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Bio-Plex Manager MP Software User Guide - Bio-Rad

1. llle 66 Importing the Calibration or Verification Values 0 0 0 67 Checking the Status of the Instrument Maintenance lulu 68 Responding to a Failed Routine 0 0 0 es 69 Calibration Fall tes cx cache ee ERU REGE Roe m eR RR RR a ue 70 Verification Failures llle RR Ta 70 Interrupting a Routine 0 0 00 es 71 Preparing Your Instrument for Nonuse 000 eee eee 71 Adjusting the Probe Height 0 0 cece eee 72 Weekly Maintenances cgo Ro ur ew nes ae eed Saw bee Sale 72 Cleaning the Sample Probe 00 2 2 cee eee ee eee 73 MAGPIX Maintenance ranea eaa EA eee 73 User Guide v Table of Contents Chapter 7 Maintenance Routines 0000000eeeneneee 75 Calibration and Verification Routine llle 75 Clear Bubbles Routine 0 000 ee enne 77 Daily Start Up Routine a 28s adda eee ede eehie eds Ghd ESAE RE UR EERS 78 Enhanced Maintenance Routine llle 79 Fluidics Preparation Routine 2 00 eee 80 Prepare for Storage Routine ss acassasrinrerierikai as es 81 Princ ROUNE sooo Ime oh ate a ears andar iu ML sd ete ides eese epe ede 82 shut Down ROUTING ser eese eu teen IGE Aaa ee a EEREERREERGUES 83 UnclogROUtllie sse teste hee oet io ine ETE das ine iN ad ee Ae od denis 84 Verification ROUTING cs ig etes euet tute Een eth gere ee aN eM Seg 85 Wake from Storage Routine 002 eee 86 Was
2. Click OK Weekly Maintenance 72 Clean the sample probe once a week to keep it free of any debris Whenever you remove the sample probe from the probe assembly you must recalibrate the probe before you read another plate Therefore cleaning the sample probe must always be followed up with running the Adjust Probe Height maintenance routine Bio Plex Manager MP Software MAGPIX Maintenance Cleaning the Sample Probe To clean the sample probe 1 Turn off the MAGPIX instrument and unplug the power cord 2 Remove the sample probe 3 Use either or both methods to clean the sample probe m Bath sonicator place the tip of the sample probe in the bath sonicator for 2 5 min 10 ml syringe force distilled water through the tip of the sample probe to its large end 4 Replace the sample probe Screw the black fitting on top of the sample probe until it clicks 5 From the Maintenance view run the Adjust Probe Height procedure MAGPIX Maintenance Within the first year of use Bio Rad recommends that you perform the 6 month and 12 month maintenance The maintenance kits are Bio Plex MAGPIX 6 Month Preventive Maintenance Kit cleans the air filters and replaces the syringe seals catalog 171 012010 x Bio Plex MAGPIX 12 Month Preventive Maintenance Kit replaces the sample probe tube and the drive fluid filter catalog 171 012012 User Guide 73 6 Maintaining the MAGPIX System 74 Bio
3. LSG Software ActGbio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Back Activate ILL 5 Navigate to where the license file is located select the file and click Open The Activation Successful window appears confirming that the software has been activated Wil Bio Plex Manager MP License Mar Activation Successful Bio Plex Manager MP is successfully activated Who Bio Rad Technical Support Email LSG_Software_Act bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST 6 Click OK to exit the activation software and start Bio Plex Manager MP 96 Bio Plex Manager MP Software Deactivating the Bio Plex Manager MP License Deactivating the Bio Plex Manager MP License You may want to deactivate the Bio Plex Manager MP license for one of the following reasons You want to move the license from one computer to another This can occur for example if you are replacing your computer You must first deactivate the license from the first computer and then activate it on the second computer You want to remove the license from the computer Deactivating the License Online To deactivate Bio Plex Manager MP online 1 2 3 Start Bio Plex Manager MP From the Help menu click Manage License Select Deactivate Bio Plex Manager MP Online and click Continue Wi Bio Plex Manager
4. Monitor the status of the MAGPIX instrument and to easily identify at any time which routines need to be run to keep your instrument operating according to the manufacturer s specifications x Run the maintenance routines including calibration and verification m Import the calibration and verification kits m Adjust the probe height ee a EA File Instrument Help Eo Calibration Not Available a Verification Not Available a Fluidics Not Available a amp Shut Down 6 11 2013 33829 PM Q Create Run Protocols ibo Additional Routines e Q e Po sett rl CAL VER Fluidics Fluidics2 Calibration Kits Analyze Export p Daily Start Up Verification Kits x Es J Aen LP sor 4 S Add 5 mL of 70 isopropanol to the appropriate reservoir in the reagent block mu Routine Log Ready Vortex CAL VER Fluidies1 and Fluidics2 each for 10 seconds Add 6 drops each of CAL VER Fluidics1 and Fluidics to the indicated wells Estimated Run Time 10 minutes Use Calibration Kit Contains Calibration Lot Use Verification Kit Contains Verification Lot Fluidics 1 Lot Fluidics 2 Lot Description Daily Start up prepares your instrument for daily use It runs different routines depending on the state of the instrument and it may include the Calibration and Verification Verification and Wake From Storage routines Run Daily Start Up each day you use the instrument before you run any
5. WARNING f any of the Bio Plex Manager MP assay panels provided by Bio Rad have been modified these will be overwritten with the Restore command If you want to save these edited panels rename the panels first before you use the Restore command To restore the Bio Plex Manager MP assay panels 1 From the protocol dialog box click Manage Assay Panels 2 Click Restore About Standard Lots Standard lots are definitions of analytes and their starting concentration for a particular assay panel When you create a protocol you select one of the defined standard lots The standard lot definitions can be reused thus eliminating the tedious task of entering the standards each time you run an experiment Bio Plex Manager MP comes with a set of predefined standard lots User Guide 49 4 Managing Assay Panels and Standard Lots A list of the predefined standard lot definitions and any standard lots you create is displayed in the Manage Standard Lots dialog box IT CX v LotName Format Assay Panel Expiration Date 4 5029511 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2016 03 29 5029510 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2016 03 29 5028692 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2016 01 29 5028196 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2015 12 19 5025848 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2015 09 20 5023534 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2015 0
6. Description Daily Start up prepares your instrument for daily use It runs different routines depending on the state of the instrument and it may include the Calibration and Verification Verification and Wake From Storage routines Run Daily Start Up each day you use the instrument before you run any protocols You do not need to keep track of the calibration and verification status if you run this routine at the start of each day 64 Bio Plex Manager MP Software Setting Up the Reagent Block LEGEND 1 The colored squares indicate which reservoirs to fill and specify the appropriate liquids 2 The wells are color coded to correspond to the reagents specified in the reagent block instructions The colors match the color of the bottle covers of the reagents 3 Routine name 4 Instructions on which liquids and reagents are required any preparation required and the amounts of the liquids and reagents to use 5 Calibration or verification kit lot numbers 6 Reagent lot numbers 7 Description of the routine Click the arrow to show or hide the description There is a diagram of the MAGPIX reagent block and well strip Important The reservoirs and wells in the diagram correspond to those in the MAGPIX reagent block and well strip as seen when you stand facing the ejected plate When you select a maintenance routine one or more reservoirs and wells are filled in The Reagent Block section displays the lot number of the
7. File Help EA Export Results Name Acquisition Time Assay Panel Analytes Description Hu Diabetes 10 Plex 4 6 20 2013 245 PM Bio Plex Pro Hu Diabetes 10 Plex 10 ME Hu Diabetes 10 Plex 3 6 20 2013 245 PM Bio Plex Pro Hu Diabetes 10 Plex 10 Hu Diabetes 10 Plex 2 6 20 2013 244 PM Bio Plex Pro Hu Diabetes 10 Plex 10 Hu Diabetes 10 Plex 1 6 20 2013 244 PM Bio Plex Pro Hu Diabetes 10 Plex 10 Hu Diabetes 10 Plex 6 20 2013 243 PM Bio Plex Pro Hu Diabetes 10 Plex 10 Hu Cytokine 27 Plex 10 6 20 2013 242 PM Bio Plex Pro Hu Diabetes 10 Plex 10 Hu Cytokine 27 Plex 9 6 20 2013 240 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex B 6 20 2013 240 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 7 6 20 2013 239 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 6 6 20 2013 2 39PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 5 6 20 2013 238 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 4 6 20 2013 238 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 3 6 20 2013 2 37 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 2 6 20 2013 2 37 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 1 6 20 2013 2 36 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cytokine 27 Plex 6 20 2013 235 PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cancer Biom
8. ef New Assay Panel dj Manage Assay Panels Assay Panel MAGPIX Quick Start Region Analyte 12 Region_12 13 Region_13 14 Region_14 E 15 Region 15 18 Region 18 Region 19 Region 20 Region 21 Region 22 Region 25 Region 26 Region 27 Region 28 Region 29 Region 30 Region 33 Region 34 Select All Unselect All ok Cane User Guide 13 2 Creating Protocols Formatting Plates 14 The array reader uses the plate formatting to identify which wells are to be read and Bio Plex Manager MP uses it to determine how to analyze the different samples in each well Note Only formatted wells are read by the array reader Undefined wells are not read To format a plate Ts 2 3 4 Navigate to the protocol dialog box Click Format Plate Click the button in the toolbar for the type of well you want to format Click the wells in the template that you want defined with this well type Formatted wells are colored blue with a specific shape to identify the well type Control Standard and Unknown wells are numbered Blank wells are specified with the letter B For more information on the well types see Well Types on page 16 p P sees RECOLHA 8 9 60000nnmpn 00000BBDBng 90000BnnEB 000000006 000000006 90000BDnpg 90000HDnBE o Standards Info Bio Plex Mana
9. 2 Clean or replace the sample probe 3 Perform the Adjust Probe Height procedure 4 Perform the Enhanced Maintenance routine 5 Runthe protocol again When emptying the waste container replace it with a different waste container that is dry The sensors on the emptied waste container may not be completely dry causing the instrument to incorrectly detect the waste container as full Problem Possible Cause Solution A Windows security The user s profile and Click Allow access alert dialog box appears permissions are set such with the message that the user must grant Windows Firewall has access to xPONENT blocked some features of this program s Firewall has blocked some features of this program Windows Firewall has blocked some features of xPONENT on all public and private networks Name Publisher Luminex Corporation Path C program flesuminex xponent42 xponent exe This program has already been blocked or unblocked for a different network location Allow xPONENT to communicate on these networks F Private networks such as my home or work network de already configured vihat are the risks of allowing a program through a frewal User Guide 109 C Troubleshooting 110 Bio Plex Manager MP Software Index A Analytes definition 12 Analytes excluding 12 Analytes selecting 13 Analyzing results in Bio Plex Manager MP 55 Assay panel list customizing
10. What to Do Next 1 Move the file to a computer where you can send email 2 Send the file as an attachment to Bio Rad Technical Support Bio Rad Technical Support Warning Email The deactivation process is not complete until the certificate LSG_Software_Act bio rad com is sent to Technical Support Until then you will not be able to move the license to another computer or reactivate the Telephone software on this computer 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST PER 8 Click OK 9 Move the deactivation certificate file to a computer where you can send email and email the file to Bio Rad Technical Support LSG Software ActQGbio rad com Technical Support will reply with an email informing you that the license has been deactivated Once you receive this email the license has been removed from the computer You have the option to reuse the license and activate it on any computer User Guide 101 A License Activation 102 Bio Plex Manager MP Software B Backing Up the Database There are two databases that need to be backed up on a regular basis m xPONENT database m Bio Plex Manager MP database User Guide 103 B Backing Up the Database Backing up the xPONENT Database 104 Bio Rad recommends that you back up the xPONENT database on a regular basis You can manually back up the xPONENT database or you can schedule automati
11. Bio Plex Pro Hu Isotyping 7 Plex Bio Plex Pro Ra Cytokine 23 Plex Bio Plex Phosphoproteins Bio Plex Total Targets Bio Plex Pro Hu Cancer Biomarker 16 Plex Bio Plex Pro Hu Cancer Biomarker 18 Plex E Bio Plex Pro Hu Group I Cytokine 27 Plex Bio Plex Pro Hu Group I Cytokine 17 Plex Bio Plex Pro Hu Group II Cytokine 21 Plex Bio Plex Pro Hu VCAM 1 ICAM 1 2 Plex E Bio Plex Pro Hu Group I Cytokine 8 Plex Bio Plex Pro Hu Cytokine Th17 15 Plex Bio Plex Pro Hu Cytokine Th17 IL 17A F Bio Plex Pro Hu Cytokine Th1 Th2 9 Plex Bio Plex Pro Hu Isotyping 6 Plex Bio Plex Pro Hu Isotyping IgE Bio Plex Pro Hu Isotyping IgG Total Bio Plex Pro Hu Diabetes 10 Plex Bio Plex Pro Hu Cancer Biomarker Panel 1 16 Plex Bio Plex Pro Hu Cancer Biomarker Panel 2 18 Plex Bio Plex Pro Hu Adipsin Region 35 44 Bio Plex Manager MP Software Creating Assay Panels Customizing an Existing Assay Panel Bio Plex Manager MP provides a list of all the assay panels it manufactures along with related analytes In many instances you will take one of these panels and use it as is If your experiment uses only a subset of the analytes Bio Rad recommends you edit the assay panel and delete any analytes you are not interested in and save the panel with a new name This customized panel makes it easier to run repeated exp
12. before Bio Plex Manager MP responds to another command Resuming a Run You can interrupt a run and make changes to your protocol including changing the analytes you are interested in or correcting the format of your plate You can run the protocol again and start where you left off or start from the beginning and read the entire plate To resume a run i 2 From the Create Run Protocols view click Start In the Run Settings dialog box either accept the default or enter a different name in the Result Name field By default the Result Name you entered for the first run is appended with a number surrounded by square brackets For example if the result name you entered is Test when you return to the Run Settings dialog box to run the protocol again the result name is Test 1 With each subsequent run the number is incremented In the Well Selection diagram specify the wells you want read Bio Plex Manager MP reads only selected formatted wells A black border indicates the selected wells You can m Readonly the wells that were not read on the last run This is the default as shown in the figure that follows In this example when the run resumes it will start with well A2 m Click Select All to read all the wells m Click on a subset of the formatted wells to read only those wells Tip Use Shift Click to select more than one well User Guide 35 3 Running Protocols i H Alcohol USES Result Name Hu C
