed by the software F
252. on different CDs it must be placed in separate wells in the reagent microplate and on separate rows in the Sample list in order to avoid evaporation during the run The number of wells for each Standard series Unknown Calibration Control Quality Control sample shall cor respond to the number of CDs in the Run on which the sample should be used on Each row in the Sample list must have unique sample identity Refer to examples in Chapter H2 9 2 Click File Save As to save the Sample list in a folder accessible by the Gyrolab com puter NOTE Do not save the file in the c ProgramData Gyros Gyrolab Tem plates Lists folder This folder should be kept for list templates only Click File Close to close the Sample list Print the Sample List and use when preparing sample microplates Quality Control samples are valid only in the reagent list H 8 Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A H2 Custom Run workflow H2 4 2 Create Reagent List The Reagent List contains information about the solutions in the reagent plate such as type of liquid concentration for Standard series samples dilution factor etc The Reagent List template must be edited for each new set of reagents used for each new Run Step Action 1 Open the Reagent List Template Reagent_list_Template xls found in C Program Data Gyros Gyrolab Templates Lists 2 From row 3 and below one row in the Reagent list represents one reagent Columns
253. on is controlled by the PMT setting in a Gyrolab method If the degree of amplification is too high the detector will be saturated If the PMT setting is too low weak signals may be lost in the background scatter To investigate proper amplification level expressed in percentage of incoming signal amplification PMT different PMT levels can be tested in the same run Normally three PMT levels are included in the methods used during assay development phase to illustrate assay performance When the assay is fully optimized it is sufficient to use one selected PMT setting Refer to Chapter D1 for guidance on how to optimize PMT setting using the Gyrolab Viewer software module Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A 23 A3 Gyrolab immunoassay workflow Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A GYROLAB USER GUIDE B Perform immunoassays on Gyrolab Instrument CCS2 Ba meo HX max ieee Na Rg Py _Rexxip A So anma a at we uat a aMi Contents B1 Labelling of capture and detection reagents B 5 B1 1 Biotinylation of capture reagent cece eee eee ee eee ee ee B 5 B1 2 Fluorophore labeling of detection reagent B 7 B1 3 Buffer exchange azide removal and protein concentration DIOLO CONS osinean EEE EEE EERE E ae ans B 9 B1 3 1 Nanosep 30K Protocol sssssssssssssssssesssessssssessseesssseese B 9 B1 3 2 Thermo S
254. onsecutively numbered 1 2 3 and so on NOTE Do not use this column for Standard series Quality Controls or Calibration Controls UNK for Unknown samples e QC for Quality Controls e CC for Calibration Controls e STD for Standard series BL for Blanks Enter Sample identity for all unknown samples Sample identity is used as basis for statistical analysis in Gyrolab Evaluator software Table B3 2 Basis for sample statistics on page 27 below Sample Group is used to group samples with common properties Sample group is used as basis for statistical analysis in Gyrolab Evaluator software Table B3 2 Basis for sample statistics on page 27 below Sample Subgroup is used to subgroup samples within a Sample Group or Sample identity with common properties for example samples given different treat ment or from different time points Sample subgroup is used as basis for statistical analy sis in Gyrolab Evaluator software Table B3 2 Basis for sample statistics on page 27 below A Microplate identity must be entered Identity of microplate well where the sample is located Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Sample identity Column C Used Used Used Used Sample group Column D Not used Used Not used Used Table B3 2 Basis for sample statistics Sample subgroup Column E Not used Not used Used Used O Copyright 2015 Gyros Gyrola
255. ontact Gyros for information 13 Click OK and proceed to Chapter By 1 1 Gyrolab xP or Chapter By 2 1 Gyrolab xPlore sample and reagents preparations D3 5 Gyrolab LIMS Interface data output One or more LIMS Run result files are generated in the format specified in Chapter D3 2 and to location specified in Chapter D3 4 The result files can be imported into a LIMS for analysis D3 6 Data evaluation When using the LIMS workflow all data analysis is performed using a LIMS system D3 7 Installation of Gyrolab LIMS Interface The Gyrolab LIMS Interface software module is available for Gyrolab Control version 5 2 or higher and is activated by the user with a licence key Licenses are instrument specific Contact Gyros to purchase Gyrolab LIMS Interface and receive a license To register the license Save the license file to the hard disk of the instrument computer at the destination C ProgramData Gyros Licenses D 46 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D4 Gyrolab Control Report Gyrolab Control Report Visit www gyros com for the latest updates on available software modules Dy 1 Introduction to Gyrolab Control Report Gyrolab Control Report is a software add on module for Gyrolab Control version 5 2 or higher that enables automatic generation of a condensed printable raw data report in pdf format after each run on the Gyrolab instrument The generated report is compliant with 21 CFR Part 11 r
256. ontent a Quansteanone version fur Assay 1 S20ENOW G ORAS ES PW reresa Ene parameter gare sure araye ace nhre aescorte Experimer yr Sa anet na Eta Detect PMT 3a e CEM Farase Awa S007 B S084 ce L asesae D asss E 1 18286 08 2 Guanstcations Z versien T fur Assay 1 SODE NOW D OP AEE ela Feros Ene parameter opaze sine analyte vaga escores meme quer Bia agag a Nata Detect PMT dem Re 0064235 Farameter Aw 825 50013098 Co 67 ME Do 33 748 0 33082 Notes Data Companson 1 Proect RooviAssay Develooment anniAssay_NN _cate using Dats Comganson module verson 2 7 4 125 n Gyrotsb Evaluator version 2 1 4 136 Logged in as Administrator e coat s e Runs in the Project are shown under Runs Analyses in the Project are shown under Analyses e Report content for selected Run or Analysis is shown in the right part of the view To change displayed report select the desired Run or Analysis Project Name Status Description Information item example from figure above Project name Assay_NN3_date For Projects not yet saved the Project name is missing Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C 17 3 Manage analysis projects Project Name Status Information item example from figure above Folder path Root Assay Devel opmenti Karin Assay_NN3_date Project version o a Approval status Not approved Runs Run name Assay 1 2009 NOV 10 03 45 55 P
257. op an ongoing Run click Abort The Run is immediately terminated and cannot be resumed Remove all CDs and microplates as described in Chap ter B6 2 1 Do not use results or CDs from aborted Runs as there is a risk that data or the CDs may have been corrupted The pause an ongoing run click Pause To resume the Run click Resume 4 The system stops automatically when the run is completed Click Finish Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B6 B6 After Run procedures and result export After Run procedures and result export NOTE There are two separate instructions one for Gyrolab xP and one for Gyrolab xPlore B6 1 Instructions for Gyrolab xP B6 1 1 Finish Run When the Run is completed microplates and CDs must be unloaded from the instrument Unloading is carried out in the same way as the system is loaded that is by following the instructions on the screen After each step has been completed a green LED is lit on the left side of each section Step Action 1 The system stops automatically when the run is completed Click Finish The Exe cute Run screen a checklist for unloading appears Run ProteinQuantification 2 CD type Gyrolab Bioaffy 200 Execution name ProteinQuantification 2 o Samples Identity Loaded No of Samp Mp1 Yes 18 o CD data 0001020 001 9 Km Unload o Reagents Name identity avaiabe R MP1 Loaded Unload IN Copyrig
258. or detection of ADAs Two parameters in the ADA methods can be controlled by the user mixing time and incubation time NOTE User level Method Developer Project Manager or System Administrator is required to edit methods For more information on user levels refer to Chapter F2 2 6 Step Action 1 In the main menu of Gyrolab Control refer to Chapter F1 1 2 select Methods 2 Select an ADA method in the method list and click Open Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D 13 D2 Gyrolab ADA Software Step Action 3 The Basic View for method editing opens Method steps that are editable are displayed in black in the Operations list Select the method step you wish to edit in the example above mix spin 1 or mix spin 2 Enter mixing and incubation times in seconds in the fields Mixing and Incubation e lick Save to save the method change e Click Save As to save the method in a new name 4 To enable editing of all method steps click Switch The Advanced View for method editing opens FEIO so e so so E mo Advanced editing is a function used for developing customized Methods to suit specific needs Contact Gyros for more information 5 Click Close to close the method editor D 14 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A D2 Gyrolab ADA Software D2 2 2 Design Run This chapter describes how to create or edit an ADA Run using the Wizard
259. or more informa tion e lick the Continue button Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A C 29 C4 Analyze data Step Action 3 The Quantification window opens The left panel of the Quantification window displays available experiments in the run Click on the plus or minus signs in the tree to expand or collapse the tree structure Experiment data is structured according to Run name Analyte name Experiment name CD number 1 2 etc Available PMT setting Detect PMT X Green symbols see below indicate that the standard curve fit succeeded a 7 GenlgG QC samples 2010 MAR 05 03 40 54 PM a ic E O Experiment 1 i Detect PMT 5 5 Q Detect PMT 25 e Red symbols see below indicate that the standard curve fit failed E Assay 1 2009 Nov 10 03 45 55 PM a O Her EQ Test ETE aha Detect PMT 5 C Detect PMT 25 e Click on the rows with green or red symbols to view results from corresponding data set bottom level in the tree in the right panel refer to steps 6 10 e Click the tick box of one or more experiments bottom level in the tree to include that those experiments in the report Click Run Info in the bottom of the left panel to display run information such as user and date Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C4 Analyze data Step Action 5 The right panel of the Quantification window di
260. or multiple CD runs If Calibration Controls are used these will be placed on each CD that do not have a corresponding Standard series Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B3 Design run Step Action 4 Click Loading List Gyrolab Control Loading screen is opened e Gyrolab Control Loading holds microplate loading information and is used when preparing microplates for a run Name concentration volume microplate and well position is included for all sample types An overview of microplates with indication of used wells is also provided e Click Printer button to print the Gyrolab Control Loading TIP Select File Export to export the Loading list in PDF or text format This is useful when printing from another computer is required 5 Close Gyrolab Control Loading 6 Click OK A screen with two tabs Targets and Reports is opened Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B3 Design run Step Action 7 In the Targets tab choose Gyrolab Evaluator Result files from the run are always saved in Gyrolab Result Database To create local copies of the result files optional mark the check box Copy file s to disc Targets Reports v Gyrolab Evaluator v Gyrolab Report 7 Process this target m Copy file s to disk Gyrolab evaluator result folder ramData Gyros Gyrolab Results user date run _ time
261. or these groups NOTE Only edit rows 8 and below Edits in other parts of the Sample list may cause the list to be incompatible with the run 3 Save the edited Sample List Sample List Mandatory Information item and Optional column Index Mandatory for The index is an identifier for Unknown samples UNK Unknown The form of the entry is predefined and the entries Column A samples not must be consecutively numbered 1 2 3 and so used for other on sam pIE types NOTE Do not use this column for Standard series Quality Controls or Calibration Controls Sample type Mandatory UNK for Unknown samples Column B e QC for Quality Controls e CC for Calibration Controls e STD for Standard series e BL for Blanks Sample Iden Mandatory Enter Sample identity for all unknown samples ay Sample identity is used as basis for statistical analysis Column C in Gyrolab Evaluator software Table B3 4 Basis for sample statistics on page 43 below Sample Group Optional Sample Group is used to group samples with common Column D Table B3 3 Details for Sample List items properties Sample group is used as basis for statistical analysis in Gyrolab Evaluator software Table B3 4 Basis for sample statistics on page 43 below Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Sample List item and column Sample Subgroup Column E Dilution Factor Column F MP Identity Column G Well Column H