13. 45 Importing an Assay Panel 0 0 eee 46 Creating a New Assay Panel 00 00s 47 Editing an Assay Panel 2 2000 e eee ee 47 Customizing Your Assay Panel List llle 48 Sharing Customized Assay PanelS 0 000 c eee eee 48 Restoring an Assay Panel 0 0 0c eres 49 About Standard Lots sce isd scene E Rav RARE LERREERPERVERCETISRERES 49 Creating Standard LotS 0 cece eee 50 Creating New Standard Lots 00 02 eee eee 50 Defining a Standard Lot with Custom Concentrations 52 Creating a Standard Lot from an Existing Lot llli 52 Importing a Standard Lot se seccu eee eee 53 Editing Standard Lots secs sse ssa ee a ee ee Sie bd ee 53 Deleting Standard Lots esdire cece eee 54 Exporting Standard Lots osese 0 ee ee 54 iv Bio Plex Manager MP Software Table of Contents Chapter 5 Analyzing Results eeeees esses 55 Chapter 6 Maintaining the MAGPIX System 57 Recommended Routine 2000 elles 58 Daily Maintenance Routines lisse re 59 Daily Start Up Routine 1 2 6 eee 59 Enhanced Maintenance s rsss ue iR r Sunni ee ee eee eee bee eee See 60 Shut Down Routine xs RR Shee eee eke RTA Re ee SES 60 Running a Routine 2 rr 60 Monitoring the Routine 0 6 eee 62 Setting Up the Reagent Block 0 00 c eee eee 64 Calibration and Verification Kits
14. 48 Assay panel lists customizing 48 Assay panels combining existing 45 Assay panels creating 44 Assay panels creating new 47 Assay panels customizing 45 Assay panels editing 47 Assay panels exporting 48 Assay panels importing 46 Assay panels naming 47 Assay panels restoring Bio Rad 49 Assays exposure to light 26 Autofill across definition 17 Autofill down definition 17 Autofilling wells 17 Auxiliary plate 27 Bead map 33 Bead map white areas of 34 Bio Plex Manager 6 1 running protocols in 28 Bio Plex Manager 6 x region events in 55 Bio Plex Manager MP differences between Bio Plex Manager 6 x and 55 Bio Plex Manager MP region events in 55 Blank wells 16 C Calibration and Verification routine 75 Calibration kit description of contents 66 Calibration kit importing values 67 Calibration kit lot numbers of 66 Calibration routine failure 70 Calibration checking status of 68 Clear Bubbles routine 77 Control wells 16 Custom concentrations specifying 52 D Daily Start Up routine 78 Daily Start Up routine recommended routine 59 Dilution Factor parameter 22 E Editing protocols 23 Enhanced Maintenance routine 79 Exporting data from Analyze Export view 41 Exporting data from Create Run Protocols view 40 Exporting data multiple times 42 Exporting data to Bio Plex Manager 6 1 39 F Filter plate 27 User Guide 111 Index Flat Bottom plate 27 Fluidics Preparation routine 8
15. 7 When you are done making your changes click OK Importing a Standard Lot You can import an xstds file that contains one or more standard lots If the imported standard lot has the same name as an existing lot Copy is appended to the name to distinguish the imported standard lot from the existing one for example Standard Lot Copy To import a standard lot from a file 1 From the protocol dialog box click Standards Info 2 Click Manage Standard Lots 3 In the Manage Standard Lots dialog box click Import 4 Navigate to where the standard lot file is select the file and click Open Note The file must have an xstds extension A dialog box appears informing you that the standard lot is successfully imported and the imported standard lot appears in the list Editing Standard Lots You can make changes to an existing standard lot To edit an existing standard lot 1 From the protocol dialog box click Standards Info 2 Click Manage Standard Lots User Guide 53 4 Managing Assay Panels and Standard Lots 3 In the Manage Standard Lots dialog box select a standard lot from the list and click Edit 4 Make any changes to the name of the standard lot the expiration date the method used to dilute the standards and the starting concentrations of the analytes When you are done making changes click OK Deleting Standard Lots You can delete standard lots you no longer need from the Manage Standard Lots
16. 83 7 Maintenance Routines Unclog Routine 84 Description of Routine This procedure performs a series of fluidics operations to remove possible obstructions from the fluidics lines When to Run this Routine If you suspect there is an obstruction in the MAGPIX system run the Unclog routine Estimated Run Time 2 minutes To Run the Unclog Routine 1 2 Navigate to the Maintenance view In the Select Routine section select Unclog from the Additional Routines dropdown list Add 5 ml distilled or deionized water and 5 ml 0 1N NaOH to the appropriate reservoirs in the reagent block Insert the plate in the microplate platform and click Start Bio Plex Manager MP Software Verification Routine Verification Routine Description of Routine The Verification routine ensures that the calibration settings are valid and ensures that well to well cross talk does not occur When to Run this Routine Run the Verification routine when its status in the Maintenance view is not up to date Bio Plex Manager MP adds verification to the Daily Start Up routine in accordance with the manufacturer s recommendation Therefore if you run the Daily Start Up routine daily you will be running the Verification routine as recommended Estimated Run Time 4 minutes To Run the Verification Routine Before you run the Verification routine you must import the verification kit information For more information see Calibrati
17. Daily Start Up may include the Calibration and Verification Verification and Wake From Storage routines When to Run this Routine Run Daily Start Up each day you use the instrument before you run any protocols You do not need to keep track of the calibration and verification status if you run this routine at the start of each day Estimated Run Time 4 12 minutes To Run the Daily Start Up Routine 1 2 Navigate to the Maintenance view In the Select Routine section select Daily Start Up Fill the reservoirs and the well strip with the solutions indicated in the Reagent Block diagram Click Start Bio Plex Manager MP Software Enhanced Maintenance Routine Enhanced Maintenance Routine Description of Routine The Enhanced Maintenance routine clears any bubbles from the system and clears any clogs from the probe and fluidics When to Run this Routine This routine is recommended when a low bead count occurs during a protocol run or when calibration or verification fails Estimated Run Time 14 minutes Before Running the Routine Before you run the Enhanced Maintenance Routine Bio Rad recommends that you check the following 1 Check that the correct calibration and control lots are being used 2 Clean the sample probe 3 Check that the waste container is not full 4 Runthe Agjust Probe Height procedure To Run the Enhanced Maintenance Routine 1 Navigate to the Maintenance view 2 Inthe Select
18. Plex Manager MP Software Maintenance Routines The maintenance routines keep the MAGPIX instrument in good working order and operating according to the manufacturer s specifications Bio Rad recommends that you run the recommended routine at the start of each day to minimize having to keep track of running the correct routines at the right time In addition to running the recommended routine you can run any of the maintenance routines as necessary Calibration and Verification Routine Description of Routine Calibration normalizes the operation of the MAGPIX analyzer when it acquires data Once calibrated the values remain until you recalibrate Verification verifies the operation of the MAGPIX analyzer When to Run this Routine Bio Plex Manager MP software adds calibration and verification to the Daily Start Up routine once a week in accordance with the manufacturer s recommendation Therefore if you run the Daily Start Up routine daily you will be running the Calibration and Verification routine as recommended In addition recalibrate the system if the any of the following is true m The delta calibration temperature exceeds 5 C m The instrument has been moved m The instrument undergoes hardware maintenance for example a part replacement User Guide 75 7 76 Maintenance Routines Estimated Run Time 10 minutes To Run the Calibration and Verification Routine Before you run the Calibration and Verifi
19. Therefore RESULT 1 is not the same as result 1 Alcohol 01N NaOH Result Name Plate ID Plate Type Flat Bottom Plate Pre Run Routine None Post Run Routine Wash Between Plates Set as Default Stop runs with low bead count Run Protocol Cancel Plate heater off Optional Enter the Plate ID You can specify anything here that will help you distinguish your experiments and results Specify the type of plate in the Plate Type List If you do not see your plate listed here see Using the Plate Heater on page 28 to determine the equivalent match for your plate type Optional In the Pre Run Routine list select any routines you want executed before the protocol run Note A Rinse routine is always run before a plate is read This routine is run in addition to any pre run routine specified here User Guide 29 3 30 Running Protocols If you select a pre run routine refer to the Reagent Block diagram and fill the appropriate reservoirs with the specified fluids Optional In the Post Run Routine list select any routines you want executed after the protocol run Note Bio Rad recommends you run the Wash Between Plates routine after each protocol run to prevent traces of sample or other debris from collecting inside the Bio Plex suspension array system If you select a post run routine refer to the Reagent Block diagram and fill the appropriate reservoir
20. dialog box Once deleted you will not be able to select the lot to use with your protocol To delete a standard lot From the Manage Standard Lots dialog box select the lots you no longer need and click Delete Exporting Standard Lots 54 You can export standard lots to a file which can then be transferred to another computer and imported into another copy of Bio Plex Manager MP Note You can export a single standard lot or multiple standard lots at one time In both instances the lots are exported to a single file When the file is imported all the standard lots are imported You cannot selectively import standard lots from a file To export a standard lot to a file 1 From the protocol dialog box click Standards Info 2 Click Manage Standard Lots 3 In the Manage Standard Lots dialog box select a standard lot from the list and click Export In the Export Standard Lots dialog box enter the name of the file and click Save Bio Plex Manager MP Software 5 Analyzing Results Bio Plex Manager MP is used to create and run your protocols Once the plate has been read you can review the fluorescence intensities of the analytes you selected and use the bead map to confirm that the bead sets are correctly selected and identified Further analysis of your results is done in Bio Plex Manager 6 x The Bio Plex Manager MP results are exported to Bio Plex Manager 6 x For more information on exporting your results see Exportin
21. of 64 Reagent block setting up 64 Recommended routine 58 Recommended routine running 25 Region Selection Severe Clog error 107 Replicate groups autofilling 18 Replicate groups defining 18 Result name default 40 Run results table description 38 Run Settings dialog box 29 S Saving protocols 11 Selecting analytes 13 Set Replicate Size 19 Shut Down routine 83 Shut Down checking status of 68 Software activation offline 91 Software activation online 89 Software activation Product activation code 89 Software deactivation 97 Software deactivation offline 99 Software deactivation online 97 Standard curve 20 Standard lots creating 50 Standard lots creating from existing lots 52 Standard lots definition 49 Standard lots deleting 54 Standard lots editing 53 Standard lots exporting 54 Standard lots importing 53 Standard lots naming convention for 22 Standard lots selecting 21 Standard wells 16 Standards Info pane disabled 21 Standards definition 20 Stop beads with low bead count parameter 30 T Troubleshooting MAGPIX 107 Troubleshooting Resolving Unstable Instrument Problem 109 U Unclog routine 84 Undefined wells 17 Unknown wells 17 V Verification kit description of contents 66 Verification kit importing values 67 Verification kit lot numbers of 66 Verification routine 85 Verification routine failure 70 Verification checking status of 68 Ww Wake from Storage routin
22. selection of analytes in the protocol dialog box User Guide 23 2 Creating Protocols 24 Bio Plex Manager MP Software 3 Running Protocols Once your protocol is created you are ready to run the protocol The result is displayed in the raw data table and bead map and it can be exported to Bio Plex Manager 6 x software for analysis You can interrupt a run at any time make any necessary changes to the protocol and resume the run with no loss of data Bio Plex Manager MP software provides graphical clues and alerts informing you when it detects problems with your run Running the Recommended Routine Run the routine in the Recommended Routine section of the Maintenance view each day you use the MAGPIX instrument This keeps the instrument free of bubbles and ensures that it is operating according to specifications To run the recommended routine 1 Navigate to the Maintenance view 2 Inthe Recommended Routine section click Select to select the routine 3 Fill the reservoirs and the well strip with the solutions indicated in the Reagent Block 4 Click Start 5 When the routine is completed a dialog box displays indicating that the routine is successfully completed You can monitor the progress of the routine for more information see Monitoring the Routine on page 62 User Guide 25 3 Running Protocols Plate Handling Guidelines 26 Before starting the run note the following plate handling guid
23. set you cannot run your protocol To use the plate heater 1 Inthe dashboard select the Plate heater off checkbox to turn the heater on The Turning on message appears When the heater is turned on Set Temp is displayed 2 Use the left and right pointing triangles to set the plate temperature The temperature can be set from 35 60 C in 0 5 increments When the temperature of the plate falls within range of the set temperature the thermometer turns green 3 When you are done select Set Temp to turn the heater off Running the Protocol 28 After you create your protocol you are ready to run it Refer to Chapter 2 Creating Protocols for more information on creating protocols Note You can run only protocols created in Bio Plex Manager MP You cannot run protocols created in other versions of Bio Plex Manager such as Bio Plex Manager 6 1 The data from each run are stored as a result in the Bio Plex Manager MP database Result names must be unique You can retrieve the data by exporting the result to Bio Plex Manager 6 x Bio Plex Manager MP Software Running the Protocol To run your protocol iz In the Create Run Protocols view click Start The microplate platform automatically ejects In the Run Settings dialog box enter the name of the result in the Result Name box The result name is the name that the data are stored under in the database This name is case sensitive and must be unique
24. 0 Fluidics checking status of 68 Instrument not connected error message 107 L License activation offline 91 License activation online 89 License deactivation offline 99 License deactivation online 97 Lot numbers 66 Low bead count 36 Low Bead Count error 108 M Maintenance of instrument checking status of 68 Maintenance routine failed 69 Maintenance routines beginning of the day 59 Maintenance routines daily 59 Maintenance routines end of the day 59 Maintenance routines interrupting 71 Maintenance routines monitoring 62 Maintenance routines running 60 Maintenance view 57 Most Concentrated Standard parameter 22 N New From 23 Nonuse preparing instrument for 71 P PCR plate 27 Plate formatting 14 Plate heater temperature range of 28 Plate heater using 28 Plate types 27 Plate types calculating probe height 27 112 Bio Plex Manager MP Software Plates formatting 14 Plates guidelines for handling 26 Post run routine 30 Prepare for Storage routine 81 Pre run routine 29 Prime routine 82 Probe height adjusting 72 Protocol dialog box 10 Protocol dialog navigating to 10 Protocol run interrupting 34 Protocol run resuming 35 Protocol setup overview of 9 Protocol definition of 9 Protocols editing 23 Protocols reusing 23 Protocols running 28 Protocols running in Bio Plex Manager 6 1 28 Protocols saving 11 R Raw data table description 32 Reagent block description
25. 2 04 5023535 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2015 02 04 7 5022130 Serial Dilution Bio Plex Pro Hu Group I 27 Plex 2014 10 29 5026346 Serial Dilution Bio Plex Pro Hu Group II 21 Plex 2015 10 10 T 5030291 Serial Dilution Bio Plex Pro Mo Group I 23 Plex 2016 07 16 5022433 Serial Dilution Bio Plex Pro Mo Group I 23 Plex 2015 12 07 5022128 Serial Dilution Bio Plex Pro Mo Group I 23 Plex 2014 09 20 5023102 Serial Dilution Bio Plex Pro Mo Group II 9 Plex 2015 02 21 5031065 Serial Dilution Bio Plex Pro Mo Group III 11 Plex 2016 09 17 5020658 Serial Dilution Bio Plex Pro Mo Diabetes 9 Plex 2014 03 12 5030980 Serial Dilution Bio Plex Pro Ra Cytokine Diabetes 24 Plex 2016 07 18 5028694 Serial Dilution Bio Plex Pro TGF Beta 3 Plex 2015 12 29 Select All Unselect All Creating Standard Lots 50 You can start with a blank standard lot and enter the required information for the standard lot definition However you are more likely to take an existing standard lot and modify it You can share standard lot definitions using the export and import features Creating New Standard Lots To create a new standard lot 1 From the protocol dialog box click Standards Info 2 Click Manage Standard Lots 3 In the Manage Standard Lots dialog box click New 4 In the New Standard Lot dialog box enter a name f
26. 320 36 580 09 14502 3626 10 Hu IL 10 56 2513344 6283 36 157084 39271 9818 11 Hu IL 12 p70 75 3316240 8290 60 207265 51816 12954 12 Hu IL 13 51 34067 84 851696 2129 24 53231 13308 4 m ok cancet_ Note Use Most Concentrated Standard to specify whether the first well or the last well contains the highest concentration of the analyte Bio Plex Manager MP Software Reusing a Protocol Reusing a Protocol You can use a saved protocol as a template for your experiment You can make changes to a copy of the saved protocol for example you might change the number of unknown samples To reuse a saved protocol iz 2 Click New From on the toolbar to open the Select Protocol dialog box Select the protocol you want to use and click OK In the protocol dialog box make any changes to the selected analytes the plate formatting and the standards information When you are done making changes click OK Editing a Protocol The Edit command opens the protocol dialog box for the protocol currently displayed in the Create Run Protocols view You might want to edit a protocol in the following situations You make changes to a saved protocol to match the changes in your experiment The most common change is to the number of unknown samples in the experiment You run a protocol and discover that there is a low bead count indicating that the wrong analytes might have been selected You can change the
27. Akt m IA S VEGFR 2 NN 3 s R 2 W e JN 2p70 NF2x8p65 a 2i b eT C m Ju iy Nuance b S N N NS S Bio Plex Manager MP Software User Guide Version 1 0 Bio Plex Manager MP Software User Guide Version 1 0 10032257 Rev A Bio Rad Technical Support Department The Bio Rad Technical Support department in the U S is open Monday through Friday 5 00 AM to 5 00 PM Pacific Time Worldwide technical support is available on the Web at www consult bio rad com Phone 1 800 424 6723 option 2 Fax 1 510 741 5802 Email LSG TechServ US Bio Rad com U S LSG TechServ IntI Bio Rad com International Web www consult bio rad com Notice No part of this publication may be reproduced or transmitted in any form or by any means electronic or mechanical including photocopy recording or any information storage or retrieval system without permission in writing from Bio Rad Bio Rad reserves the right to modify its products and services at any time This user guide is subject to change without notice Although prepared to ensure accuracy Bio Rad assumes no liability for errors or omissions or for any damage resulting from the application or use of this information Luminex MAGPIX and xPONENT are trademarks of Luminex Corporation Windows is a trademark of Microsoft Corporation MaxiSorp Nunc and PolySorp are trademarks of Thermo Fisher Scientific By opening the packaging containing this unit of Luminex ins
28. M eP New Assay Panel g Manage Assay Panels Assay Panel MAGPIX Quick Start Region Analyte 12 Region_12 E 13 Region 13 7 14 Region 14 15 Region 15 Region 18 Region 19 Region 20 Region 21 Region 22 Region 25 Region 26 Region 27 Region 28 Region 29 Region 30 Region 33 Region 34 Select All OK 10 Bio Plex Manager MP Software Creating a Protocol Creating a Protocol The following are the steps to create a new protocol To create a new protocol i 2 3 4 5 6 2 10 11 12 Click Create Run Protocols in the navigation bar Click New to open the New Protocol dialog box Click the Assay Panel dropdown list and select an assay panel Select the analytes for your experiment Click Format Plate Format the wells to use in the experiment For more information on formatting wells see Formatting Plates on page 14 Click Standards Info From the Standard Lot dropdown list select the standard lot you want to use with this protocol Note If no standard lots appear in the list you must first create a standard lot for your assay panel For more information see Creating New Standard Lots on page 50 Select the dilution factor from the Dilution Factor dropdown list For more information see Selecting a Standard Lot on page 21 Click OK Optional Click Save As to save the protocol Note Save the protocol if you want to r
29. MAGPIX Bio Plex Data Pro Bio Plex Manager MP Software 2 Creating Protocols About Protocols A protocol contains the parameters of a Bio Plex Manager MP software run It includes information about the analytes included in the run the plate wells to be read the concentrations of standards and instrument settings These parameters are saved in the result along with the data from the reading You can save a protocol and reuse it or modify it for another reading Each time you run the protocol a new result is created and stored in the database You set up your protocol from the protocol dialog box There are three phases to setting up your protocol that correspond to the three panes in the protocol dialog box m Select Analytes select an assay panel and the analytes for your experiment m Format Plate specify which wells are to be read and the sample type of each well x Standards Info specify the concentrations of your standards User Guide 9 2 Creating Protocols Navigating to the Protocol Dialog Box Protocols are created from the protocol dialog box There are a number of ways you can get to the protocol dialog box To navigate to the protocol dialog box 1 Click Create Run Protocols in the navigation bar 2 Doone ofthe following m Click New m Click New From and select a protocol from the Select Protocol dialog box With an open protocol in the Create Run Protocols view click Edit G neve N
30. MP License Manager 44 Who Bio Rad Technical Support Email LSG_Software_Act bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Bio Plex Manager MP Is Activated Bio Plex Manager MP is activated Do you want to deactivate C Do not deactivate Deactivate Bio Plex Manager MP Online I have an Internet connection C Deactivate Bio Plex Manager MP through Technical Support I do not have an Internet connection Deactivation will remove the license on this computer This allows you to move your license to another computer or to upgrade the license s User Guide 97 A License Activation 4 Enter your activation code and click Deactivate Note The Activation Code field will be populated with the activation code If the field is empty you can find the activation code in the CD folder W Bio Plex Manager MP License Mar Deactivate Bio Plex Manager MP ox Enter your activation code and click Deactivate e Activation Code 295700 000099 178102 Installation ID 3399 8442 6114 7692 0170 6186 5832 8300 Bio Rad Technical Support Email LSG Software ActGbio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Deactivate e The Deactivation Successful window appears confirming the software has been deactivated I Bio Plex Manager MP License Deactivation Succes
31. Plates Routine Description of Routine The Wash Between Plates routine performs a series of fluidics operations to prevent traces of sample or other debris from collecting inside the Bio Plex suspension array system When to Run this Routine Bio Rad recommends that you wash the fluidics lines after each plate reading Note In the Run Settings dialog box the default is to run the Wash Between Plates routine after the reading Estimated Run Time 6 minutes To Run the Wash Between Plates Routine 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Wash Between Plates from the Additional Routines dropdown list 3 Add 5 ml distilled or deionized water 5 ml 70 isopropanol and 5 ml 0 1N NaOH to the appropriate reservoirs in the reagent block 4 Click Start User Guide 87 7 Maintenance Routines 88 Bio Plex Manager MP Software A License Activation To have access to all of the features of Bio Plex Manager MP software you must activate the product with a valid product license You will need a separate license for each computer on which you install Bio Plex Manager MP Note If you purchased a new MAGPIX instrument the computer included with the instrument comes with the software already activated Therefore you can skip this step Activating the Bio Plex Manager MP License You can activate the product either online if you have access to the Internet or through Technical Suppo
32. Routine section select Enhanced Maintenance 3 Add 5 ml distilled or deionized water 5 ml 70 isopropanol and 5 ml 0 1N NaOH to the appropriate reservoirs in the reagent block 4 Click Start User Guide 79 7 Maintenance Routines Fluidics Preparation Routine Description of Routine The Fluidics Preparation routine prepares the fluidics system for daily use When to Run this Routine Run the Fluidics Preparation routine when you replace an empty drive fluid container or if the drive fluid line is not aspirating drive fluid because the line has become dislodged Estimated Run Time 2 minutes To Run the Fluidics Preparation Routine 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Fluidics Preparation from the Additional Routines dropdown list 3 Add 5 ml 70 isopropanol to the appropriate reservoir in the reagent block 4 Click Start 80 Bio Plex Manager MP Software Prepare for Storage Routine Prepare for Storage Routine Description of Routine The Prepare for Storage routine clears all fluids from the instrument When to Run this Routine Run the Prepare for Storage routine if you will not be using the instrument for more than two weeks or before you ship the instrument to Bio Rad Estimated Run Time 6 minutes To Run the Prepare for Storage Routine 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Prepare for Storage from the Additiona
33. Up m Enhanced Maintenance Continue to run the recommended routine until maintenance is up to date and None is displayed in the Recommended Routine section At the End of the Day At the end of each day run the Shut Down routine before you shut down the instrument Daily Start Up Routine The Daily Start Up routine runs different procedures depending on the state of the instrument Bio Plex Manager MP detects whether the instrument needs to be verified calibrated or both and it runs the appropriate commands as part of Daily Start Up This routine can take 4 12 minutes Note When you turn on the MAGPIX instrument Daily Start Up is generally the routine that is recommended However there may be times when Enhanced Maintenance is recommended for example if calibration and verification previously failed Run whatever routines are recommended until maintenance is up to date and no routines appear in the Recommended Routine section Tip If verification calibration or both routines fail after successive attempts contact Bio Rad Technical Support for assistance User Guide 59 6 Maintaining the MAGPIX System Enhanced Maintenance The Enhanced Maintenance routine will be recommended for example if calibration or verification failed on the previous day Once this routine is successfully completed it is followed with a recommendation to run the Daily Start Up routine Shut Down Routine If you do not run the Shut Down
34. ancer Biomarker Panel 1 1 Plate ID Plate Type Flat Bottom Plate Pre Run Routine None Well Selection Post Run Routine Wash Between Plates NC ess M aie Set as Default 4 eo eo e Q o E 7 Stop runs with low bead count o000EBH o0000EH o0BHEBNNH CORRE CORRES C9ORERER CORRES Selecta Clearan Buo Protocol uma Cancel Plate heater off Encountering and Resolving Low Bead Counts Bio Plex Manager MP notifies you when a low bead count is detected m The well with the low bead count displays a warning symbol A warning symbol is displayed for the region in the Raw Data table if a low bead count occurred for that particular analyte You can specify that Bio Plex Manager MP stop the run if it encounters three or more consecutive wells with low bead count of less than 20 In the Run Settings dialog box select Stop runs with low bead count If a low bead count is encountered the run is stopped and a dialog box appears with a suggested solution In addition a warning symbol is displayed in the affected wells in the plate template and for the applicable analytes in the raw data table 36 Bio Plex Manager MP Software Encountering and Resolving Low Bead Counts Q Bio Plex Manager MP m Af New Gl NewFom eti F saveas EA Export Results A tjet D gt start Maintenance Protocol New Protocol Results MAGPIX Quick Start 1 R