262. orescence data into a binding profile revealing the interaction taking place on the column within each CD microstructure The binding profiles are accessed through Gyrolab Evaluator Gyrolab Viewer is used during assay development to aid in the selection of optimal reagents and during quality control and assay troubleshooting to investigate outliers D1 2 View binding profile images Binding profile images are accessed through the analysis modules for example Quantification or Data Comparison Refer to Chapter C4 1 and Chapter C4 2 for information on Quantification and Data Comparison modules Step Action 1 In the analysis window select a sample in a data table Right click on the sample identity and select View Images Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 6 D1 Gyrolab Viewer Step Action 2 Gyrolab Viewer window opens The binding profile is a 3D representation of the response intensity in each Gyrolab CD microstructure The binding profile color ranging from dark blue to dark red corresponds to signal intensity from o to 1 For alternative profile coloring refer to step 3 For further information on binding profile interpretation refer to Chapter D1 3 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Di Gyrolab Viewer Step Action 3 Click within the 3D image and drag to change the view angle To control the 3D bi
263. pproved Yes Modified 2008 12 18 15 23 Complete Yes Ea Bioaffy 200 CD type Gyrolab Bioaffy 1000 Status Approved 6 6 Service System version 9 version Not valid Bioaffy 1000 2 step C D wiz v1 1 Bioaffy 1000 wie v1 It is possible to perform six different administration actions Cut Paste Delete Import Export and Export Readable NOTE Select a method in the list to activate inaccessible task buttons Button Action Cut and Cut and Paste are used to move a Method within the folder structure Paste Browse the folder structure to the left in the Methods screen to locate the folder that holds the Method to be cut Select folder Select Method to be cut in the list to the right in the Methods screen e Click Cut Browse the folder structure to the left in the Methods screen to locate a new folder for the run e Click Paste The Method is now located in the new folder NOTE To paste a Method into a folder the folder must have status Allow Method refer to Chapter F2 2 2 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A F 37 F2 Gyrolab Administration Tool Button Action Delete Delete is used to delete a Method e Browse the folder structure to the left in the Methods screen to locate the folder that holds the Method to be deleted Select folder Select the Method to be deleted in the Method list to the right in the Methods screen e Click Delete e Click OK in
264. pyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D3 Gyrolab LIMS Interface Step Action 6 e Check One MP per CD to place all samples for one CD on individual microplates e Un check One MP per CD to let the software distribute samples on microplates 7 Click Loading List Gyrolab Control Loading screen is opened o crbcomumi a He view Ma aim GYRUS Gyrolab Control Loading atein Quantification Gyrolab Bioaffy 200 0 4 4 4 4 4 4 4 100 100 4 4 4 4 4 4 e Gyrolab Control Loading holds microplate loading information and is used when preparing microplates for a run Name concentration volume microplate and well position is included for all sample types An overview of microplates with indication of used wells is also provided e Click Printer button to print the Gyrolab Control Loading TIP Select File Export to export the Loading list in PDF or text format This is useful when printing from another computer is required 8 Close Gyrolab Control Loading 9 Click OK A screen with two tabs Targets and Reports is opened Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A Step 10 11 D3 Gyrolab LIMS Interface Action In the Targets tab choose Gyrolab LIMS LIMS result files are always saved in Gyrolab Result Database To create local copies of the LIMS result files optional mark the check box Copy file s to disc Tages
265. r setting up experiments and running assays on the Gyrolab sys tem called Wizard Run Custom Run and LIMS run LIMS is an optional add on module Loading List A list generated during Execute Run procedures Wizard Run containing information of microplate location and volumes of samples and reagents Method The method describes how the instrument handles samples reagents and CDs Project In Gyrolab Evaluator a Project is a folder into which data from One or more Runs can be added Within the Project Run data is analyzed and the analyzed data is saved and stored Reagent list Used only for runs of design type Custom The list holds infor mation about samples and solutions in the transfer list e g sample type and concentration Run A Run is a collection of information required to perform a set of experiments on the instrument Sample List The Sample List holds information about the samples in a run A 16 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Term Sample Target Transfer list A2 Introduction to the Gyrolab platform Description Sample is the common name for Unknown samples samples to be analyzed Standard series samples with known concentration used for standard curves e Blanks samples without protein added Calibration Controls selected Standard samples used in CDs as controls in multi CD runs Quality Controls spiked samples with known concentration used for qualit
266. rameters e Save Wizard Run Set result file output format Chapter B3 1 2 Gyrolab xP e Save LIMS Run Chapter B3 2 2 Gyrolab xPlore Chapter D3 2 Sample List or Sample List generated by Worklist s generated by Worklist s e Gyrolab Control e LIMS or Chapter D3 3 e manual editing xls Chapter B3 1 3 Gyrolab xP Chapter B3 2 3 Gyrolab xPlore Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 37 D3 Gyrolab LIMS Interface Step LIMS Run Prepare Run Select Wizard Run e Select LIMS Run Select Sample List Select Worklist s Enter experimental parameters Enter experimental parameters Set name and folder for result e Set name and folder for result files files Set name and folder for reports Set name and folder for reports Generate Loading List e Generate Loading List Chapter B3 1 4 Gyrolab xP Chapter D3 4 Chapter B3 2 4 Gyrolab xPlore D3 2 Create or edit a LIMS Run There are three options available when setting up a new run e Create a new Run proceed with D3 2 Edit an existing Run use when similar but not identical experiment design is wanted proceed with D3 2 Use an existing Run use when identical experiment design is wanted go to D3 4 Step Action 1 Click Design Run on the Main menu The Run screen appears E DADA Root t rare Content 2 folders O runs Attribute Folders and Runs allowed 2 e To create a new Run click New Enter a Run name in the Run
267. re and detection reagents Please refer to Chapter B1 H2 3 Gyrolab instrument startup procedure Please refer to Chapter B2 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A H2 Custom Run workflow H2 4 Experimental design Chapter H2 9 contains detailed information and examples on how to prepare Sample Reagent and Transfer lists to achieve intended mapping of samples against standard curves H2 4 1 Create Sample List The Sample List is designed to transfer sample information to Gyrolab Control Gyros provides a Sample List template in Microsoft Excel format Step 1 2 TIP TIP Action Open the Sample List Template Sample_list_template xls found in Cc Pro gramData Gyros Gyrolab Templates Lists From row 8 and below one row in the Sample list represents one sample Columns labelled M are mandatory columns labelled 0 are optional and columns labelled N A are not used M Mandetory MPSE PCR O Optonal Figure H2 1 Sample list template NOTE Cells with a red mark in the upper right hand corner have a comment attached The comment is a description of the information to be included in the column cell Fill in sample information according to Table B3 1 in Chapter B3 1 3 Gyrolab xP or Table B3 3 in Chapter B3 2 3 Gyrolab xPlore For multi CD runs If designing multiple CD Run where a Standard series Unknown Calibration Control Quality Control sample is repeated
268. re optimized for all types of applications and CDs and for a variety of molecules with different analytical properties Suitable Rexxip buffer should be selected considering sample type and species analyte and assay format Refer to Product Information Sheet for Rexxip buffers for recommendations on buffer selection The following solutions and reagents are required PBS T for recipe refer to Chapter E1 2 e Capture and Detection reagents Standard Protein e Rexxip buffer Refer to Product information sheet for Rexxip buffers for recommendations on buffer selection B4 1 Instructions for Gyrolab xP B4 1 1 Reagents and samples By 1 1 1 Capture reagent 1 Vortex Capture reagent stock solution gently 2 Dilute in PBS T or Rexxip to working concentration usually 700 nM for an antibody this corresponds to 0 1 mg ml For minimum required reagent volumes please refer to the Gyrolab Control Loading list Chapter B3 1 4 NOTE Use fresh Capture reagent Use new aliquots from the Capture reagent stock solution kept in refrigerator or freezer at least every week and prepare fresh dilutions of Capture reagent daily B4 1 1 2 Detection reagent 1 Vortex Detection reagent stock solution gently 2 Spin at12 000 x g for 4 minutes to pellet any aggregates that may have formed during storage 3 Dilute the detection reagent in Rexxip buffer usually Rexxip F to the optimal working concentration Use a dark vial to minimize fluorophore e
269. reagent Nanosep cen trifugal devices exist in 3K 10K 30K and 100K Protein Desalting Spin Columns Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H1 Products accessories and consumables Recommended supplier Pall Life Sciences Thermo Scientific Product no 0D030 34 89849 H 6 H1 Products accessories and consumables Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A H2 H2 Custom Run workflow Custom Run workflow This chapter it is describes how to perform immunoassyas in Gyrolab Instrument using the Custom Run workflow design type Refer to Chapter A3 1 for recommendations of when to use which Run design type Only instructions that are unique for Custom Run is included in this chapter For the parts of the workflow that are identical between Custom Run and Wizard Run refer to relevant section in Chapter B H2 1 Introduction to Custom workflow The Custom Run workflow is designed for maximal flexibility and allows the user to customize what samples are quantified towards what reagent set Custom Run can be used when non standard transfer from microplates to CD microlaboratories is required or when a variation of replicates for different samples and standard points for example during assay development is required No Loading List is generated during experiment set up Transfer and Reagent Lists are required to define a Custom Run H2 2 Preparation of captu
270. rent Runs This can for example be used when comparing different assay development Runs when comparing routine analyses performed at different occasions or for quality tests Data to be compared must be analyzed in the same Project 1 2 2 Analysis settings There are several settings available for data analysis Examples of analysis settings for the Quantification module are curve fit models and acceptance criteria Analysis settings can be set for an entire Project option to lock settings refer to Chapter 3 8 or for a specific analysis refer to Chapter Cy 1 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C 5 G Introduction to data evaluation 1 2 3 Storage of analyses In order to store analyses of Run results in a traceable way compliant to GxP requirements the following features are used Project Run results from one or more Runs are added to analysis entities named Projects Within a Project selected Run results are analyzed using one or several analysis modules The resulting Analyses are included in the Project Analysis setting may be locked for a Project All analyses are logged in the Audit trail If the Project is set to Approved status it can be opened and viewed but no additional analyses can be made Folder structure In order to organize Projects a folder structure is available Run result files Analyses Projects and Structure folders are stored in a specific Gyrolab database connected to t