35. arker 16 Plex 6 6 20 2013 2 34PM Bio Plex Pro Hu Group I Cytokine 27 Plex 12 Hu Cancer Biomarker 16 Plex 5 6 20 2013 2 27 PM Bio Plex Pro Hu Cancer Biomarker Panel 1 16 Plex 16 Hu Cancer Biomarker 16 Plex 4 6 20 2013 2 24 PM Bio Plex Pro Hu Cancer Biomarker Panel 116 Plex 16 Hu Cancer Biomarker 16 Plex 3 6 20 2013 2 23 PM Bio Plex Pro Hu Cancer Biomarker Panel 1 16 Plex 16 The following table describes the information in the run results table Column Name Description Name Name of the result set Acquisition Time Time stamp of when the protocol was run Assay Panel Assay panel used in therun EE Analytes MEM Number of analytes selected in the protocol f definition Description User defined description Tip Click the column header of any column to sort the table by that column 38 Bio Plex Manager MP Software Exporting Data to Bio Plex Manager 6 x Exporting Data to Bio Plex Manager 6 x Before data can be analyzed in Bio Plex Manager 6 x the Bio Plex Manager MP run result must first be saved to a file This file can then be exported to Bio Plex Manager 6 x You can export your results in either of the following ways Export your results immediately following a protocol run from the Create Run Protocols view For more information see Exporting Data from the Create Run Protocols View on page 40 Export your results at a later time from the Analyze Export view For more informati
36. at is currently displayed and it does not load the new file Therefore you will continue to see the old result Tip Give your result files unique names to avoid running into this problem By default a time stamp is appended to the end of the name of the result file making it unique 42 Bio Plex Manager MP Software 4 Managing Assay Panels and Standard Lots In Bio Plex Manager MP software you can select any of the Bio Rad assay panels for use in your experiments These panels can be customized for your experiments and reused or shared with colleagues who are using Bio Plex Manager MP on other computers or in other locations Bio Plex Manager MP makes it easy to manage your standards through predefined standard lots Standard lots are panels of assays with starting concentrations for Bio Rad kits You can use the standard lot as provided or customize it to your experiment Standard lots can be shared with colleagues User Guide 43 4 Managing Assay Panels and Standard Lots Creating Assay Panels You can create assay panels in the following ways from the Manage Assay Panels dialog box Customize an existing assay panel Edit button Create an assay panel by combining one or more existing panels New From button Enter your analytes into a new assay panel New or New From buttons Import an assay panel Import button Senes v Assay Panel MagPix Quick Start Bio Plex Pro Hu Angiogenesis
37. ated on the computer select the file and click Open The lot number of the calibration kit or the verification kit appears in the Reagent Block section of the Maintenance view Use this number to verify that you are using the correct calibration or verification values with your reagents User Guide 67 6 Maintaining the MAGPIX System Checking the Status of the Instrument Maintenance The Status section of the Maintenance view displays the status of the following routines m Calibration m Verification m Fluidics m Shut Down Ls es Calibration Passed 4 26 2013 2410 PM v Verification Passed 4 26 2013 2 41 10 PM w Fluidics Passed 4 26 2013 2 41 10 PM Shut Down 4 25 2013 11 50 32 AM Q Calibration Kits B27801 11 20 2013 v Sa The Status section displays information about the last time the routine was run It shows whether the routine was successfully completed or not Passed or Failed and atime stamp 68 Bio Plex Manager MP Software Responding to a Failed Routine Status also shows the current status of the routine with the following symbols Symbol Description m This routine is current and up to date io This routine is not current or the routine failed The Shut Down routine is in one of two states m It has either never been run since the software was installed m t has not been run in the current day This is a reminder to run the Shut Down routine at the e
38. been defined for your analytes To select a standard lot for your protocol run 1 From the protocol dialog box click Standards Info The table displays the analytes you selected on the Select Analytes pane Each analyte appears as a row in the table There is a column for each standard well you defined on the Format Plate pane In this example eight standard wells were selected on the Format Plate pane and therefore there are eight columns S1 S2 and so on New Protocol An i oe 96 o Select Analytes Format Plate b amp Af New Standard Lot jg Manage Standard Lots Standard Lot lt None gt Dilution Factor 4 x Most Concentrated Standard Analyte Si S2 S3 S4 S5 S6 S7 S8 Hu IL 1b 39 Hu IL Lra 25 Hu IL 2 38 Hu IL 4 52 Hu IL 5 33 Hu IL 6 19 Hu IL 7 74 Hu IL 8 54 Hu IL 9 77 10 Hu IL 10 56 11 Hu IL 12 p70 75 12 Hu IL 13 51 13 Hu IL 15 73 o0 OQ u RwiWN o Cancel Note The Standards Info pane is disabled until you select your analytes and format your standard wells 2 From the Standard Lot dropdown list select the standard lot you want to use with this protocol User Guide 21 2 22 Creating Protocols Only the standard lots that contain the selected analytes appear in the list If the list is empty then there are no defined standard lots that include the analytes you selected and
39. bottom Bio Plex Pro flat bottom plate black 3 94 plate plate comes with Bio Plex Pro assays catalog 171 025001 Filter plate Millipore multiscreen plate for example 3 05 MSBVN1210 PCR plate Bio Rad low profile unskirted PCR plate 2 79 for example MLL 9601 Auxiliary plate Nunc PolySorp for example 475094 3 30 Nunc MaxiSorp for example 445105 This is the distance between the platform and the inside bottom of the plate well For other plate types check the manufacturer s specifications to determine the distance from the surface of the MAGPIX platform to the bottom of the well The probe backs off 1 mm after it makes contact with the probe height adjustment plate Therefore you need to add 1 mm to the distance in the table to get the correct probe height For example if the specification for your plate type is 3 4 mm you can use the auxiliary plate 3 3 mm because the actual setting after running the probe height adjustment is 4 3 mm This gives an allowance of 0 9 mm above the plate s well bottom for sample aspiration User Guide 27 3 Running Protocols Using the Plate Heater For some experiments for example nucleic acid testing you may need to heat and maintain the temperature of the plate with the MAGPIX plate heater You can turn the heater on from any view in Bio Plex Manager MP and set the temperature of the plate from 35 60 C in 0 5 increments Note While the plate temperature is being
40. c backups The default is manual backups Database backups are managed with the Archive Utility Unless you specify otherwise you will get the following reminder to back up your database Please initiate a Scheduled Archive or you will eventually run out of disk space and not be able to run Batch in xPONENT Click Yes to open the Archive tool You can also run the utility by navigating to the application To open the Archive Utility 1 Navigate to the following location All Programs Luminex Common 2 Click xPONENT Archive to start the utility 6o Instructions Setup a schede for Automatic Reminders ar Archives Select Manus Archive fo iedvhaly archive Wes Backup the enire system by selecting Backup System and restore system from a previous backup by selecting Restore System Schedule Overview Archive Events ERKENNEN EN 08 00 AM SS Ea EO TEES Daily Reminder Only To Be Archived Note If he first twe nol checked all batches wil be archived c 4 Days Batches han 30 Days Archive Folder C Users Public Documents Archive Edit System CurentflesinxPONENT Batches 117 Protocols o Kis o Lots o LIS Records o Current Local Disk Space Current Database Space Current Local Archive Space 55 o 55 Used Used Used Version 1 0 490 0 System Backup System Restore Manual Archive Close Bio Plex Manager MP Software Backing up the Bio Plex Manager MP Database You can specify th
41. cal Support I do not have an Internet connection Bio Rad Technical Support Email Deactivation will remove the license on this computer This allows you to move your LSG_Software_Act bio rad com license to another computer or to upgrade the license Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Exit a User Guide 99 A License Activation 4 Inthe Export Deactivation Certificate window click Save Wii Bio Plex Manager MP License Manager Export Deactivation Certificate Enter your activation code and click Save to g generate your deactivation certificate i X Activation Code 295700 000099 178102 Installation ID 3399 8442 6114 7692 0170 4806 2940 6669 Bio Rad Technical Support Email LSG Software Act amp bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST A dialog box appears asking you to confirm the deactivation 5 Click Yes 6 In the File browser navigate to where you want to save the deactivation certificate 7 Enter the name of the file and click Save 100 Bio Plex Manager MP Software Deactivating the License through Technical Support The File Successfully Saved window appears with instructions on how to send the deactivation certificate file to Technical Support I Bio Plex Manager MP License Manager a File Successfully Saved N g
42. calibration kit and verification kit currently selected It also displays the lot numbers of the reagents that belong to the calibration and verification kits Use this information to ensure that you are using the correct reagents Important Do not mix reagents from different verification kits All of the reagents must belong to the same lot If you select a different kit from the Select Kit section the lot information in the Reagent Block section automatically updates with the new kit information User Guide 65 6 Maintaining the MAGPIX System To set up the Reagent Block 1 Fill any colored reservoir with the indicated liquid 2 Foreach colored well in the well strip locate the appropriate calibration or verification kit 3 Vortex each bottle for at least 10 sec 4 Fill the well with 6 drops of the solution from the bottle with the matching cap color Calibration and Verification Kits 66 Calibration and verification kits are sold separately Each calibration kit comes with the following m 1bottle of MAGPIX calibrator m 1 calibration kit CD m 1 pack of well strips Each verification kit comes with the following m 1bottle of MAGPIX verifier m 1 bottle of MAGPIX fluidics 1 m 1 bottle of MAGPIX fluidics 2 m 1 verification kit CD m 1 pack of well strips About Kit Lot Numbers The lot number on the box identifies the kit Use this lot number to coordinate the reagents with the calibration or verificatio
43. cation routine you must import the calibration and verification kit information For more information see Calibration and Verification Kits on page 66 1 2 D Ee o9 Navigate to the Maintenance view In the Select Routine section select Calibration and Verification from the Additional Routines dropdown list Add 5 ml 7096 isopropanol to the appropriate reservoir in the reagent block Vortex CAL VER Fluidics1 and Fluidics2 each for 10 sec Add 6 drops each of CAL VER Fluidics1 and Fluidics2 to the indicated wells Click Start Bio Plex Manager MP Software Clear Bubbles Routine Clear Bubbles Routine Description of Routine The Clear Bubbles routine performs a series of fluidics operations to force out air bubbles that may be trapped in the cuvette When to Run this Routine If you suspect there is air in the MAGPIX system run the Clear Bubbles routine Estimated Run Time 3 minutes To Run the Clear Bubbles Routine 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Clear Bubbles from the Additional Routines dropdown list 3 Add 5 ml distilled or deionized water and 5 ml 70 isopropanol to the appropriate reservoirs in the reagent block 4 Click Start User Guide 77 7 Maintenance Routines Daily Start Up Routine 78 Description of Routine Daily Start Up prepares your instrument for daily use It runs different routines depending on the state of the instrument
44. column can be displayed or hidden using a toggle command Total bead events recorded within the 50 defined regions This column can be displayed or hidden using a toggle command When bead region counts are displayed there are two numbers The first number is the fluorescence intensity for that analyte The second number in parentheses is the number of bead events for that region If there are low bead counts for any of the selected analytes the following symbols appear There are fewer than the recommended 50 beads for one or more analytes ANY There are fewer than 20 beads for one or more analytes The bead color map is a density dot plot of the events in a reading for a selected well Different colored dots in the map represent different numbers of events at those data points There are 50 available regions in the bead map User Guide 33 3 Running Protocols The x axis is the Classification 1 channel and the y axis is the Classification 2 channel These channels measure the embedded fluorochromes in each bead which are used to identify the bead set and corresponding analyte The resulting data point clusters in the map represent the different bead sets in the assay and their associated analytes Tip Use Maximize View to expand the bead map to fill the entire window Once maximized you can use the Zoom tool to focus further on a particular area in the bead map Note Each bead set generates a cluster of data poi
45. different name for the file Click Save A message appears informing you that the result file has been exported If Bio Plex Manager 6 x is installed on the same computer where you are running Bio Plex Manager MP you are also asked if you want to open the result in Bio Plex Manager 6 x In the Export Results dialog box click Yes Bio Plex Manager 6 x is launched and the run result appears in the Raw Data table Note You are now in the Bio Plex Manager 6 x application Bio Plex Manager MP continues to run and you can switch back and forth between the two application windows Bio Plex Manager MP Software Exporting Data to Bio Plex Manager 6 x Exporting Data from the Analyze Export View The result from a protocol reading is stored in the run results table See Run Results Table on page 38 for more information You can export your run result at a later time from the Analyze Export view To export data from the Analyze Export view 1 is ge d Click Analyze Export in the navigation bar Click the row of the run result you want to export Click Export Results Enter the name of the file The default file name is the run result name followed by the time stamp of the time of the export For example Experiment 2013 02 12 13 04 08 You can accept the default name or enter a different name for the file Click Save A message appears informing you that the result file has been exported If Bio Plex Manager 6 x is install
46. e 86 Index Wash between Plates routine 87 Waster container is full error 108 Well formats removing 20 Well formatting changing 20 Well types 16 Wells autofilling 17 Wells blank 16 Wells control 16 Wells standard 16 Wells undefined 17 Wells unknown 17 UserGuide 113 Index 114 Bio Plex Manager MP Software Life Science Group 10032257 Rev A US EG Bio Rad Laboratories Inc Web site www bio rad com USA 800 424 6723 Australia 61 2 9914 2800 Austria 01 877 89 01 Belgium 09 385 55 11 Brazil 55 11 5044 5699 Canada 905 364 3435 China 86 21 6169 8500 Czech Republic 420 241 430 532 Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65 Germany 089 31 884 0 Greece 30 210 9532 220 Hong Kong 852 2789 3300 Hungary 36 1 459 6100 India 91 124 4029300 Israel 03 963 6050 Italy 39 02 216091 Japan 03 6361 7000 Korea 82 2 3473 4460 Mexico 52 555 488 7670 The Netherlands 0318 540666 New Zealand 64 9 415 2280 Norway 23 38 41 30 Poland 48 22 331 99 99 Portugal 351 21 472 7700 Russia 7 495 721 14 04 Singapore 65 6415 3188 South Africa 27 861 246 723 Spain 34 91 590 5200 Sweden 08 555 12700 Switzerland 026674 55 05 Taiwan 886 2 2578 7189 Thailand 800 88 22 88 United Kingdom 020 8328 2000 13 0782 0413 Sig 1212
47. e Bio Plex Manager MP Enter your activation code below and click activate Activation Code 3399 8442 6114 7692 0170 4074 8732 1639 Who Installation ID Please take a few moments to activate your product now No personal data is sent during the activation process Enter the activation code in the box above and click Activate The activation code can be found in your product folder 90 Bio Rad Technical Support Email LSG Software Act amp bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST During the activation process the software will connect to the Internet If you have a firewall or proxy server this may prevent the software from successfully connecting If you see a message prompting you to unblock control activation exe click OK to unblock the file Back Bio Plex Manager MP Software Activating the License through Technical Support The Activation Successful window appears confirming that the software has been activated Wi Bio Plex Manager MP License Manager _ Activation Successful Bio Plex Manager MP is successfully activated Wo d Bio Rad Technical Support Email LSG Software ActObio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST 5 Click OK to exit the activation software and start Bio Plex Manager MP Acti
48. e frequency with which you receive reminders to back up the database or you can schedule automatic database backups For more information on the Archive Utility see XPONENT for MAGPIX 4 2 Software User Manual available on the Luminex web site Backing up the Bio Plex Manager MP Database It is a best practice to back up the database frequently and keep the backup copies in a safe location A USB or network hard drive is a good backup solution Keep in mind that it can take several minutes to back up a large database To back up the database 1 Exit the Bio Plex Manager MP software 2 Navigate to C ProgramData Bio Rad Bio Plex Manager MP Note If you do not see the ProgramData directory the directory may be hidden and you must show the hidden files See Showing Hidden Files on page 105 3 Copy the database file BioPlexManagerMP 214 db3 to a backup location Showing Hidden Files If you do not see the directory specified in the database path the cause may be that the directory is hidden from view You must display the hidden directory before you can back up your database To display hidden files 1 Goto the Windows Start menu select Settings and select Control Panel 2 Click Folder Options 3 Inthe Folder Options dialog box click the View tab 4 Under Advanced Settings click Show hidden files folders and drives 5 Click OK User Guide 105 B Backing Up the Database 106 Bio Plex Manager MP Software C T
49. e s quedes bue qns 23 Editing a Protocolo eere acera nm Rx Rev xen REX be REIHE 23 Chapter 3 Running Protocols leere 25 Running the Recommended Routine 0 cee eee 25 Plate Handling Guidelines llle 26 Plate Lyp6S 2k ueees Re uus Pe Ra prid chew GREER sees Ee ewes rex 27 Using the Plate Heater 0000s 28 Running the Protocol 2 i065 e208 lue mm rl a rd rm ea Rr dos 28 User Guide iii Table of Contents Reading the Plate esseri ecl mro ee e Rc ew Semi eer ee 31 Raw Data Table i2ulula do ilk Dee Eum nee RR eda rok ect has 32 Bead Map eod eet oo a tp eee eee Seeders s Red cendres 33 Interruptingia RUN iure de Pio eem RD Ru RES qure deque der 34 Resuming A RUF 4 ce esa mE xm bem e ede weds CE EE Re ru Ri E E CS 35 Encountering and Resolving Low Bead Counts 000 eee eae 36 Run Results Table o24 4 iseds ont bh EIEEE amp LEGAS Red Pes Ru E ERES 38 Exporting Data to Bio Plex Manager 6 x llle 39 Exporting Data from the Create Run Protocols View 20 55 40 Exporting Data from the Analyze Export View 0020 cee eee 41 Exporting Data Results Multiple Times l i 42 Chapter 4 Managing Assay Panels and Standard Lots 43 Creating Assay Panels ess sireisri tsis traku EESE lere 44 Customizing an Existing Assay Panel 0 0 00 cee eee ee 45 Creating an Assay Panel by Combining Existing Panels
50. ed on the same computer where you are running Bio Plex Manager MP you are also asked if you want to open the result in Bio Plex Manager 6 x In the Export Results dialog box click Yes Bio Plex Manager 6 x is launched and the data result appears in the Raw Data table Note You are now in the Bio Plex Manager 6 x application Bio Plex Manager MP continues to run and you can switch back and forth between the two application windows User Guide 41 3 Running Protocols Exporting Data Results Multiple Times As you analyze your data result in BPM 6 x you may want to rerun the protocol and generate a new result As you switch between BPM MP and BPM 6 x you should be aware of how you name your result files For example assume you save your result to a file called Exp Region 21 After you examine the result in BPM 6 x you decide you want to make some changes to the protocol and run it again You return to BPM MP edit the protocol rerun the protocol and export the result a second time When you are prompted to save the result if you use the same file name that you used for the first run that is Exo Region 21 you will overwrite the result file from the first run Note Before you export your result from BPM MP to BPM 6 x you must close the Report Table view for Exp Region 21 in BPM 6 x If you do not close the Report Table view for the first result file BPM 6 x does not recognize the new result file as an updated version of wh
51. elines and warnings Protect your assay microspheres from light Once photobleached the beads are no longer usable You must care for the microspheres properly to maintain your product warranty When using a filter plate and wrapping the plate avoid touching the bottom of the wells The sample may wick or leak from the well bottom Should this occur it can cause problems when reading the plate Make sure you have added at least 125 yl of sample to all the wells specified in your plate template before starting a protocol run If the array reader attempts to draw sample from an empty well air is sucked into the sample loop and injected into the flow chamber When this happens bubbles form in the cuvette and interfere with the analysis Should this occur perform a Clear Bubbles procedure see Clear Bubbles Routine on page 77 then rerun the protocol Shake the microplate on a plate shaker for 30 seconds prior to performing a reading For some experiments the temperature of the plate must be maintained at a particular temperature See Using the Plate Heater on page 28 for more information Bio Plex Manager MP Software Plate Types Plate Types The plate height adjustment procedure adjusts the probe setting for four consumables the well strip and the reservoirs in the reagent block When you run your protocol you must specify one of the following plate types Plate Type Compatible Consumable Distance from Platform mm Flat
52. ends you perform the following steps in the order shown Performing the steps in order increases the likelihood that when you run the verification routine again it will succeed To correct a verification failure 1 e Ol d ps Check that the beads are in the correct wells Check that the correct verification and or calibration control values are being used Clean the sample probe Check that the waste container is not full Run the Adjust Probe Height procedure Run the recommended maintenance routine Bio Plex Manager MP Software Interrupting a Routine 7 Run the Calibration and Verification routine If verification fails a second time contact Bio Rad Technical Support Interrupting a Routine You can interrupt a maintenance routine before it has finished for example if you forgot to fill the reagent block with the necessary liquids and reagents To interrupt a maintenance routine gt Click Stop Note When you click on the Routine Log link while a routine is running the Routine Commands window opens You must close the Routine Commands window before you will be able to click Stop to interrupt the routine Preparing Your Instrument for Nonuse When the MAGPIX instrument is not used for a period of time microbes may grow in the water reservoir and traces of liquids and reagents in the lines can crystallize Therefore if you do not plan to use your instrument for 14 or more days Bio Rad recommends you prepare
53. eriments using the same panel For more information on editing an existing assay panel see Editing an Assay Panel on page 47 Creating an Assay Panel by Combining Existing Panels You can create a new assay panel by combining existing panels Once this panel is created you can cull the list and delete any analytes you are not interested in To create a new assay panel by combining existing panels 1 From the protocol dialog box click Select Analytes 2 Click Manage Assay Panels 3 Inthe Manage Assay Panels dialog box select the panels from the Assay Panel list Note You can select up to four assay panels 4 Click New From 5 In the New Assay Panel dialog box enter a name for your assay panel 6 Use the Add and Delete buttons to add or remove analytes from the list Tip Click the number of the analyte to select the entire row 7 Use the Up and Down buttons to reorder the analytes 8 When you are done making changes to the panel click OK In the Manage Assay Panels dialog box the new panel appears at the top of the list 9 Click Close User Guide 45 4 46 Managing Assay Panels and Standard Lots From the protocol dialog box you can now select this new assay panel from the Assay Panel dropdown list Importing an Assay Panel The Import feature can be used to share assay panels among users working on different computers or to add new Bio Rad assay panels Once the panel is imported you can edit the panel o
54. erved concentration of the control wells is compared to the expected concentration and calculated at the end of the reading m Standard Wells Standard wells contain analytes of known concentration A series of known concentrations of an analyte is used to generate a standard curve of fluorescence intensity compared to analyte concentration The regression equation for the curve is used to calculate the concentration of analytes in the unknown samples and controls Bio Plex Manager MP Software Formatting Plates Unknown Wells The unknown wells contain samples of unknown concentration These samples are taken from the subjects of your experiments Undefined Wells Use the Undefined wells button to remove the definition of a well Undefined wells are not read by the array reader Autofilling Well Numbers Use the Autofill feature to quickly define a well type for multiple wells Autofill Across numbers the wells sequentially from left to right then top to bottom Autofill Down numbers the wells sequentially from top to bottom then left to right To use Autofill to format the plate 1 zu i cu In the New Protocol window click Format Plate Click Autofill Across or Autofill Down Click the well type Click and drag your cursor in the plate over the wells you want to format User Guide 17 2 18 Creating Protocols In the following example Autofill Down was used to create 20 Unknown wells Note the numberi
55. fication kit Note The lot number on the MAGPIX Calibration Kit or the MAGPIX Verification Kit CD must match the lot number of the kit to which the reagents belong For more information on calibration and verification kits see Calibration and Verification Kits on page 66 6 Click Start Once the routine is completed a dialog box appears informing you that the routine is completed Note You cannot run a protocol while a routine is running You must wait for the routine to complete User Guide 61 6 Maintaining the MAGPIX System Monitoring the Routine From the Maintenance view you can monitor the status of the routine in any of several ways Select Routine Daily Start Up Enhanced Maintenance Shut Down Prime Additional Routines ES Routine log Routine Log Fluidics2 Routine status Progress bar Estimated Run Time 4 minutes The following table describes the methods for monitoring the routine status Routine status The progress of the commands in the routine are displayed here The status changes displaying each command as it is being executed When the routine is finished running the status displays Completed Routine log Click the Routine Log link to open a Routine Commands dialog box displaying a complete list of all the commands in the routine the reagents used and the status of the commands 62 Bio Plex Manager MP Software Monitoring the Routine Progress bar T
56. g Data to Bio Plex Manager 6 x on page 39 Note Analysis of Bio Plex Manager MP results is supported only with Bio Plex Manager 6 0 or higher Earlier versions of Bio Plex Manager are not supported The following are differences between Bio Plex Manager MP and Bio Plex Manager 6 x m TheBio Plex Manager MP results cannot be viewed in a histogram or bead map in either software application Bio Plex Manager 6 x results can be viewed in both a histogram and bead map in the Bio Plex Manager 6 x software application m Region events are calculated differently in Bio Plex Manager MP and Bio Plex Manager 6 x n Bio Plex Manager MP the total region events includes all beads within the 50 regions whether or not they were selected for analysis x nBio Plex Manager 6 x the total region events includes only beads in the selected regions The same data result will reflect this difference in total region events when viewed in the two software programs User Guide 55 5 Analyzing Results x n Bio Plex Manager MP there are no gated events MAGPIX is a CCD camera based system and the gating of beads in the assay is accomplished through the software without user input For more information on analyzing your results in Bio Plex Manager 6 x refer to Bio Plex Manager Software 6 1 User Guide and the online help in the software 56 Bio Plex Manager MP Software 6 Maintaining the MAGPIX System The Maintenance view is used to
57. ger MP Software Formatting Plates The template diagram in the Create Run Protocols view displays the formatted wells in your protocol and the raw data table is populated with the well location and sample type Create Run Protocols view Formatted wells Name of assay panel Raw data table droning File Edit Instrument Help Af New G NewFrom etr F saveas lemon Results d tjet Pp start Protocol New Protocol R Run Log Maintenance 5 6 z 8 9 10 n i2 x Ee Assay Panel MAGPIX Quick Start Well Type Error Total Events Total Region Events Region 12 12 Regio 2 B 3 B 4 Di B 5 B 6 A2 C1 User Guide 15 2 16 Creating Protocols Well Types The following are different well types that you can specify on the plate Blank Standard Undefined ee a iol Control Unknown Blank Wells In certain types of assays such as the Bio Plex phosphoprotein assay it might be useful to subtract the assay background from the readings of standards controls and unknown samples Prepare blank wells that contain all of the assay components excluding the sample Blank wells are read along with the rest of the assay Bio Plex Manager 6 x then subtracts the mean background reading of these wells from the fluorescence intensity values of the wells containing standards controls and unknowns m Control Wells Control wells contain samples of known concentration The obs