271. rent than normal Structure Structures are either common structures named Common left or Com mon right or individual structures 1 8 For each segment there are Column B one Common left one Common right and eight individual structures All operations will begin in the first microstructure of the first unused segment of the CD Common left is used for adding liquid to all structures in one seg ment starting from the left Common right is used for adding liquid to all structures in one seg ment starting from the right e The microstructure numbers 1 2 3 indicate individual structures in a segment Inlet Inlet specifies where samples and reagents are applied on the CD micro laboratory either to a common inlet common distribution channel or Column C to a structure inlet individual microstructure Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A H 13 H 14 H2 Custom Run workflow Transfer List item Op_Capture reagent addi tion Column D Op_Analyte addition Column E Op_Detect reagent addi tion Column F Op Column G information First operation in the method The name must be written as Op lt your customized transfer name from method gt for example Op_Capture reagent addition Nam ing is case sensitive The entries here are the names from the reagent list or a number for example 1 if it comes from a Sample List This specifies where the reagent or sample will be p
272. right 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A GYROLAB USER GUIDE G Troubleshooting Contents G1 G2 Instrument ISSUOS 6 ccacace eee aor ae ee wa ace ho ee a G 3 G1 1 Instrument initialization ProbDleMS c eceeceeseeeeeees G 3 G1 2 Instrument computer CONTACT cece cece eect ee ee eee eeeee G 7 G1 3 Gyrolab xPlore front panel LEDS cece cece eee ee ee eens G 7 Software ISSUES ari ics hw we aa wo RO SR G 9 G21 Gyrolab Control seres casairese snes zen nessa cama cadre cornea G 9 G2 2 Gyrolab Result Database Backup Manager G 9 G2 3 Gyrolab Evaluator c eee ecceccesceeceeceecesceeeeeeeesseeees G 10 Application issues eee ee ee ee eee G 11 G3 1 No response values are generated eceeeeeeee eee ee sees G n G3 2 Unexpected appearance of standard curve G 11 G3 2 1 Laboratory and instrument generated errors G 11 G3 2 2 LOW response scecceceecesceeceeeeeceseecensencesceaeeaesseenenes G 12 G3 2 3 Extensive VariatiONn cccesccesccesceectenceecceesseeeecseess G 12 G3 2 4 Detect result Not OK in Gyrolab Evaluator result file G 13 G3 2 5 Elevated background eenen iene G 14 G3 3 Problems with outliers cc cece cece esc ceesceeneeeesseeseees G 15 O Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A G3 4 Poor recovery of proteins after
273. rime Gyrolab instrument to ensure function ality of Wash Station pump Refer to Chap ter B2 4 for details To remove air bubbles centrifuge microplate at 3000 x g for four min If bubbles still remain increase time or speed until all bub bles are gone Ensure that loaded volumes are according to volumes specified in Loading List Ensure that each CD contain Unknown Stan dard series samples with a concentration larger than the limit of quantification for the assay and at least four structures with Unknown Standard series samples with a response value of 0 5 Use a fresh aliquot of detecting reagent Gyrolab methods with extended wash proce dures are available for analytes with specific biochemical properties Contact Gyros for sup port G3 2 4 Detect result Not OK in Gyrolab Evaluator result file Possible cause The fluorescence signal is saturated in the Fluorescence detector e The quantifier fails to calculate the response The fluorescence signal generated from this particular structure in the CD microlaboratory is of poor quality Were serum or plasma samples analyzed in the Run Was a partially used CD used in the Run Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Action e Results should be disregarded e Adjust PMT setting Ensure that recommendations regarding sam ple preparation were followed Serum and plasma samples should be thawed on ice vortexed and centrifuge
274. ring assay development and validation D 24 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software Step Action 1 In the ADA Analysis window Chapter D2 4 click on Screening Settings The Screen ing Settings panel opens Screening Settings Cut point formula a Help You can enter a formula used to calculate the cut point The formula may contain numbers and operators Parantheses may be used In addition the following predefined parameters cam be used AvgNcResp Average of the response of all included NC sample replicates AvgNcAvgResp Average of the average response of all NC samples SdNcResp Standard deviation of the response of alll included NC sample replicates SdNcAvgResp Standard deviation of the average response of all NC samples Write the parameters directly in the formula or use the parameter selection and insert button Note All numerical values must be written in american English e g decimal point not decimal comma ADA Controls Detect 1 Detect 5 Identity Type Max CV Lower Limit Upper Limit Lower Limit Upper Limit NC 1_spiked NC NC 1 unspiked NC NC 2 NC sited AE ef ee ee NC 2__unspiked NC PCi_spiked PC PC1 unspiked PC PC2 spiked PC PC 2_unspiked PC CV unknown samples 3 In the Evaluation section enter cut point formula in th
275. rm analysis on DADA 2 2011 MAY 09 02 52 58 PM 2 screening 2 Confirmation 7 Quantification Screening Settings Confirmation Settings Quantification Settings Select what analysis Functionalities to use by marking check boxes as appropri ate e Inthe Runs section select desired Run for analysis Analysis Settings for each functionality are set in the Screening Settings Confir mation Settings and the Quantification Settings sections Click on the section to expand it For Screening analysis continue to Chapter D2 4 1 Screening assays are performed to screen for ADA positive samples The Screening functionality is used during assay development and validation and for routine analysis e For Confirmation analysis continue to Chapter D2 4 2 Confirmation assays are performed to investigate whether positive samples from screening assays are true positives Confirmation functionality is used during assay development and validation and for routine analysis For Quantification analysis continue to Chapter D2 4 3 The Quantification functionality is used during ADA assay development and validation It offers the same functionality as the Quantification module used when analyzing results from immunoassays performed in Gyrolab Bio affy CDs described in Chapter Cy 1 D2 4 1 Screening During ADA analysis clinical samples are screened for ADA positives in a Screening assay The Screening functionality is also used du
276. rophore labeled detection reagent Dilute the fluorophore labeled reagents to 1000 nM in PBS 0 2 BSA Calbio chem e Aliquot and store fluorophore labelled detection reagent at 20 C protected from light Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B1 Labelling of capture and detection reagents Step Action 7 Verify fluorophore labeling e For all new assays assay formats and newly labelled reagents perform a titra tion Run to find the optimal concentration for the detection reagent refer to Chapter A3 4 2 e Foran established assay perform a test Run using previously established con centration Compare the result from the new batch of labelled reagent with results from previous batches in previous titration Runs B1 3 Buffer exchange azide removal and protein concentration protocols This chapter contains protocols for buffer exchange and reagent concentration B1 3 1 Nanosep 30K Protocol The Nanosep 30K protocol Pall Life Sciences is used for buffer exchange and azide removal Nanosep columns come in different cut off values 3 10 30 and 100K The optimal filter size of the spin column depends on the size of the reagent The following solutions and consumables are required e Nanosep 30K membrane Pall Life Sciences and sample reservoir e Deionized water 1xPBS without NaN Step Action 1 e Pre rinse the Nanosep by filtering 500 pl deionized water or buffer through the mem
277. rted in the list to the right in the Maintenance screen Click Export Readable to open Export Maintenance in readable format dialog Browse and select desired export readable folder Click OK in the Export Readable Maintenance dialog to confirm export readable The selected Maintenance method is now present in a readable format in the selected export folder Click on Close in the top right hand corner of the Maintenance screen to exit Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 41 F 42 F2 Gyrolab Administration Tool F2 2 6 Users Click on Users on the main menu to access the Users screen The Users screen lists Gyrolab software users with their user levels Four different user levels can be assigned to users There is also a Service user level used by Gyros during services Each user level has a defined set of user privileges A System Administrator is allowed to perform all actions whereas a Operator has more limited user privileges focused on performing Gyrolab experiments Using different user levels it is possible to control the workflow and give access to critical steps to a limited number of users All users log in to Gyrolab software with their user name and a password The password must be changed the first time a user logs in and then every 90th day During introductory customer training Gyros provides temporary User Name and Password for the computer controlling Gyrolab instrument and for
278. rvoir e Deionized water e 1xPBS without NaN3 Thermo Scientific spin column protocol Step Action 1 e Pre rinse the Nanosep by filtering 500 pl deionized water or buffer through the membrane twice Spin up to 11 000 x g for a couple of minutes Do not allow the membrane to dry out prior to use 2 Pipette the required volume of protein 50 to 500 pl into the sample reservoir e Cap the Nanosep device Spin up to 11 000 x g for 2 20 minutes 3 If the reagent appears to have spun dry in the device the reagent is easily recov ered by pipetting several times with approximately 50 ul buffer 4 Dilute the reagent with buffer to get a concentration of 1 mg ml Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Bi Labelling of capture and detection reagents B 12 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B2 B2 Gyrolab instrument startup procedure Gyrolab instrument startup procedure The following steps must be performed prior to start a Run on the Gyrolab instrument Turn on the instrument and laser Chapter B2 1 Start Gyrolab Control Chapter B2 2 e Initialize the system Chapter B2 3 e Prime the system Chapter B2 4 The following solutions are required refer to Chapter E1 2 for recipes e Bioaffy Pump Liquid e Bioaffy Wash Station Solution 1 B2 1 Turn on instrument and GL Degasser NOTE GL Degasser is only delivered with Gyrolab xP In Gyrolab
279. s Would you like to set the system in standby mode Yes No e If another Run is scheduled later during the day click No and start the new run e If it is the last Run of the day click Yes The Ensure enough standby solution is available dialog opens Connect tubings for Standby solutions and click OK Standby procedures will start Standby procedures means priming Syringe Pumps and Wash Stations with Standby Solution It is recommended to put system in Standby mode at least three times a week For more information refer to Gyrolab Instrument Guide for Gyrolab xPlore How to turn Gyrolab off Before turning the instrument off for a longer period of time it is recommended to put the instrument in Standby mode see Gyrolab Instrument Guide for Gyrolab xPlore B6 2 2 Step 1 2 1 Shut down the Instrument Action Right click on the Gyrolab server icon and select Instrument Shutdown This will unload the instrument software and power off the instrument Press the power button on the Instrument for more than 5 seconds Chapter A2 2 2 NOTE The instrument will shutdown even if a run is in progress After the button has been pressed down for 5 seconds the following will happen Instrument software is unloaded Power is cut Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B6 After Run procedures and result export B6 2 3 Generated Gyrolab Control files There are four types of
280. s for this project Wis Test D12153 ADA 2011 SEP 13 03 08 41 PM x Le Select OK Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A C 23 3 Manage analysis projects Step Action 6 In Quantification tab edit settings for the quantification module Analysis Settings e Evaluation These settings affect curve appearance and limit of detection factor e Matrix Settings Specify if the acceptance criteria LLOQ and ULOQ refers to the back calculated Neat concentration values or the Diluted concentration values Acceptance criteria These settings are used to determine which result values are considered acceptable Result that fall outside of acceptance criteria will be highlighted in the result report For detailed descriptions of analysis settings for the Quantification module refer to Chapter Cy 4 C 24 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 3 Manage analysis projects Step Action 7 In General tab edit general project settings Analysis Settings ADA Analysis Quantification General Plug in Selection CJrequire a reason for modificabons to key fields Eq excluding samples changing concentrations Number format e If Require a reason for modification of key fields box is ticked a change description is required if a sample is excluded or included and if concentration or dilution values are changed The change descriptions