58. h Between Plates Routine 200 eee 87 Appendix A License Activation elles 89 Activating the Bio Plex Manager MP License esee 89 Activating the License Online 200 e eee 89 Activating the License through Technical Support 000 eee eee 91 Generating the Credentials File llis 92 Activating the Software with a License File llle 94 Deactivating the Bio Plex Manager MP License llls eres 97 Deactivating the License Online l l 97 Deactivating the License through Technical Support 006 99 Exporting the Deactivation Certificate llle 99 Appendix B Backing Up the Database 103 Backing up the xPONENT Database sselseeeleee eee 104 Backing up the Bio Plex Manager MP Database 0 000 105 Showing Hidden Files 0002 e eee eee eee 105 Appendix C Troubleshooting Lee 107 Ue ioa aesackx ka ee ee E RR RR Reda 111 vi Bio Plex Manager MP Software 1 Introduction Bio Plex Manager MP is an application that allows you to run and maintain your MAGPIX instrument MAGPIX monitors the state of your instrument and recommends routines to keep the instrument in good working order and it also recommends maintenance routines to resolve problems With Bio Plex Manager MP you do not have to keep track of when to calibrate your
59. he progress bar is a visual display of the duration of the routine The progress bar fills from left to right as the routine is run When it is completely filled in the routine is finished running The following figure is an example of the Routine Commands dialog box Rovtne Commands a a Daily Start Up Name Reagent Status Prime None y Completed Alcohol Flush Alcohol Completed Rinse None Completed Rinse None F4 Completed Rinse None PA Completed Verify VER y Completed Rinse None Jf Completed Fluidics1 Fluidics1 Jf Completed Fluidics2 Fluidics2 y Completed Rinse None P4 Completed Rinse F4 Completed User Guide 63 6 Maintaining the MAGPIX System Setting Up the Reagent Block The Reagent Block section of the Maintenance view provides you with the information you need to set up the reagent block before you run your routine Reagent Block Alcohol CAL VER Fluidicsi Fluidics2 3 Daily Start Up 4 Add 5 mL of 70 isopropanol to the appropriate reservoir in the reagent block Vortex CAL VER Fluidics1 and Fluidics2 each for 10 seconds Add 6 drops each of CAL VER Fluidicsi and Fluidics2 to the indicated wells Use Calibration Kit B27801 Contains 9 Calibration Lot B26139 Use Verification Kit B29056 Contains Verification Lot B28334 Fluidics 1 Lot 828548 Fluidics 2 Lot 828338 o ao Oo
60. hnical Support do not have an Internet connection Bio Rad Technical Support C Activate Bio Plex Manager MP later You must activate this product before you can use it Email LSG Software ActGbio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Exit 3 Select Import license file and activate product and click Continue Wi Bio Plex Manager MP License Manager Activate Through Technical Support She Select one of the following options Send credentials to Technical Support Start here to initiate the activation process Importlicense file and activate product I have requested and received a license file from Bio Rad Technical Support Bio Rad Technical Support Email LSG Software ActGbio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Continue IL User Guide 95 A License Activation 4 Click Activate Wil Bio Plex Manager MP License Activate Bio Plex Manager MP Click Activate to select your license file and SX activate Bio Plex Manager MP OX L4 Follow these Steps Make sure the license file is available on your local hard drive an external drive a flash drive or a network drive Click Activate Bio Rad Technical Support Use the File Browser to naviagate to your license file Email Open the file to activate Bio Plex Manager MP mail
61. instrument or verify the calibration settings Its easy to use interface facilitates creating and running your protocols Bio Plex Manager MP works with any MAGPIX instrument purchased from any vendor You will use two software applications Bio Plex Manager MP 1 0 and Bio Plex Manager 6 x to run your experiments and analyze your results Both software applications are required and are shipped along with the MAGPIX instrument Use Bio Plex Manager MP to do the following m Operate the MAGPIX instrument m Maintain the instrument Define protocol parameters and initiate plate readings Use Bio Plex Manager 6 x to do the following m Review and optimize results m Exportresults to Microsoft Excel or other third party analysis software m Export results to Bio Plex Data Pro for analysis of your experiment grouping biological replicates and identifying statistically significant changes User Guide 7 1 8 Introduction Bio Plex Data Pro is an optional software application that allows you to do further analysis of your results x Identify and group biological replicates Determine statistically significant changes m Generate and export charts heat maps and tables Bio Plex Data Pro catalog 171 001513 and 171 001523 is a separate product that can be purchased from Bio Rad MAGPIX Operation Data Review and Optimization Bio Plex Manager MP Bio Plex Manager 6 x Experimental Analysis and Interpretation
62. l Routines dropdown list 3 Add 5 ml distilled or deionized water 5 ml 0 1N NaOH and 5 ml 10 bleach to the appropriate reservoirs in the reagent block 4 Click Start User Guide 81 7 Maintenance Routines Prime Routine Description of Routine The Prime routine primes the fluidics system by forcing drive fluid through the fluidics lines When to Run this Routine If the Unpack MAGPIX routine fails during the initial instrument set up then run the Prime routine Estimated Run Time 1 minute To Run the Prime Routine 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Prime from the Additional Routines dropdown list 3 Click Start 82 Bio Plex Manager MP Software Shut Down Routine Shut Down Routine Description of Routine The Shut Down routine cleans the fluidics lines and prevents a buildup of debris within the system When to Run the Routine Bio Rad recommends that you run the Shut Down routine at the end of each day that you use the instrument Refer to the Shut Down entry in the status section in the Maintenance view to determine whether the Shut Down has been run that day Estimated Run Time 2 minutes To Run the Shut Down Routine 1s 2 Navigate to the Maintenance view In the Select Routine section select Shut Down Add 5 ml distilled or deionized water and 5 ml bleach to the appropriate reservoirs in the reagent block Click Start User Guide
63. l Support m pm P Wil Bio Plex Manager MP License Manager gt File Successfully Saved What to Do Next Bio Rad Technical Support 1 Move the file to a computer where you can send email Email 2 Send the file as an attachment to Bio Rad Technical Support LSG_Software_Act bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST PER 7 Move the credentials file to a computer where you can send email and email the file to Bio Rad Technical Support LSG_Software_Act bio rad com Activating the Software with a License File Technical Support will generate a file with the license and email the file to you When you receive the email transfer the file to the computer where Bio Plex Manager MP is installed The file can be copied to a local hard drive flash drive or network drive Bio Plex Manager MP Software Activating the License through Technical Support To activate Bio Plex Manager MP with the license file 1 Start the Bio Plex Manager MP software 2 Inthe Product Activation Required window select Activate Bio Plex Manager through Technical Support and click Continue Wil Bio Plex Manager MP License Manager Product Activation Required Bio Plex Manager MP is not activated Do you want to activate P C Activate Bio Plex Manager MP Online I have an Internet connection Activate Bio Plex Manager MP through Tec
64. n values on the CDs The bottle for each reagent is not identified with the lot number for the kit Each bottle is identified with its own lot number but this number is different from the lot number for the kit Bio Plex Manager MP Software Calibration and Verification Kits Important The reagents must be used with the calibration or verification values with the same lot number If the values and reagents have different lot numbers the calibration and verification routines will fail Tip When you open a new kit continue to store the bottles in the original box or write the lot number of the kit on each of the reagent bottles This will make it easier to keep track of which reagents are associated with a particular lot Importing the Calibration or Verification Values The calibration kit CD and the verification kit CD contain values required to calibrate the MAGPIX instrument and verify the results Only one set of calibration values and one set of verification values can be used at a time Best Practice Import the calibration or verification values as soon as you open a new kit To import the calibration or verification values 1 Navigate to the Maintenance view 2 In the Select Kit section click Import Kit 3 Load the kit by doing one of the following m If you have the CD place the calibration or verification kit CD in the DVD drive and click Load from CD m If the file is on your computer navigate to where it is loc
65. nd of the day before you turn the instrument off If the Calibration Verification or Fluidics routines display the hourglass icon then run all routines in the Recommended Routine section Once the routine is successfully completed the routines in the Status pane will display as current If the Shut Down routine displays the hourglass icon then run the Shut Down routine before running any recommended routines Responding to a Failed Routine A routine may fail due to instrument problems or user error When failure occurs follow the instructions in any messages that appear and perform the recommended routines User Guide 69 6 70 Maintaining the MAGPIX System Calibration Failures If the calibration routine fails Bio Rad recommends you perform the following steps in the order shown Performing the steps in order increases the likelihood that when you run the calibration routine again it will succeed To correct a calibration failure 1 2 189 CEN Qe DO C9 Check that the beads are in the correct wells Check that the correct calibration control values are being used Clean the sample probe Check that the waste container is not full Run the Adjust Probe Height procedure Run the recommended maintenance routine Run the Calibration and Verification routine If calibration fails a second time contact Bio Rad Technical Support Verification Failures If the verification routine fails Bio Rad recomm
66. ng of the wells is top to bottom then left to right The arrow shows the path of the cursor as it is dragged across the plate template Defining a Replicate Group You can quickly format a replicate group To define a replicate group 1 Click Turn Autofill Off 2 Click and drag your cursor over the wells that contain the same sample The wells are labeled with the same number Autofilling Replicate Groups You can quickly format multiple replicate groups at one time To format a replicate group 1 Click Autofill Across or Autofill Down Bio Plex Manager MP Software Formatting Plates 2 Click the Set Replicate Size dropdown list and pick the number of replicates in the group Note The maximum size you can specify with the Set Replicate Size dropdown list is eight Tip You can create replicate groups that are larger than eight by clicking Turn Autofill Off setting the replicate size to 7 and selecting the number of wells you want in your replicate group 3 Click the well type 4 Click and drag your cursor over the wells on your plate In the following example Autofill Across is selected and the replicate size is set to 2 Eight groups of replicates of Unknown well type were created Each row represents a replicate group The arrow shows the path of the cursor as it is dragged across the plate template New Protocol we Jw eoo User Guide 19 2 Creating Protocols Remo
67. ngineer the Luminex Instrument or any such beads The Bio Plex suspension array system includes fluorescently labeled microspheres and instrumentation licensed to Bio Rad Laboratories Inc by the Luminex Corporation POW ERFUL CST antibodies exclusively developed and validated for Bio Plex phosphoprotein and total target assays Cell Signaling TECHNOLOGY CONTENT Copyright 2013 by Bio Rad Laboratories All rights reserved Table of Contents Chapter 1 Introd ctlOli sss sn mx nc cece eda eneee n me Rin 7 Chapter 2 Creating Protocols 22000ee eee eee eee 9 About Protocols eseri dee rre doe ER ee eo ee nde ie Bh ae ee ed 9 Navigating to the Protocol Dialog Box sselele ele 10 Creating a Protocols es seems e rre grece ene REG eee ia EIE E A 11 About Analytes cese mh a9 eRRORG Y ERR RENE OX R3 R Bee ee URL 12 Selecting Analytes s erre craro ills ln ee denen RA nd b oy d E E e dut 13 Formatting Plates uses iidem eb xe more n qeu beww ne us 14 Wel TYPES DT 16 Autofilling Well Numbers oe snsrssreisr erriei III 17 Defining a Replicate Group 000 eee 18 Autofilling Replicate Groups 2 2 0 0 00 ee 18 Removing the Well Formatting 000 e eee ee eee 20 Changing the Well Formatting llle 20 About standards ss cy seno rw bep E Rx Smut a uos aU R RR EORR X RR E EUR 20 Selecting a Standard Lot 00 eere 21 Reusing a Protocol suia hue as caves chee ede t
68. nts rather than a single point because of minute variations in fluorochrome levels and intensity among the beads in the set The white areas on the map indicate the expected regions of the selected analytes When you move your cursor over these areas the name of the analyte appears in a tool tip The data point clusters should fall within these regions If one or more clusters do not fall within the white areas there may be a problem with the beads such as photobleaching Or the analyte selections in the protocol may be incorrect If all the data clusters have shifted out of the white regions there may be microbubbles in the cuvette The bead map can be used to confirm that the bead sets are correctly selected measured and identified Interrupting a Run 34 The results for each run whether the run is completed or interrupted are saved to a unique result which can later be retrieved and viewed Any data that were read up to the point the run is interrupted are saved to the result name you specify in the Run Settings dialog box When you are ready to run the protocol again return to the Run Settings dialog box To interrupt a run P Click Stop to interrupt a run Bio Plex Manager MP Software Resuming a Run When a sample is being read the Start button changes to a Stop button Note When you click Stop Bio Plex Manager MP finishes reading the current well before it stops the run Therefore you may have to wait up to a minute
69. on see Exporting Data from the Analyze Export View on page 41 Note You can export your data once the plate reading is completed If you select a post run routine to be run once the run is completed you do not have to wait for the routine to complete before exporting your data Once the file is saved it can be viewed in Bio Plex Manager 6 x in one of the following ways If Bio Plex Manager 6 x is installed on the same computer where you are running Bio Plex Manager MP then you are prompted to view the result in Bio Plex Manager 6 x after the file is saved If you respond Yes the result file is opened in Bio Plex Manager 6 x If Bio Plex Manager 6 x is not installed on your computer then you must copy the saved file to a computer where Bio Plex Manager 6 x is installed and import it into the software User Guide 39 3 40 Running Protocols Exporting Data from the Create Run Protocols View You must first export the result to a file before you can analyze the data To export data from the Create Run Protocols view T 2 From the Create Run Protocols view click Export Results In the Export Results dialog box navigate to where you want the run result to be saved Enter the name of the file The default file name is the Result Name assigned in the Run Settings dialog box followed by a time stamp of the time of the export For example Experiment 2013 02 12 13 04 08 You can accept the default name or enter a