281. s screen to locate the folder that holds the Method to be exported readable Select folder Select Method to be exported in the Method list to the right in the Methods screen e Click Export Readable to open Export Methods in readable format dia log Browse and select desired export readable folder e Click OK in the Export Readable Methods dialog to confirm export The selected Method is now present in a readable format in the selected export folder Click on Close in the top right hand corner of the Methods screen to exit F 38 O Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H Doo23573 A F2 Gyrolab Administration Tool F2 2 5 Maintenance Click on Maintenance on the main menu to access the Maintenance screen Select a folder in the folder structure to display its content amp Maintenances System versions supported 1 9 Maintenance amp Maintenance Approved maintenances allowed Yes Approved maintenances 3 Draft maintenances 0 Draft maintenances allowed Yes Needle desorb v2 1 Needle sanitize v2 Needle wash v2 It is possible to perform six different administration tasks Cut Paste Delete Import Export and Export Readable NOTE Select a maintenance method in the list to activate inaccessible task buttons Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F2 Gyrolab Administration Tool Button Act
282. s supported by the Gyrolab system when analysis is exported Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A C 19 3 Manage analysis projects 3 4 Open a Project Step Action 1 ae NOTE The Open Project dialog is also available from the Gyrolab Evaluator start view 2 The Open window opens In the folder structure in the left panel browse to the Folder in which the desired Project is present 3 Click to highlight Project name in the right panel and click Open 3 5 Save a Project NOTE If no change has been made in a Project it is not possible to save it Step Action In the Project view select File Save Project or click ud 2 The Save Description window opens C 20 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A 3 Manage analysis projects Step Action 3 Enter a comment in the text box to describe the reasons for Project changes The comment is saved in the Audit trail F save Description Describe the reasons for your changes in the text box below before saving Change description Change list Add Run Added Run Assay 1 Add Run Added Run Run Demo 1 Add Run Added Run Run Demo 2 New analysis Created version 1 of Quantification 1 New analysis Created version 1 of Quantification 2 New analysis Created version 1 of Quantification 3 New analysis Created version 1 of Quantification 4 New analysis Created version 1 of Data Compari
283. s with known concentration Quality Controls may be used for quality control or when comparing results from different Runs and experi ments Reagents Standard series Replicates RA Quality control name j i Add QC 1 20 0 10 0 QC 2 40 0 10 0 Delete Qc 3 80 0 10 0 QC 4 160 0 10 0 Concentration unit pM Set number of replicates in the Replicates list Highest number of replicates is 8 e Specify Quality control name Concentration and Dilution for each Quality Con trol sample The concentration value corresponds to Quality Control sample con centration before dilution The dilution value corresponds to the dilution of the Quality Control sample A value of 1 corresponds to an undiluted sample Dilu tion values must be 1 or larger e Specify the unit in the Concentration unit text box Note that the same unit must be used as used for the Standard series refer to Step 7 Click Add for adding an additional Quality Control sample e Highlight Quality control sample and click Delete to remove 9 The ADA Control section contains settings specific for the software module Gyrolab ADA Software Refer to Chapter D2 2 for more information 10 Select Analytes For each Run one or more Analytes are defined For each Analyte one or more Experiments are defined Experiment settings deter mine which Reagents Standard series Calibration Controls and Quality Controls define
284. scanning the identity of a MP B 64 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Bs Start Run procedures B5 2 2 Load CDs Step Action 1 Put CDs in room temperature for 30 minutes in the unopened aluminium pouches 2 Click Load in the CD Data section The Load CD dialog opens 1 Insert CD into instrument and close the hatch 2 Press Load to load CD Method requires Gyrolab Bioaffy 200 CD id 3 Open the aluminium pouch and place the CD in loading position refer to Chap ter A2 2 2 Touch only the outer edge of the CDs Do not touch the surface of the CD Start the Run within 15 minutes after the CD has been taken out from its pouch Protect the CD from extended illumination from indoor lighting or sunlight since this may affect data quality Close the hatch and click Load in Load dialog The system identifies the CD and the CD identity appears in the list on screen Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B 65 B5 Start Run procedures B5 2 3 When loading is completed as confirmed by all green LEDs being lit on screen the Run can be started Step Start Run Action 1 Close the instrument hatch 2 Click Start An event log is displayed where all steps of the Run are registered along with event time Run Protein Quantification 2 CD type Gyrolab Bioaffy 200 Execution name Protein Qua
285. screen NOTE Different Syringe Pumps can handle different liquids Syringe Pumps Wash Stations Needles Use pump for Connected Samples Reagents Syringe Volume Needles Pump 1 E 100 0 ul 1 2 Pump 2 q 100 0 ul 3 4 Pump 3 e 100 0 ul 5 6 Pump 4 r 100 0 ul 7 8 Pump 5 m 100 0 ul 9 10 General pump settings Pump to needle prime volume 2000 0 ul Minimum needle volume 0 1 E Bottle to pump prime volume 6000 0 ul Maximum needle volume 60 0 ul Standby Liquid Standby solution Prompt for priming needles before run execution x Figure 9 Example of syringe pump configuration tab Step Action 1 Indicate the role of the syringe pump by marking one or both of the check boxes Samples and Reagents for each pump 2 Enter the Syringe Volume in ul 3 Enter the Connected Needles if not already completed 4 In the General Pump Settings section enter Pump to Needle Prime Volume in ul The Pump to Needle Prime Volume is the volume used to rinse the tubing between the syringe pump and its connected needles during priming 5 In the General Pump Settings section enter Bottle to Pump Prime Volume in ul The Bottle to Pump prime Volume is the volume used to rinse the tubing between the pump liquid bottle and the syringe pump during priming 6 Enter the Minimum Needle Volume in wl 7 Enter
286. ser Guide P0004354 H D0023573 A B 15 B2 Gyrolab instrument startup procedure B2 4 Prime instrument For optimal results it is important to prime the Gyrolab instrument before the first Run of the day Gyrolab priming requires 15 20 minutes Refer to Gyrolab Instrument Guide for priming instructions NOTE If the instrument has not been used for at least two weeks extra priming must be performed Refer to Gyrolab Instrument Guide B 16 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B3 B3 Design run Design run NOTE There are two separate instructions one for Gyrolab xP and one for Gyrolab xPlore This chapter describes the how to design runs in Gyrolab Control using the Wizard design type For instructions on how to design a run using Custom design type refer to Chapter H2 4 For instruction on how to use the optional add on LIMS design type refer to Chapter G1 2 B3 1 Instructions for Gyrolab xP B3 1 1 Wizard run design introduction The two workflow Wizard and LIMS differ in run design Design of runs are described in separate chapters Chapter B3 1 2 and Chapter B3 Sample preparations run start and run finish procedure are the same for both workflow and will be described in chapters Chapter B4 Chapter B6 Step Create or Edit Run Select Wizard Run design type Chapter B3 1 2 e Enter experimental parameters e Save Wizard Run Sample List Sample List generated by Chapter B3 1 3 Gyrolab Con
287. ser is working refer to GL Degasser manual e Inspect the syringes to ensure that there is no leakage Refer to Gyrolab Instrument Guide e To remove air bubbles prime Gyrolab instrument refer to Chapter B2 4 If there still are air bubbles in the Syringe Pumps remove the bubbles as described in Gyrolab Instrument Guide Action Frozen samples should be thawed on ice vor texed and centrifuged before transfer to microplate wells refer to Chapter B4 1 1 4 or Chapter By 1 1 3 Gyrolab xP or Chap ter By 2 1 4 or Chapter By 2 1 3 Gyrolab xPlore for details Refer to Instruction For Use supplied with the Rexxip buffer Refer to Chapter B1 1 and Chapter B1 2 for details Titrate detection reagent concentration refer to Chapter A3 4 for details Remove unbound labeling reagent refer to Chapter B1 2 Further assay development and optimization may be needed refer to Chapter A3 4 for details Action Refer to Chapter B1 2 for details Refer to Chapter B1 2 for details Refer to Chapter B2 4 for details Possible cause Was the Wash Station pump moving during Run Were there air bubbles in microplate wells Was enough volume of reagents and sample added to microplate wells Does the fluorescent signal image in Gyrolab Viewer show extensive variation Was an old aliquot of detecting reagent used Did sample to sample carryover interfere with results G3 Application issues Action P
288. signal to Background croup Subgroup E Calculated Concentration Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H Doo23573 A Step 10 11 12 13 14 15 C4 Analyze data Action To view specific data points click desired Table Standards Quality Controls Cali bration Control and Unknowns to expand Click again to collapse a e TIP If not the entire name of the analysis set is visible in a Table increase the column width decrease number of columns refer to step 9 or refer to complete name under Selected Data Optional Add general experiment comments in the Notes text box located at bot tom of the right panel Optional To export data from the Data Comparison module to tab separated text format txt or to Excel XML spreadsheet format xIs click Copy Data To File but ton browse for desired location and click Save NOTE No traceability of results is achieved using Copy Data To File A copy of a Result file is created but this can be done for example before an analysis is saved and it is NOT logged in the Audit Trail To fulfil the requirements of 21 CFR part 11 data must be exported from a saved Project refer to Chapter 3 5 Click Create Report to save the analysis Set Analysis Name and click OK The analysis is now saved under Analyses Data Comparison in Gyrolab Evaluator Project view Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C 37 C4 Ana
289. software for example when a new user logs in or if 90 days have passed since last password change Password may also be changed when desired by the user To change password e Mark the check box Change Password e Enter current password in Password field new password in New Password field and confirm new password in Confirm Password field e Click OK NOTE User name and password are case sensitive E E d z User Name l Password l Change Password Gyrolab Control GYR f S Version Nf Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B2 Gyrolab instrument startup procedure Step Action 4 Once logged in the main screen will appear GYROS j f aaa i NOTE If no instrument access restart the instrument B2 3 Initialize the system During initialization hardware tests of the instrument components are performed for example robot arm movements carousel rotation and CD stations vacuum Step Action 1 Close the instrument hatch if open Click Initialize System on the Main menu The Initializing System dialog box is displayed as initialization proceeds Details of the initialization can be viewed by clicking on the Details button NOTE To re initialize the system click on Logout in the Main menu Choose Restart from the drop down menu in the Shut Down dialog then click OK 2 Click Finish when initialization is complete Copyright 2015 Gyros Gyrolab U
290. son 1 Com 4 Click Save 3 6 Close a Project Step Action In the Project view select File Close or click K E 2 If the Project has unsaved changes the Save Project dialog opens e Click Yes to save changes The Save Description window opens refer to Chap ter 3 5 e Click No if the changes are not to be saved 3 7 Approve Unapprove a Project Approved Projects are locked for further action It is possible to open it but no new analyses can be saved To approve a Project user level Project Manager or System Administrator is required Approved projects can be unapproved It is possible to edit unapproved Projects To unapprove an approved Project user level System Administrator is required Select Edit Approve Project to approve a project The action is logged in the system audit trail Chapter 2 3 e Select Edit Unapprove Project to unapprove an approved project The action is logged in the system audit trail Chapter 2 3 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C 21 3 Manage analysis projects 3 8 Set analysis settings for a Project Analysis settings for a Project determines the default settings for data evaluation for all analyses within the Project It is possible to lock analysis settings for a Project This will facilitate that all analyses performed within the Project are carried out in a consistent manner Step Action 1 To edit and set analysis settings