70. on and Verification Kits on page 66 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Verification from the Additional Routines dropdown list Add 5 ml 70 isopropanol to the appropriate reservoir in the reagent block Vortex VER Fluidics1 and Fluidics2 each for 10 sec Add 6 drops each of CAL VER Fluidics1 and Fluidics2 to the indicated wells Dn o9 Click Start User Guide 85 7 Maintenance Routines Wake from Storage Routine 86 Description of Routine The Wake from Storage routine prepares the instrument to be used after it has been idle for a long period of time When to Run this Routine Run the Wake from Storage routine if the instrument has been idle for 2 weeks or longer or if it has been prepared for storage Bio Plex Manager MP adds Wake From Storage to the Daily Start Up routine if it detects that the instrument has been idle for 2 weeks or longer Therefore if you run the Daily Start Up routine daily you will be running this routine as recommended Estimated Run Time 2 minutes To Run the Wake From Storage Routine 1 Navigate to the Maintenance view 2 Inthe Select Routine section select Wake From Storage from the Additional Routines dropdown list 3 Add 5 ml distilled or deionized water and 5 ml 70 isopropanol to the appropriate reservoirs in the reagent block 4 Click Start Bio Plex Manager MP Software Wash Between Plates Routine Wash Between
71. or the standard lot Bio Plex Manager MP Software Creating Standard Lots D gt New Standard Lot Standard Lot Name Expiration Date Select a date 1 Assay Panel Select a panel X Define Standard Lot By Serial Dilution Custom Analyte Starting Concentration Ce Tip Bio Rad recommends you include the lot number of the standards This will help you select the correct standard to use when running your protocol In the Expiration Date field enter the expiration date for this standard lot Tip Click on the calendar and select a date From the Assay Panel dropdown list select the assay panel you are using Select how the standard lot is defined by choosing one of the Define Standard Lot By options In most instances you will be using a serial dilution For information on defining custom concentrations see Defining a Standard Lot with Custom Concentrations on page 52 Specify the starting concentration for the analytes User Guide 51 4 52 Managing Assay Panels and Standard Lots The starting concentrations are specified on a label or product insert in the standard lot kit Tip If the starting concentration for all of your analytes is identical enter the concentration for the first analyte Select the entire row by clicking in the first column in the table Right click and select Apply starting concentration to all analytes from the men
72. ow 20 bead events 1 The bead count for one or more No data were found or an error e occurred while reading the well The results are displayed in the Raw Data table and the Bead Map Raw Data Table 32 As the wells are read the Raw Data table is populated with the results The table displays the well location and the well type for all formatted wells As Bio Plex Manager MP completes reading each well the Raw Data table is populated with the results for that well The fluorescence intensities of the analytes you selected are displayed for each well Note During a reading the array reader detects all of the analytes in the sample including any that you have not selected However any analytes that are not selected in the protocol are not included in the table even if they are detected After a reading you can edit the protocol and change the selection of Bio Plex Manager MP Software Bead Map your analytes The new analytes if detected during the run will then appear in the table Column Heading Well Type Total Events Total Region Events Region_ Bead Map Description Location of the well on the plate template Identifies the type of well Blank Control Standard Unknown and the sample For example C1 is the first control sample and S4 is the fourth standard sample Total bead events recorded for that well including unclassified events events that fall outside the 50 regions This
73. ox click Select Analytes 2 Click Manage Assay Panels 3 From the Manage Assay Panels dialog box select one or more assay panels and click Delete Sharing Customized Assay Panels 48 If there are multiple users of Bio Plex Manager MP in your environment you can customize an assay panel for your environment once and share it with other users Export the assay panel to a file and have your users import the panels into Bio Plex Manager MP on their computers You can also use the Export feature to archive assay panels that you no longer need Note You can export any number of assay panels at a time All selected assay panels are exported to a single file When the file is imported all panels are imported Users will not be able to selectively import panels from the file Bio Plex Manager MP Software Restoring an Assay Panel To export an assay panel 1 From the protocol dialog box click Select Analytes Click Manage Assay Panels Select the panel you want to export and click Export 25 399 H9 In the Export Assay Panels dialog box enter the name of the file and click Save Restoring an Assay Panel You may inadvertently delete an assay panel or you may want to return to the original version of a Bio Rad panel that you modified In these instances you can restore the assay panels that were originally distributed with the Bio Plex Manager MP software using the Restore command Any assay panels you created are not affected
74. previously omitted and the data for those analytes will appear in the tables Each analyte is listed by name and region The region number refers to the area of a fluorescent color map that identifies the analyte s bead region Each bead region is embedded with specific quantities of two fluorescent dyes The array reader detects the combination of these fluorochromes and associates the bead region with a unique region on the color map Therefore the location on the map identifies the bead region and its associated analyte Each analyte on a Bio Rad preconfigured panel is identified by a unique region However analytes on different panels may occupy the same region If you pick analytes from more than one panel only one analyte for a particular region can be selected Bio Plex Manager MP warns you if there is a conflict Bio Plex Manager MP Software Selecting Analytes Selecting Analytes After you select the assay panel you want to use in your experiment you select the analytes you are interested in To select an analyte 1 2 3 4 From the protocol dialog box click Select Analytes From the Assay Panel dropdown list select an assay panel Click the checkboxes to select the analytes to include in your protocol or click Select All to select all analytes Click OK The following figure shows the MAGPIX Quick Start assay panel with analytes in regions 20 21 and 25 through 27 selected la Sema 00 E
75. protocols You do not need to keep track of the calibration and verification status if you run this routine User Guide 57 6 Maintaining the MAGPIX System Recommended Routine Bio Plex Manager MP software monitors the MAGPIX instrument and identifies what routines need to be run to keep the instrument in good working order You do not have to keep track of whether you have run the correct routines at the right time Bio Plex Manager MP informs you what routine needs to be run in the Recommended Routine section When all recommended maintenance has been performed None is displayed r File Instrument Help A Eject p Start Daily Start Up Select Routine Daily Start Up Create Run D Enhanced Maintenance Protocols F Shut Down Additional Routines zj Best Practice m At the start of each day of operation Bio Rad recommends that you run the recommended routine Before you run a protocol check to see that all maintenance is up to date and the Recommended Routine section displays None 58 Bio Plex Manager MP Software Daily Maintenance Routines Daily Maintenance Routines Bio Rad recommends that you run the following routines each day you use the MAGPIX instrument At the Beginning of the Day Run the routine in the Recommended Routine section One or both of the following routines are recommended each day Daily Start
76. r select it in your protocol You import an xpnl file that contains one or more assay panels If the imported panel has the same name as an existing panel Copy is appended to the name to distinguish the imported assay panel from the existing one for example Assay Panel Copy To import an assay panel T 2 3 4 5 From the protocol dialog box click Select Analytes Click Manage Assay Panels From the Manage Assay Panels dialog box click Import In the Import Assay Panels dialog box navigate to the file you want to import Select the file and click Open A message informs you of the number of panels that were successfully imported for example Successfully imported 3 assay panels The imported panels appear at the top of the Manage Assay Panels list Click Close From the protocol dialog box you can now select any imported assay panels from the Assay Panel dropdown list Bio Plex Manager MP Software Editing an Assay Panel Creating a New Assay Panel You can create a new panel by starting with an empty assay panel and entering the details for the assay To create a new assay panel 1 From the protocol dialog box click Select Analytes 2 Click New Assay Panel 3 In the New Assay Panel dialog box enter a name for the assay panel 4 Enter the region and name of each analyte 5 Click OK In the protocol dialog box the new panel is added to the Assay Panel list Tip You can also create a new as
77. roubleshooting Problem Instrument is not connected Region Selection Severe Clog Possible Cause The connection to the MAGPIX instrument has been lost One or more of the analytes selected has little or no data Solution Try each of these suggestions in order until you reconnect to the instrument 1 Confirm that the instrument is turned on 2 Reconnect to the instrument From the Instrument menu select Reconnect Instrument 3 Turn off the instrument and exit Bio Plex Manager MP Turn the instrument on and restart the software 4 Restart the computer Restart Bio Plex Manager MP Perform the following steps 1 Stop the run 2 Review your data and verify that you have selected the correct analytes in the protocol definition Make any necessary changes to the selected analytes 3 Clean the probe and run the Enhanced Maintenance routine 4 Run the protocol again User Guide 107 C Troubleshooting Problem Possible Cause Low Bead Count Three or more consecutive wells have bead counts lower than the recommended number You empty the waste The instrument detects container but continue some moisture in the to see the following waste container and error message The triggers an alert waste container is full Empty the waste container and replace it with a dry waste container 108 Bio Plex Manager MP Software Solution Perform the following steps 1 Stopthe run
78. routine at the end of the previous day when you start up the instrument the next day the Status section in the Maintenance view shows that Shut Down is not current Run the Shut Down routine first This routine takes 2 minutes Once that routine has successfully completed then run the routine in the Recommended Routine section Running a Routine 60 In addition to running the recommended routines as part of daily maintenance all routines may be selected and run at any time To run a routine 1 From the Maintenance view select the routine from the Select Routine list 2 Ifthe routine does not appear in the list click the Additional Routines dropdown list and select the desired routine 3 Fill the reservoirs as indicated in the Reagent Block The Reagent Block is colored with the reservoirs and wells that need to be filled for the selected routine For more information on filling the reservoirs see Setting Up the Reagent Block on page 64 4 If indicated in the Reagent Block fill the well strip with the appropriate reagents For more information on filling the well strip see Setting Up the Reagent Block on page 64 5 Ifthe routine involves calibration and or verification select the kit in the Select Kit section Bio Plex Manager MP Software Running a Routine a Click the Calibration Kits dropdown arrow to select the correct calibration kit b Click the Verification Kits dropdown arrow to select the correct veri
79. rt if you do not have Internet access Note To activate your license you will need the product activation code which can be found in the Bio Plex Manager MP CD folder Activating the License Online Follow the procedure below if the computer on which Bio Plex Manager MP is installed has an Internet connection With this method the software uses your activation code to automatically activate your software To activate Bio Plex Manager MP online 1 Start the Bio Plex Manager MP software User Guide 89 A License Activation 2 Ifthe product license has not been activated the Product Activation Required window appears Wil Bio Plex Manager MP License Product Activation Required Bio Plex Manager MP is not activated Do you want to activate So Activate Bio Plex Manager MP Online l have an Internet connection Activate Bio Plex Manager MP through Technical Support do not have an Internet connection Bio Rad Technical Support C Activate Bio Plex Manager MP later Email You must activate this product before you can use it LSG_Software_Act bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST 3 Select Activate Bio Plex Manager MP Online and click Continue 4 Enter your activation code in the text box and click Activate Note The activation code can be found in the CD folder Wil Bio Plex Manager MP License Manager Activat
80. s with the specified fluids Accept the default for Stop runs with low bead count or clear the checkbox if you do not want the run interrupted By default the run is interrupted if three consecutive wells have a bead count of less than 20 Click Create Run Protocols The plate retracts and Bio Plex Manager MP starts the run Bio Plex Manager MP Software Running the Protocol Reading the Plate In the template diagram in the Create Run Protocols view the blue wells indicate which wells have been formatted Only formatted wells are read Each well is read in turn from top to bottom then from left to right A pulsing triangle shows you which well is currently being read Protocol name Run commands status EA export Results A cea Protocol Hu Cancer Biomarker 10 Plex Run Log Well E2 started 1 2 3 4 c 6 AAAA OO00NN oOo00BH Template diagram Analyze Export Well E2 The Run Commands status displays about the well that is currently being read In the preceding example Well E2 is being read The Run Commands status indicates when the reading begins and ends for the current well User Guide 31 3 Running Protocols Once the reading for a well is complete the pulsing triangle resolves into one of the following symbols indicating the result of the reading Symbol Description The bead count for all analytes is 20 or higher analytes is bel