291. splays collapsable expandable views for Analysis settings used to view and edit analysis settings refer to step 6 Standards which hold standard curve data table and corresponding graph refer to step 8 e Quality Controls Calibration Control and Unknowns which hold result data tables refer to steps 9 to 11 Other available functionalities e Options for viewing of data tables and graph refer to step 7 e Notes refer to step 12 e Data export refer to step 13 e Report generation refer to step 14 to 16 6 Click Analysis Settings in the right panel to view and or edit Evaluation and or Acceptance Criteria settings for the analysis refer to Chapter C4 4 for information on settings parameters If changes are made only settings for currently opened data set will be changed The calculated Limit of detection as well as Fit data parameter values are displayed in the bottom of this view a Analysis Setbngs View Ongral Ditechude blanks in curve fitting LLOQ conc Fit model Five parameter logestx curve v ULOQ conc Weeght Response Eo mer timit of detection factor 3 Onex CY conc Odikted Avg Sias 36 D a Limit of detecton response 0 095304 Fat data Modal equation y A 5 1 yC 8 amp 0 05915 E 9 86544E 07 C 1 84161E 08 D 0 99081 E 0 25157 R 0 93931 Click Analysis Settings again to collapse the Analysis Settings view Copyright 2015 Gyros G
292. syringe pump during priming 6 Enter the Minimum Needle Volume in wl 7 Enter the Maximum Needle Volume in ul Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 9 Fi Gyrolab Control Step Action 8 Click Standby Liquid The standby liquid is the solution used to put the system in Standby mode The Pump Liquids dialog displays a list of available liquids F Pump Liquid xl Standby solution New Pump Liquid Delete Pump Liquid 9 Select Standby Solution by clicking its name in the list To add new liquids to the list click New Pump Liquid Type a new name and click OK e To remove a liquid from the list select a name in the list and click Delete Pump Liquid and click OK to confirm deletion 10 Click Set The standby liquid appears on the tab 11 Click Save to save syringe pump settings Configure Wash Stations The system is equipped with two wash station pumps one for each Wash Station The wash station pumps are primed with wash station solutions The two Wash Stations are configured on the Wash Stations tab in the Configure System screen Syringe Pumps Wash Stations Needles cD Stations Prime Volume Wash station 1 100000 0 ul Wash station 2 100000 0 ul General wash station settings Standby Solution Standby solution Prompt for priming wash stations before run execution I Figure 3 Example of Wash Station configuration tab F 10 Copyright 201
293. t TIP Macros can be used to construct file names and locations refer to Chap ter B3 1 5 for a list of available macros TIP The settings in the Targets tab can be exported and imported which enables settings to be shared between users instruments and projects Other targets tabs may be available as well for example Gyrolab Report The Gyrolab Report tab contains settings specific for the software module Gyrolab Control Report and is only available if a licence for Gyrolab Control Report has been acquired Refer to Chapter D4 2 for more information Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D3 Gyrolab LIMS Interface Step Action 12 Open Reports tab Targets Reports tylesheet Destination ProgramData Gyros Gyrolab Templates Styleshe c ProgramData Gyros Gyrolab Results user l Add Edit Remove Import Output Settings Export Output Settings A report file with information on the Run can be generated To import default settings for report file Stylesheet and Destination lick Import Output Settings Inthe Import Settings dialog browse to C ProgramData Gyros Gyro lab Templates Stylesheets select GyrolabStandardReport xsl and click Import e If no report file is wanted select the file present in Stylesheet and click on Remove button TIP Customized reports can be generated C
294. t 3 mM 0 02 remove the sodium azide refer to Chapter B1 3 e If the detection reagent solution is in amine containing buffer exchange buffer to 0 1 M Sodium bicarbonate buffer pH 7 2 8 0 refer to Chapter B1 3 e If concentration of detection reagent is lt 1 mg ml concentrate detection reagent solution refer to Chapter B1 3 e If concentration of detection reagent is gt 1 mg ml dilute with 0 1 M Sodium bicarbonate buffer e Ifthe reagent to be labeled is a powder lyophilized from an appropriate buffer it is reconstituted in 0 1 M Sodium bicarbonate buffer Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 7 B1 Labelling of capture and detection reagents Step 2 Action Fluorophore labeling procedure Add 1 10 volume of 1 M Sodium bicarbonate buffer to the 1 mg ml detection reagent solution NOTE This is not required if the starting material is lyophilized and already reconstituted in 0 1 M sodium bicarbonate buffer e Transfer 100 ul of detection reagent solution to vial containing Component A reactive dye Vortex gently to dissolve the reactive dye e Protect vial from light by wrapping it with aluminum foil e Incubate 1 hour at room temperature while shaking the vial gently Preparation of purification column e Moisten purification column filter with 1 ml PBS Pressured air may be required to elute the PBS e Stir purification resin Component C and add 1 ml to the column al
295. t and run finish procedure are the same for both workflow and will be described in chapters Chapter B4 Chapter B6 Step Create or Edit Run Select Wizard Run design type Chapter B3 2 2 Enter experimental parameters e Save Wizard Run Sample List Sample List generated by Gyrolab Control or Chapter B3 2 3 manual editing xIs or Prepare Run Select Wizard Run Chapter B3 2 4 Select Sample List Enter experimental parameters Set name and folder for result files Set name and folder for reports Generate Loading List B3 2 2 Create or edit a Wizard Run There are three options available when setting up a new run e Create a new Run proceed with Chapter B3 2 2 Edit an existing Run use when similar but not identical experiment design is wanted proceed with Chapter B3 2 2 Use an existing Run use when identical experiment design is wanted go to Chapter B3 2 4 Step Action 1 Click Design Run on the Main menu The Run screen appears CADA Root GBioaffy o Service Content 3 folders 4 runs Attribute Folders and Runs allowed Run Y Complete Approved 2 e To create a new Run click New Enter a Run name in the Run Name field To edit an existing Run browse and select the desired Run and click Open B 32 Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A B3 Design run Step Action 3 e Select Wizard in the Design Type list and click Select The Wizar
296. t most column if With replicates box is ticked and View list is set to Extended NOTE The number and titles of columns may differ depending on the Run and if replicates are shown or not Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Step 8 10 11 12 13 1h 15 16 Cy Analyze data Action Click Standards to view Standard samples data and Standard curve e Use buttons to display Px Standard samples data and Standard curve E Standard samples data zZ Standard curve Standard Samples that fail acceptance criteria are highlighted in the table Acceptance criteria were set in 6 e Click Chart settings above the Standard Curve to set linear logarithmic scales on the X axis and the Y axis Click again to close the Chart settings window Standard Curve zooming Zoom in by clicking in the graph and drag the cursor down and right to select area with the rectangle Zoom out by clicking in the graph and drag the cursor up and left The original graph will be shown Standard points can be excluded included by clicking in the graph Right click on the point and chose ExcludelInclude The graph and the data will be updated e Click Standards again to close the Standards view Click Quality Controls to view Quality Control samples data e If desired Exclude include samples and make notes as described in 7 e lick Quality Controls again to close the Quality Controls view Click Calibra
297. t one blank sample must be included Include at least duplicates of all unknown samples in the Run A3 3 2 Calibration Controls The purpose of Calibration Control samples is to save CD structures for analysis of unknown samples in multi CD runs For each experiment a standard series must be present on at least one CD With the use of Calibration Controls on the remaining CDs instead of an entire Standard series structures are saved It is recommended to use at least two Calibration Controls with concentrations corresponding to two different Standard sample concentrations When analyzing results check that Calibration Control data do not differ from Standard series data for corresponding concentration values If there is a significant difference discard the sample results from that particular CD It is very important that the Standard sample and Calibration Control of the same concentration are from the identical aliquot A3 3 3 Unknown samples Unknown samples are placed in designated sample microplates and information about each Unknown sample is entered into a Sample List to allow traceability of the generated results Include at least duplicates of all unknown samples in the Run A3 3 4 Quality Controls Quality Controls are samples that have been spiked with known analyte concentrations into identical sample matrix as present in your unknown samples Quality Controls are used to ensure that the assay is working properly within a CD run and
298. tect PMT 1 5 25 B 34 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A B3 Design run Step Action 5 Select Setup 6 Select Reagents NOTE The software will automatically add reagents to the design depending on selected method 1 step 2 step 3 step or 4 step This can be edited by the user ee Dette t Delete Specify Name for capture Cap_ and detect Det_ reagents The Condition field is optional and can be used for additional information such as concentration value or matrix Click Add to add more capture and detect reagents Add and name one reagent in the software for each different reagent required for the design Highlight reagent and click Delete to remove reagent Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B 35 B3 Design run Step Action 7 Select Standard series Delete b Number Replicates Blank k I Standard points 7 2 v Calibration Controls cc o0 v 2 Cc only used in mutico runs Standard point name Concentration cc Standard A_Blank 0 0 Standard A 1 0 0 Standard A 2 0 0 Standard A 3 0 0 Standard A 4 0 0 Standard A 5 0 0 Standard A 6 0 0 Standard A 7 0 0 Concentration unit Specify Name for Standard series Condition is optional and can be used for ad
299. tenance methods import export export readable cut paste and delete Manage users and user permissions create user edit user export user list audit trail and delete Manage CD types import export export readable and delete Manage microplate types import export export readable and delete Manage liquids import export export readable and delete Manage targets used to process Run results import export export readable and delete Manage list loader files Logs out user from the Administration Tool Launches the Gyrolab User Guide in pdf format Provides information of Gyrolab Control version Copyright 2015 Gyros Gyrolab User Guide Pooo4354 H D0023573 A F2 Gyrolab Administration Tool F2 2 1 Design types Click on Design types on the main menu to access the Design types screen The Design types screen lists available design types 6 Design Types System version supported 2 No design type selected 5 0 RCOS v1 Dom J sts leti di It is possible to perform four different administration tasks Import Export Export Readable and Delete NOTE Select a design type in the list to activate unavailable task buttons Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A F 31 F2 Gyrolab Administration Tool Button Action Import Import is used to import design types to Administration Tool to make them available for use in Gyrolab Control e Click Import to open
300. tes Gyrolab Set System Time dialog opens Gyrolab Set System Time posar msi mim Retest o a Set New system time date and time e Click Refresh to update the fields in New System Time to the current system time e Click Apply e Click Close Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A F 67 F5 Gyrolab Set System Time F5 3 Non logged system time changes System time can also be changed manually using the regular Windows tools or by automatic updates However system time changes will only be added to the audit trail if the Change System Time tool is used Automatic updates of system time can occur when The instrument computer is included in a Windows domain where system time is controlled by domain policies The instrument computer is configured to automatically adjust the system time to correlate with an external time server The instrument computer is set to automatically adjust to daylight saving time changes If it is vital to include all system time changes in the audit trail make sure to exclude these time change sources by taking the following steps Do not add the instrument computer to a windows domain or make sure that there are no policies adjusting the system clock on the instrument computer e Disable synchronization with external time servers and daylight saving adjustments using the Windows Control Panel Date and Time tool F 68 Copy
301. th information on user identity time and version are in the Audit trail This is done to ensure full traceability of results It is possible export and print Audit trail reports This chapter describes Audit trail for Gyrolab Evaluator refer to Chapter 3 10 for information on Project specific Audit trail Step Action de Select History Audit trail in Gyrolab Evaluator main view to display the Audit trail log 2 The Audit Trail window opens PP Audit Trail System Renamed project Root Study_1 Assay_AAA to Administrator 6 7 2011 7 32 46 PM_Assay_A2 Rename Project 6 7 2011 7 32 45 PM Renamed Project Assay_AAA to Assay_A2 Administrator 6 7 2011 7 07 57 PM Renamed folder Root Study 2 to Study 3 Rename Folder 6 7 2011 7 07 57 PM Renamed Folder Study 2 to Study 3 6 7 2011 7 06 52 PM sdfc Remove 6 7 2011 7 06 52 PM Removed Project Assay BBB Renamed project Root Study 2 Assay BBB2 to Administrator 6 7 2011 6 45 17 PM Assay BBB Rename Project 6 7 2011 6 45 16 PM_ Renamed Project Assay BBB2 to Assay BBB Renamed project Root Study 2 Assay BBB to Administrator 6 7 2011 6 45 11 PM Assay BBB2 Rename Project 6 7 2011 6 45 10 PM_ Renamed Project Assay BBB to Assay_BBB2 Administrator 6 7 2011 6 36 20 PM Renamed folder Root Study 22 to Study 2 Rename Folder 6 7 2011 6 36 19 PM Renamed Folder Study 22 to Study 2 z To review details click the Open button for desired Project Version That version of th
302. th replicates must be ticked If required by Project settings the reason for exclusion must be specified The change description is included in the Audit Trail To include an excluded sample right click on the sample and select Include To perform this With replicates box must be ticked If required by Project settings the reason for inclusion must be specified The change description is included in the Audit Trail It is possible to edit Dilution values If required by Project settings the reason for editing must be specified The change description is included in the Audit Trail It is possible to add Notes for individual samples in the right most column if With replicates box is ticked and View list is set to Extended NOTE The number and titles of columns may differ depending on the Run and if replicates are shown or not 6 Optional Add general experiment comments in the Notes text box located at bot tom of the right panel 7 To export data or generate analysis report continue to Chapter D2 4 4 D2 4 2 1 Data table descriptions Confirmation Columns that are displayed in the Confirmation view will be included in reports generated If Original view is selected only columns indicated with a Yes below will be displayed If Extended view is selected all available columns are shown Column heading Identity Subgroup Response Average Response SD Response CV Response Original Description view
303. the Delete Methods dialog to confirm deletion The selected Method is now deleted from the Methods list Import Import is used to import Methods into the Administration Tool to make them available for use in Gyrolab Control Browse the folder structure to the left in the Methods screen to locate the folder into which the Method is to be imported Select folder e Click Import to open Import Methods dialog Browse and select desired Method Methods must be in zm1 format e Click Import e Click OK in the Import Methods dialog to confirm import The selected Method is now present in the Methods list Export Export is used to export Methods from the Administration Tool Exported Method can be imported into another Gyrolab instrument Browse the folder structure to the left in the Methods screen to locate the folder that holds the Method to be exported Select folder e Select Method to be exported in the Method list to the right in the Methods screen e Click Export to open Export Methods dialog Browse and select desired export folder e Click Export e Click OK in the Export Methods dialog to confirm export The selected Method is now present in the selected export folder Export Export Readable is used to export a readable copy of a Method This copy readable cannot be used in Gyrolab Control but it can be useful for example when contacting Gyros for support e Browse the folder structure to the left in the Method
304. then the concentration of the detection reagent concentration must also be higher to still be in sufficient excess at the high concentration end of the measuring range Always optimize detection reagent concentration towards expected sample concentration The data in Figure 1 displays results from a titration run in which detection reagent concentration was varied whilst capture reagent concentration was held fixed For this assay a detection reagent concentration of 10 nM is recommended since this option gives the lowest limit of detection while still sufficiently concentrated to allow measurements in high end of the calibration curve w e S 10 nM detection 9 A 50 nM detection T O 25 nM detection 10 Limit of detection 0 1 0 01 0 1 1 Concentration nM Figure 1 Standard curves for human IL 8 sandwich assay The concentration of the detection antibody was varied to determine the optimal working concentration Diamonds mark the limit of detection for the different concentrations Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A3 Gyrolab immunoassay workflow A3 4 3 Evaluation of PMT Fluorescence detector settings The fluorescent signal from the microstructure column is amplified by a photo multiplier tube PMT when the signal reaches the detector The degree of amplification needed to obtain a sufficient response value depends on the signal intensity of the measured sample The signal amplificati
305. tion Controls to view Calibration Control samples data e If desired Exclude include samples and make notes as described in 7 e Click Calibration Controls again to close the Calibration Controls view Click Unknowns to view Unknowns samples data and Standard curve e If desired Exclude include samples and make notes as described in 7 e Click Unknowns again to close the Unknowns view Optional Add general experiment comments in the Notes text box located at bot tom of the right panel Optional To export data from the Quantification module to tab separated text for mat txt or to Excel XML spreadsheet format xIs click Copy Data To File button browse for desired location and click Save NOTE No traceability of results is achieved using Copy Data To File A copy of a Result file is created but this can be done for example before an analysis is saved and it is NOT logged in the Audit Trail To fulfil the requirements of 21 CFR part 11 data must be exported from a saved Project refer to Chapter 3 5 Click Create Report to save analysis Set Analysis Name and click OK The analysis is now saved under Analyses Quantification in Gyrolab Evaluator Proj ect view Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C 33 Cy Analyze data 4 2 Data Comparison module The Data Comparison module is used to compare result data and charts produced by the Quantification module for different data sets Comparison anal
306. tion buttons on the main screen Instrument Access When the instrument access LED is lit the main power is on and the connection between instrument and computer is functioning NOTE Even if the instrument access LED is not lit indicating no instrument access methods and Runs can still be created and edited F1 1 3 14 Instrument modes Instrument mode is indicated by a LED below the instrument access LED refer to Chapter F1 1 3 13 in the main menu o Operating Mode Instrument mode and user privileges refer to Chapter F2 2 6 determine what functions are available in the main menu The change of instrument mode is triggered by actions from the user or the control software These actions differ depending on the status of the Gyrolab instrument F 16 Copyright 2015 Gyros Gyrolab User Guide P0004354 H Doo23573 A Gyrolab instrument modes Mode Description LED appearance Power off Gyrolab Con Off trol software is started Sys tem is ready to be initialized Initializing Hardware Not indicated testsare being by LED performed Operating System is On ready for use Standby System has Flashing been primed with standby solutions Accessible from e Initializing Standby Operating Power off e Initializing Standby Operating Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Fi Gyrolab Control Activated by Initialization failure User log out Switchi
307. tions to occur These additional assay steps typically add complexity and time to existing assays while the Gyrolab Mixing CD not only integrates sample pretreatment but also shortens assay and incubation times with its nanoliter scale workflows See Figure 8 for details of an individual Gyrolab Mixing CD microstructure Inlet for Inlet for wash solutions 4 SS samples reagents buffers or capture reagents for AA specific assay formats es Volume definition As gt 200 nL Volume definition o o Mixing chamber for 200 nL SE incubation steps Z Consistent volume deli d l few cade Affinity capture column hydrophobic Di E 15 nt packed with barriers stop streptavidin coated liquid flow Dynospheres Y Y Overflow channels for excess liquid and reproducible volume definition Figure 8 Gyrolab Mixing CD microlaboratory microstructure showing functional units Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A A2 Introduction to the Gyrolab platform A2 5 Rexxip buffers Gyros provides Rexxip buffers for reagent and sample dilution Rexxip buffers are optimized for all types of applications and CDs and for a variety of molecules with different analytical properties Suitable Rexxip buffer should be selected considering sample type and species analyte and assay format Refer to Product Information Sheet for Rexxip buffers for recommendation on buffer selection A2 6 Gyrolab sof
308. trol or manual editing xIs or Prepare Run Select Wizard Run Chapter B3 1 4 Select Sample List Enter experimental parameters Set name and folder for result files Set name and folder for reports Generate Loading List Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 17 B3 Design run B3 1 2 Create or edit a Wizard Run There are three options available when setting up a new run e Create a new Run proceed with Chapter B3 1 2 Edit an existing Run use when similar but not identical experiment design is wanted proceed with Chapter B3 1 2 Use an existing Run use when identical experiment design is wanted go to Chapter B3 1 4 Step Action q Click Design Run on the Main menu The Run screen appears 2 e To create a new Run click New Enter a Run name in the Run Name field To edit an existing Run browse and select the desired Run and click Open 3 e Select Wizard in the Design Type list and click Select The Wizard panel appears Run name 8 Design type Wizard Select Reselect To change design type highlight the design type in the Design Type list and click Reselect Comments for the Run can be made in the Comments window for example what type of assays the run is intended for B 18 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H Doo23573 A B3 Design run Step Action 4 Click Design Run on the M
309. trument 5 Click Close to close the CD information screen F1 2 3 9 Logout Logout is used for shut down log off or restart of Gyrolab Control Step Action i Click Logout The Logout dialog opens r Logout ip Administrator is currently logged on to the system What would you like to do Shut down Ir Ends your session and shuts do so that you safely can tum pow the system off Le A 2 Select desired function Shut down Log off or Restart and click OK 3 Gyrolab Control performs desired function Additional windows may open Select desired function and click OK to complete Shut down Log off or Restart F1 2 3 10 Help To access the help section a pdf version of Gyrolab User Guide click Help on the main menu and browse for needed Gyrolab User Guide chapter F1 2 3 11 About Click About to get information about the software versions and licences for Gyrolab Control F1 2 3 12 View Alarm Gyrolab Control has a built in warning system A traffic light icon in the bottom left hand side of the main menu indicates alarm state e o T E Cream Figure 12 Alarm LEDs F 26 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A Fi Gyrolab Control Alarms LED Level Requires action Green No active alarm No Yellow Warning alarm Optional A warning means that the system cannot operate according to configuration set up A warning d