81. say panel from the Manage Assay Panels dialog box Editing an Assay Panel You can make changes to an existing assay panel To edit an assay panel 1 From the protocol dialog box click Select Analytes 2 Click Manage Assay Panels 3 Select the panel you want to edit and click Edit 4 n the Edit Assay Panel dialog box you can make the following changes xm Rename the assay panel Tip Bio Rad recommends you give the edited panel a new name This preserves the original Bio Rad assay panel and it eliminates problems with overwriting your edited panels if you use the Restore command or import updated panels from Bio Rad User Guide 47 4 Managing Assay Panels and Standard Lots m Use the Add and Delete buttons to add or remove analytes from the list Tip Click the number of the analyte to select the entire row m Use the Up and Down buttons to reorder the analytes 5 When you are done making changes to the panel click OK Customizing Your Assay Panel List The Assay Panel list includes all the assay panels provided by Bio Rad as well as any panels you create You may want to delete assay panels from the list because you use only a subset of the published assays If you delete a Bio Rad assay panel you can always return it to the Assay Panel list using the Restore command For more information on restoring an assay panel see Restoring an Assay Panel on page 49 To delete an assay panel 1 From the protocol dialog b
82. sful Bio Plex Manager MP is successfully deactivated Who Bio Rad Technical Support Email LSG_Software_Act bio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST 5 Click Exit 98 Bio Plex Manager MP Software Deactivating the License through Technical Support Deactivating the License through Technical Support If the computer on which Bio Plex Manager MP is installed does not have an Internet connection you can deactivate your license through Bio Rad Technical Support This is a two phase process 1 Generate a deactivation certificate file and email it to Technical Support 2 Technical Support informs you that the license has been deactivated Important Until Technical Support sends you a confirmation that the license is deactivated you will not be able to move the license to another computer or reactivate it on the current computer Exporting the Deactivation Certificate To export the deactivation certificate 1 Start Bio Plex Manager MP 2 From the Help menu click Manage License 3 Select Deactivate Bio Plex Manager MP through Technical Support and click Continue Bi o Pier Maraga MP ccs Maras Bio Plex Manager MP Is Activated Bio Plex Manager MP is activated Do you want to deactivate C Do not deactivate C Deactivate Bio Plex Manager MP Online have an Internet connection Deactivate Bio Plex Manager MP through Techni
83. trumentation or using this unit of Luminex Instrument in any manner you are consenting and agreeing to be bound by the following terms and conditions and the terms and conditions set forth in the End User License Agreement for the Luminex software included with this unit You are also agreeing that all such terms and conditions constitute a legally valid and binding contract that is enforceable against you If you do not agree to all of such terms and conditions you must promptly return this unit of Luminex instrumentation for a full refund prior to using it in any manner No rights or licenses under any of Luminex Corporation s Luminex patents are granted by or shall be implied from the sale of this unit of Luminex Instrument or license of Luminex software to you the purchaser and you do not receive any right under Luminex s patent rights by virtue of your purchase of Luminex Instrument or license of Luminex software You agree that the Luminex Instrument and Luminex software are sold only for use with fluorescently labeled microsphere beads authorized by Luminex and you may obtain a royalty free license under Luminex s patents if any to use this unit of Luminex Instrument with fluorescently labeled microsphere beads authorized by Luminex by purchasing beads authorized by Luminex and registering this unit of Luminex Instrument with Luminex dealer in accordance with the instructions accompanying the Luminex Instrument You agree not to reverse e
84. u to populate the starting concentration for all the analytes with the same number Defining a Standard Lot with Custom Concentrations There may be times when you want to customize the dilutions of your standards For example you might start with a dilution factor of 4 for the first three wells then dilute the standard in smaller increments for the next three wells To define custom concentrations for the analytes 1 In the New Standard Lot dialog box select Custom for Define Standard Lot By The table displays a column for each standard well Select the number of standard wells in your protocol For each analyte enter the concentration values for each standard When you are done click OK Creating a Standard Lot from an Existing Lot You can create a new standard lot from an existing lot This is useful if you use the same assay panel repeatedly because it saves the time of reentering the starting concentration values To create a new standard lot from an existing lot Ts 2 3 From the protocol dialog box click Standards Info Click Manage Standard Lots In the Manage Standard Lots dialog box select a standard lot from the list and click New From Bio Plex Manager MP Software Editing Standard Lots 4 Enter anew name for the standard lot 5 Enter the expiration date for the standard lot Tip Click on the calendar and select a date 6 Make any changes to the starting concentration of the analytes
85. un Log The protocol is complete Well F2 1e 44 1e 34 1e 2 Classification 2 Analyze Export 1e 1 160 1e 1 Assay Panel MAGPIX Quick Start Well Type Error Region 20 20 Region 21 21 Region 22 22 Region 25 25 Re 3 Cl X3 RegionSelection Severe Clog 4 2 Ragion Selection SevereClog a 5 E1 X8 Region Selection Severe Clog 90 1 6 Fi X9 Region Selection Severe Clog 4 a 3 A2 X4 Region Selectien Severe Clog i A 4 8 B2 X5 Region Selection Severe Clog 4 a 9 C2 X6 Region Selection Severe Clog 4 y 10 D2 X10 Region Selection Severe Clog 4 a LEGEND 1 Warning symbol indicating wells with a low bead count 2 Warning symbol indicating region in which there is a bead count of fewer than 20 beads 3 Asterisk indicating region in which the bead count is lower than the recommended 50 beads Important Bio Plex Manager MP will provide warning messages when a low bead count occurs with recommended steps to resolve the problem These include reviewing your protocol performing maintenance on the instrument and running maintenance routines It is important that you perform the steps in the recommended order because this increases the likelihood that the problem will be resolved User Guide 37 3 Running Protocols Run Results Table The data from each run are saved as a result in the MAGPIX database Each result is a row in the run results table
86. un it again at a later time or if you want to use it as a template for another protocol For more information on using the protocol as a template see Reusing a Protocol on page 23 Optional In the Save Protocol dialog box enter the protocol name and click OK Note Protocols created on one computer cannot be exported and used on another computer running Bio Plex Manager MP User Guide 11 2 Creating Protocols About Analytes 12 Bio Plex Manager MP software groups analytes by panels Preconfigured panels of analytes that correspond to off the shelf Bio Plex assays can be selected These assays include human mouse and rat cytokines and phosphoproteins as well as the newer human angiogenesis diabetes isotyping and acute phase assays The following assays are currently not available for the MAGPIX instrument nonhuman primate diabetes canine kidney tox rat and human kidney tox angiogenesis and acute phase You can add other panels to this list or create custom panels that include only the analytes you use in your experiments Note After you select the assay panel you select which analytes you want to appear in your reports During a reading the array reader detects all the analytes in the sample including any analytes you excluded from selection However only the selected analytes are included in the final reports and tables After the run is completed you can always edit the protocol select any analytes that were
87. vating the License through Technical Support If the computer on which Bio Plex Manager MP is installed does not have an Internet connection you can request a product license from Bio Rad Technical Support to activate the software This is a two phase process 1 Generate a credentials file and email it to Technical Support Technical Support uses the credentials file to generate a license and emails the file back to you 2 Use the license file to activate your software The procedures that follow describe this two phase process User Guide 91 A License Activation Generating the Credentials File To generate the credentials file 1 Start the Bio Plex Manager MP software 2 Ifthe product license has not been activated the Product Activation Required window appears 3 Select Activate Bio Plex Manager MP through Technical Support and click Continue Wi Bio Plex Manager MP License Manager Product Activation Required Bio Plex Manager MP is not activated Do you want to activate NOx E Activate Bio Plex Manager MP Online I have an Internet connection Activate Bio Plex Manager MP through Technical Support I do not have an Internet connection Bio Rad Technical Support C Activate Bio Plex Manager MP later You must activate this product before you can use it Email LSG Software ActObio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST E
88. ving the Well Formatting Removing the formatting of a well returns it to its unformatted state Unformatted wells are not read by the array reader To remove the formatting of a well 1 Click Undefined 2 Click and drag your cursor over the wells you want to clear The formatting is removed and the wells return to their unformatted state Changing the Well Formatting You can overwrite the formatting of a well by simply applying another sample type over the wells To change the formatting of a well 1 Click the button for the sample type you want to use 2 Click and drag your cursor over the wells whose format you want to change The wells are now formatted with the new well type About Standards Standards are analytes of known concentration Standards are used to generate a standard curve of values using one of the several regression methods included in Bio Plex Manager 6 x This curve is used to calculate concentrations of your unknowns In Bio Plex Manager MP you define your standard lot including the starting concentration for each of the analytes This definition is stored and it can be reused each time you run a plate with those analytes 20 Bio Plex Manager MP Software Selecting a Standard Lot Selecting a Standard Lot Before you can select the standard lot to use with your protocol you must first select your analytes format the standard wells and create a standard lot for the assay panel you are using if one has not already
89. xit 92 Bio Plex Manager MP Software Activating the License through Technical Support 4 Select Send credentials to Technical Support and click Continue I Bio Plex Manager MP License Manager Activate Through Technical Support ox Select one of the following options e Send credentials to Technical Support Start here to initiate the activation process C Importlicense file and activate product I have requested and received a license file from Bio Rad Technical Support Bio Rad Technical Support Email LSG Software ActGbio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST Continue C e 5 Enter your activation code in the text box and click Save Note The activation code can be found in the CD folder Wil Bio Plex Manager MP License Manager Save License Credentials to a File Enter your activation code and click Save Sox Activation Code Installation ID 3399 8442 6114 7692 0170 5353 4420 9050 Bio Rad Technical Support Email LSG Software ActGbio rad com Telephone 1 800 424 6723 option 2 Hours 5 00 a m 5 00 p m PST 6 Inthe Save Licensing Credentials to a File dialog box enter the name of the file and click Save User Guide 93 A 94 License Activation The File Successfully Saved window appears with instructions on how to send the credentials file to Technica
90. you must create a standard lot Or if the list does not include the standard lot you are using then you must create a standard lot definition For more information on creating standard lots see Creating New Standard Lots on page 50 Note The predefined standard lots are identified by their lot numbers Included in parentheses is the name of the assay panel and the expiration date In the example 5029511 Bio Rad Pro Hu Group 27 Plex Exp 2016 03 30 5029517 is both the name of the standard lot and its lot number Select the dilution factor from the Dilution Factor dropdown list The table autopopulates with the concentrations using the starting concentration specified for that standard lot and the dilution factor 9 New Protocol PF Ff New Standard Lot a Manage Standard Lots E Standard Lot 5029511 Bio Plex Pro Hu Group I 27 Plexj Exp 2016 03 2 va Dilution Factor x Most Concentrated Standard S1 S8 penn Analyte s1 s2 3 S4 5 HE 1 HulL 1b 39 29484 80 7371 20 184280 46070 11518 tH 2 Hull lra 25 4409488 1102372 2755 93 68898 17225 4 pms 3 Hu l 2 38 11348 64 2837 16 70929 17732 4433 _ 4 Hull 4 52 391488 97872 24468 6117 1529 i 5 Hull 5 33 40258 56 10064 64 2516 16 629 04 15726 o 6 Hull 6 19 26085 76 652144 163036 40759 10190 Standards o1 74 3329216 832304 208076 520 19 13005 8 HulL 8 54 22232 96 5558 24 1389 56 347 39 8685 9 HulL 9 77 928144 2
91. your instrument for a period of nonuse Taking these steps before the instrument is idle will minimize the maintenance required when you resume using it To prepare your instrument for nonuse 1 Run the Prepare for Storage maintenance routine 2 Remove the drive fluid container from the instrument 3 Remove and empty the waste container 4 Empty any liquids from the reagent block Wash and dry the reagent block 5 Empty any liquids from the well strip User Guide 71 6 Maintaining the MAGPIX System Adjusting the Probe Height The probe must be calibrated in order to work correctly with the different plate types Adjust the probe height in the following situations After you set up the MAGPIX instrument and the computer you must first adjust the probe height before you run any protocols After you remove and clean the probe you must adjust the probe height If you experience sample problems adjusting the probe height may resolve these errors To adjust the probe height 1 From the Maintenance view click Adjust Probe Height The Adjust Probe Height dialog box appears Empty the reagent block and the well strip The rightmost reservoir in the reagent block and the rightmost well in the well strip must be empty Insert the MCV plate well strip and reagent block Click Adjust Probe Height When the calibration is completed a dialog box appears confirming that the adjust probe height procedure is completed

Bio-Plex Manager MP Software User Guide - Bio-Rad

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