310. tware A2 6 1 Standard software e Gyrolab Control Gyrolab Control is the software used to control the Gyrolab instrument set up experiments process runs and recover experimental data Refer to Chapter Fi for details e Gyrolab Evaluator Gyrolab Evaluator is used for evaluation of experiment raw data created by Gyrolab Control Refer to Chapter C for details e Gyrolab Administration Tool Gyrolab Administration Tool is used to manage administration and import export of users user access levels CD microlaboratories methods etc For details Refer to Chapter F2 for details e Gyrolab Result Database Explorer Gyrolab Result Database Explorer is used for viewing results and report files customize the database view export results and report files and to generate status reports refer to Chapter F3 for details e Gyrolab Database Backup Manager Gyrolab Database Backup Manager is used for backing up of the database at a desired location either regularly or at specified time points refer to Chapter Fy for details e Gyrolab Set System Time Gyrolab Set System Time is used for changing system time All changes of system time will be recorded in the audit trail refer to Chapter F5 for details e Gyrolab Service Application Gyrolab Service Application is intended only for Gyros service personnel A2 6 2 Additional software A number software add on modules are available e Gyrolab Viewer The Gyrolab Viewer module for Gyrolab Contro
311. type MP id MP well CD id CD structure Gyrolab response D4 Gyrolab Control Report D4 4 Installation of Gyrolab Control Report The Gyrolab Control Report software module is available for Gyrolab Control version 5 2 or higher and is activated by the user with a licence key Licenses are instrument specific Contact Gyros to purchase Gyrolab Control Report and receive a license To register the license Save the license file to the hard disk of the instrument computer at the destination C ProgramData Gyros Licenses Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D 49 D4 Gyrolab Control Report D 50 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D5 Gyrolab Serial Dilution Analysis Gyrolab Serial Dilution Analysis Visit www gyros com for the latest updates on available software modules Ds 1 Introduction Gyrolab Serial Dilution Analysis is a software add on module for Gyrolab Evaluator version 3 2 or higher The software is used for automatic evaluation of spike recovery to verify the sample analysis accuracy using dilution series of spiked and unspiked unknown samples Gyrolab Serial Dilution Analysis loads data from the quantification analysis using the information in the analysis settings fields Spiked subgroup prefix Unspiked subgroup prefix and Requested PMT name refer to Chapter D5 5 Data results of unspiked and spiked aliquotes for different dilutions are pa
312. umn in 1 5 2 ml microcentrifuge collection tube e Centrifuge at 1500 x g for1 minute to remove excess liquid 2 Perform four column washes Add 400 ul of equilibration buffer to the top of column e Centrifuge the column at 1500 x g for1 minute to remove excess liquid Discard buffer from the collection tube Sample Loading Step Action 1 e Place column in a fresh collection tube and remove the cap Apply 30 120 pl of sample proteins with My greater than 7000 to the center of the compacted resin bed Be careful not to disturb the resin or to allow sample to flow around the resin bed 2 Optional To improve recovery percentage of low molecular weight proteins or for small sample volumes add 20 40 ul of equilibration buffer to top of resin Do not exceed a total of volume of 120 ul 3 Centrifuge column at 1500 x g for 2 minutes The desalted sample is collected in the collection tube 4 Discard the desalting column after use B 10 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B1 Labelling of capture and detection reagents B1 3 3 Concentrate reagent solution This protocol for reagent concentration uses Nanosep 30K Pall Life Sciences Nanosep columns come in different cut off values 3 10 30 and 100K The optimal filter size of the spin column depends on the size of the reagent The following solutions and consumables are required e Nanosep 30K membrane Pall Life Sciences and sample rese
313. unique names for results files and folders will be created automatically without having to change the settings for different Runs A selection of macros are provided for this Insert macros by typing them into folder and result file name fields Macro user run S cdid date time Description Expands to the full user name Expands to the Run name Expands to the CD id for example 1234567 123 Expands to the executed Run start date Expands to the executed Run start time Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 47 B3 Design run B 48 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Bu B4 Prepare samples and reagents Prepare samples and reagents NOTE There are two separate instructions one for Gyrolab xP and one for Gyrolab xPlore This chapter describes sample and reagent preparation when working with Gyrolab Bioaffy CDs For sample and reagent preparation for Gyrolab Mixing CDs refer to Chapter D2 Preparation of Capture and Detection reagents Standard series Calibration Controls Quality Controls and Unknown samples for Gyrolab Bioaffy CDs and their loading into microplates is described in this chapter Refer to Chapter A3 3 for more info on sample types Minimum required reagent and sample volumes are specified in the Gyrolab Control Loading list Chapter B3 1 4 Gyros provides Rexxip buffers for reagent and sample dilution Rexxip buffers a
314. up the data stored in Gyrolab Result Database Backup of the database is not performed automatically by Gyrolab software Gyrolab users must create their own routines and set time intervals for data backup Backup can be performed manually at certain time points or set up as a scheduled repetitive task TIP It is strongly recommended to store the backup data at a different location than the Gyrolab computer Fy 1 Perform Gyrolab database back up Step Action 1 To open Gyrolab Database Backup Manager Select Start All Programs Gyros Gyrolab Control Gyrolab DB Backup Manager Gyrolab Database Backup Manager dialog opens The list displays backup history Gyrolab Database Backup Manager 10 47 07 CAGyrolabiDbBackup GyrolabDBDump dmp 27170816 Yes 10 51 36 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 10 54 00 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 11 34 39 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 11 34 45 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 11 36 07 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 11 36 52 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 11 37 29 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 11 38 41 C Gyrolab DbBackup GyrolabDBDump dmp 27170816 Yes 2 To set location for database backup e Click Set folder path NOTE Note that it is recommended to save the backup separate from the C drive if the C drive would crash It is also r
315. v 2 v Calibration Controls CC O I 2 CC only used in multi CD runs Standard point name Concentration cc Standard A_Blank 10 0 Standard A_1 loo Standard A_2 0 0 Standard A_3 0 0 Standard A_4 0 0 Standard A 5 10 0 Standard A_6 jo o Standard A 7 10 0 Concentration unit Specify Name for Standard series Condition is optional and can be used for additional information such as Standard samples dilution buffer Set Replicates for Blank samples Highest number of replicates is 20 Set Number and Replicates for Standard series samples and Calibration Controls Highest number of replicates is 8 For each Standard series sample specify the Concentration Specify unit in the Concentration unit text box For multi CD runs the use of calibration controls is added by ticking Calibration check boxes for standard samples of choice A marked check box means that for every CD that does not have a standard curve calibration control s with con centration corresponding to that of the standard sample will be placed instead of the Standard series Additional functions To add additional Standard series click Add To copy settings of one Standard series to a new Standard series highlight desired Standard series and click Copy The new Standard series can be edited and saved by a new name Highlight Standard series and click Delete to remove a Standard series NOTE Maximum 8 rep
316. verage Response value Identity of the microplate where the sample was placed Well position on the microplate where the sample or standard was placed e OK The results are approved e Not OK The results are not approved The fluorescence sig nal is of poor quality which may be caused by inadequate PMT setting detector is saturated or errors in sample preparation For ADA controls Negative control or Positive control For unknown sample Unknown The needle used to transfer the sample from the MP to the CD structure It is possible to add comments to individual samples Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software D2 4 3 Quantification The Quantification functionality is used during ADA assay development and validation It offers the same functionality as the Quantification module used when analyzing results from immunoassays performed in Gyrolab Bioaffy CDs Chapter C4 1 Step Action 1 In the ADA Analysis window Chapter D2 4 Click on Quantification Settings The Quantification Settings panel opens R Quantification Settings linclude blanks in curve fitting LLOQ fone Fit model Five parameter logistic curve ULOQ conc xd a g Tetest 4 Limit of detection factor 2 m Neat CV conc Orne se T Set or edit analysis setting in the Evaluation Matrix Settings and Acceptance Criteria ref
317. verse _ _ 512 1 08 28 1802823 PWT Dent emt 2 5 To display a 2D image of the binding profile click Chart Settings e Mark check box Show Chart in the 2D image Intensity Sum section Click Chart Settings again to close the settings window A two dimensional contour plot appears The 2D image displays the sum of the intensity across the microstructure in radial direction e Zoom in by clicking in the 2D graph and drag the cursor down and right to select an area with the rectangle Zoom out by clicking in the graph and drag the cursor up and left The original graph will be shown Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D1 Gyrolab Viewer Step Action 6 To copy or save the 2D image to file right click in the image and select e Save As to save the 2D image to disc In the Save As dialog enter desired file name and choose between available file formats svg jpg vml xaml gif png tiff bmp Click Save e Copy to place a copy of the image on the clipboard 7 To export 2D data to file click Copy 2D Data To File button A dialog appears Export Data Data will be exported to a file Please note that no Further traceability of the file and data is supported by the Gyrolab system The dialog is to remind the user that further analysis of the 2D image data is not supported by the Gyrolab Viewer software Click OK e Inthe Save As dialog enter desired file name
318. wn lists in the experiment set up Acidic reagent addition and Detection reagent mix addition Select number of Standard series in the Number of Standard series list For multi CD runs When Use on all CDs is ticked unknown samples will be quantified against Standard series on the same CD One analysis per CD will be created e If Use on all CDs is not ticked all unknown samples are quantified against the same Standard series NOTE Instead of Standard series on all CDs Calibration Controls can be used Refer to step 7 e Select Standard series in the Standard series name list Only Standard series specified in step 7 are available Select number of Quality Controls in the Number of Quality controls list For multi CD runs e If Use on all CDs is selected the Quality Controls samples will be applied on all CDs included in the Run e If Use on all CDs is not selected the Quality Controls samples will be applied on one CD even if the experiment is included on several CDs Select Quality Controls in the Quality control name list s Only Quality Controls specified in step 8 are available e Select number of ADA controls in the Number of ADA controls list For multi CD runs e f Use on all CDs is selected the ADA control samples will be applied on all CDs included in the Run If Use on all CDs is not selected the ADA control samples will be applied on one CD even if the experiment is included on several CDs
319. xPlore GL degasser is embedded Step Action 1 Switch on power The power switches are located on the rear of the Gyrolab instru ment and GL Degasser For optimal performance turn on the instrument in advance before starting the Run e Gyrolab instruments with serial number MW10010 MW10035 GW10036 GW10044 and GW10046 GW10065 3 hours before starting a Run All other instruments 30 minutes before starting a Run 2 For systems without a LIF button the laser is turned on automatically e For systems with a LIF button check that the LIF button is in pressed down position For LIF button position refer to Chapter A2 2 1 B2 2 Start Gyrolab Control software Gyrolab Control software consists of a server software and a client software The server must be running before the client is started Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A B 13 B 14 B2 Gyrolab instrument startup procedure Step Action Start Gyrolab Server e Click Start All Programs Gyros Server e Gyrolab Instrument Log is displayed and Gyrolab server icon appears on the task bar 1 Start Gyrolab Control software e Select Start All Programs Gyros Client Enter user name and password in the Login dialog box and click OK The user name and password is the same for all Gyrolab software For further infor mation on user and password administration refer to Chapter F2 2 6 Password must be changed if requested by the
320. xposure to light Avoid pipetting from the bottom of the detection reagent stock tube to avoid transferring aggregates Aggregates may affect the performance of the assay For minimum required reagent vol umes please refer to the Gyrolab Control Loading list Chapter B3 1 4 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A B 49 B 50 Bu Prepare samples and reagents NOTE Prepare fresh dilutions of Detection reagent daily By 1 1 3 Standard series and Calibration Controls Standard series samples and Calibration Controls are crucial parts of the experiment They must be prepared and handled with care since errors during this process will affect all concentration values for the Unknown samples For minimum required volumes for Standard samples please refer to the Gyrolab Control Loading list Chapter B3 1 4 1 Take a new vial from the freezer or from other appropriate storage 2 Reconstitute lyophilized standards for dilution according to their product data sheet 3 Make serial dilutions of the Standard sample proteins in appropriate Rexxip buffer 4 Ensure sufficient mixing but do not shake NOTE For the Standard series samples used as Calibration Controls one must prepare extra volume during dilution to ensure that the volume is sufficient for both the Standard series and Calibration Control It is very important that the Standard series sample and Calibration Control are from the identical dilution
321. y evaluation but not used for standard curve Targets define the output format and location for result files generated by the control software that are stored in the data base and accessed by evaluation software Used only for runs of design type Custom The list defines to which CD segments and structures samples and solutions are transferred and in what order Terminology used specifically in Gyrolab Evaluator Structure folder Project Run Analyte Experiment Data set PMT setting Quantification analysis Data Comparison anal ysis Structure folders are used to organize Projects in Gyrolab Evalu ator for example collect Projects within an experimental series or all assay development Projects in a specific Structure folder Projects are entities in which analyses of one or more Runs is kept in Gyrolab Evaluator Analysis setting may be locked for a Project All analysis made in a Project are tracked in the Audit trail Results from a Gyrolab Run Results from Gyrolab Runs are selected by Run name for analysis in a Project The Analyte subset of the Run results comprises all results using a certain assay for a certain substance There can be one or more Analyte subsets in a Run The Experiment subset of the Analyte results comprises all results using a certain combination of reagents at specific con centrations There can be one or more Experiment subsets in a Analyte subset of a Run The Data set subset o
322. y generated lists can be edited prior to run start refer to Chapter B3 1 3 However Gyros recommends using the automatically generated Sample Lists as this will reduce the risk or errors 14 Comments for the Run can be made in the Comments window for example what type of assays the run is intended for 15 Save the Run 16 Click Close to finish the Design Run procedure D 20 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A D2 Gyrolab ADA Software D2 3 Prepare Run Sample preparation is carried out as described in Gyrolab ADA assay protocol The protocol is included in the purchase of Gyrolab ADA Software This chapter describes run preparation for an ADA Run Step Action 1 Click Execute Run in the Main menu of Gyrolab Control refer to Chapter F1 1 2 2 Browse and select desired Run from the list and click OK Runs that are not complete and thus not ready to execute are marked with a zigzag line More information is needed before the Run can be 9 executed Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A D2 Gyrolab ADA Software Step Action 3 The Execute Run screen is opened Coene Let loade Sangietstlosse Number of sampes 40 Sample replicates 2 v indude medah narba of fee segments ise sohed urephed Number of CDs e To load a Sample List click Sample List File browse and select desired list e List Loader file sets rules for how to import
323. y specific column by clicking on column title Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A C2 Log in main menu functions and analysis administration 2 2 3 2 Explore folder structure Step 1 2 Action Click Manage in Gyrolab Evaluator start view and click Explore in the Manage win dow A window opens where it is possible to browse Folders jj Projects 3 Runs and Analyses 4 analysis icon differs depending on analysis type It is also possible to create new Folders and Projects and to move rename and remove Folders and Projects refer to step 3 step 5 F Gyrolab Evaluator Results Explorer BBB Gj Run Demo 1 2009 FEB 26 09 38 18 AM 4 Run Demo 2 2009 FEB 04 11 54 45 AM gt Analysis_1 Analysis_2 Z Curve Comparison e Select a project and click Open to open a Project e Click Cancel to close the Explore window To create a new Folder or a new Project right click on desired parent Folder and select New Folder or New project Gyrolab Evaluator Results Explorer A dialog opens I New Folder Enter a name for the new Folder or new Project and click OK e Click Cancel to abort Project Folder creation C 12 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A C2 Log in main menu functions and analysis administration Step Action 4 To move an existing Folder or Project right click on the Folder or the Project and select Move
324. y week and prepare fresh dilutions of Capture reagent daily B4 2 1 2 Detection reagent 1 Vortex Detection reagent stock solution gently 2 Spin at 12 000 x g for 4 minutes to pellet any aggregates that may have formed during storage 3 Dilute the detection reagent in Rexxip buffer usually Rexxip F to the optimal working concentration Use a dark vial to minimize fluorophore exposure to light Avoid pipetting from the bottom of the detection reagent stock tube to avoid transferring aggregates Aggregates may affect the performance of the assay For minimum required reagent vol umes please refer to the Gyrolab Control Loading list Chapter B3 2 4 NOTE Prepare fresh dilutions of Detection reagent daily By 2 1 3 Standard series Standard series samples are a crucial part of the experiment They must be prepared and handled with care since errors during this process will affect all concentration values for the Unknown samples For minimum required volumes for Standard samples please refer to the Gyrolab Control Loading list Chapter B3 2 4 1 Take a new vial from the freezer or from other appropriate storage 2 Reconstitute lyophilized standards for dilution according to their product data sheet 3 Make serial dilutions of the Standard sample proteins in appropriate Rexxip buffer 4 Ensure sufficient mixing but do not shake B4 2 1 4 Unknown samples and Quality Controls Quality Controls are prepared in the same manner as
325. ype dialog to confirm deletion The selected design type is now removed from the Design type list Click Close in the top right hand corner of the Design types screen to exit F 32 Copyright 2015 Gyros Gyrolab User Guide P0004354 H D0023573 A F2 Gyrolab Administration Tool F2 2 2 Folders Click on Folder on the main menu to access the Folders screen Select a folder in the folder structure to the left to display its content Folders Method system versions supported 1 9 Run system versions supported 1 2 EME Root EBS Bioaffy amp Root Bioaffy Wizard methods Bioaffy 1000 wiz E Custom methods i Runs Child folders 0 Folders allowed Yes B Wizard methods i F Bioaffy 1000 wiz Runs 0 Runs allowed Yes E Bioaffy 20 HC wiz E L E Bioaffy 200 wiz Approved methods 3 Approved methods allowed Yes H 0 Service Draft methods O Draft methods allowed Yes Vivi a Bioaffy 1000 2 step C D wiz v1 y y 7 Viv PS Bioaffy 1000 wiz v1 Cut Paste Delete It is possible to perform five different administration tasks Cut Paste Delete Create Folder and Edit Folder NOTE Select a folder in the list to activate unavailable task buttons Button Action Cut and Cut and Paste are used to move a folder within the folder structure Paste Browse the folder structure to the left in the Folders screen to locate folder to be cut Select folder e Click Cut
326. yrolab User Guide Poooy354 H D0023573 A C 31 C 32 C4 Analyze data Step T Action General commands for Standards Quality Controls Calibration Control and Unknowns tables Were Orignal 7 with repicstes KE lA Standard Curve Bennie o 1 10 10 1 900 10 000 Concectration ng ml C Cos Gece Cae In the View list select display option for data tables Original A selected number of data columns default e Extended All available data column Refer to Chapter C4 3 for description of data table columns If the With replicates box is ticked default all replicates for samples are shown Untick the box to display average values for samples To exclude a data point right click on the sample and select Exclude To perform this With replicates must be ticked If required by Project settings the reason for exclusion must be specified The change description is included in the Audit Trail To include an excluded sample right click on the sample and select Include To perform this With replicates box must be ticked If required by Project settings the reason for inclusion must be specified The change description is included in the Audit Trail It is possible to edit Expected Concentration and Dilution values If required by Project settings the reason for inclusion must be specified The change descrip tion is included in the Audit Trail It is possible to add notes for individual samples in the righ
327. yros Gyrolab User Guide P0004354 H D0023573 A B3 Design run Step Action 7 In the Targets tab choose Gyrolab Evaluator Result files from the run are always saved in Gyrolab Result Database To create local copies of the result files optional mark the check box Copy file s to disc Targets Reports v Gyrolab Evaluator v Gyrolab Report 4 Process this target v Copy file s to disk Gyrolab evaluator result folder ramData Gyros Gyrolab Results user date run _ time Browse Gyrolab evaluator result file name EvaluatorResult_ run _ date _ time xml Info This target generates a result file from a Gyrolab run for further analysis in Gyrolab Evaluator The result file is copied to the selected file destination The user sets the name and destination for the result folder and file name The settings from the last run of the current user will be pre selected Note that result files are always saved in Gyrolab Result Database Import Target Settings Export Target Settings Files are saved to the location specified in Gyrolab Evaluator result folder field and with the name specified in Gyrolab Evaluator result file name Settings are pre served from the user s last Run e To import default settings for Gyrolab Evaluator result folder and Gyrolab Eval uator result file name Click Import Tar
328. yses can be made between Quantification module analyses within a Project Step Action 1 In Gyrolab Evaluator Project view Chapter 3 1 click the Data Comparison button Data 2 The Data Comparison window opens EB Data Comparison Quantification 1 Version 0 Assay 1 2009 NOW 10 03 45 55 PM Quantification 2 Version 0 Run Demo i 2009 FEB 26 09 38 18 AM Three main panels are available e Available Data Selected Data e Data Comparison 3 In the Available Data panel browse and select analysis set Detect PMT X in figure below for data comparison by clicking the corresponding Add button Repeat until all desired analysis sets are selected Data Comparison E Quantification 1 Version 0 Assay 1 2009 NOV 10 03 45 55 PM E HCP E Test 1 1 Detect PMT 1 Detect PMT 5 Detect PMT 25 Quantification 2 Version 0 Run Demo 1 2009 FEB 26 09 38 18 AM NOTE The Add button will only be available if that specific analysis set is avail able in an Analysis Report C 34 Copyright 2015 Gyros Gyrolab User Guide Poooy354 H D0023573 A Cy Analyze data Step Action 4 The selected analysis sets are listed in the Selected Data information on analysis set can be found in the tool tip Hover with the cursor over selected data to display the tool tip An overlay chart is displayed in the Data Comparison panel sara veran 1 2219021 Optemge DOSS FEB 11 2 27 02 PM C

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