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LabChip XT User Manual

1. 14 77 Select the Auto Export Settings 31 Smear button 169 Export As Assay button 157 F File menu 104 Filter View 124 Filter Width 44 161 243 Filter Width changing 54 Filtered Peaks only 137 Filtering parameters 53 Finding peaks 250 First Peak Time 256 Flashing software 234 POCUSING s 4 ses a ur cote 219 OR ER N Ed 122 Forcing expected peaks 50 Front view 212 FUSOS tes ds ado 11 218 G CPP EN EE PER NE ET TT 66 128 COPYING ss cor 66 exporting 76 Gel color 60 Gel View 128 Gel View Properties 131 DUE sos carre sers 69 V2 1 LabChip XT XTe User Manual Index 265 Gel Color 131 Gel Contrast Range 131 Gel View Properties 131 Global Analysis settings 157 Global Peak Find 44 SAP ses 44 60 66 256 GOD ING 44 sisi sus 66 Electropherograms tab 121 Graph View Properties 122 max per page 122 overlay 63 Overlay Electropherograms Tab 120 printing 69 selected gels only 122 Standard curve 44 256 Graph selected gels only 122 Graph View 117 Green laser
2. 215 GORE ee sos ne 218 H Hardware Diagnostics 244 Heat Emission 218 Help menu 108 Hide excluded peaks 137 Hiding views 62 High Concentration Size Correction 171 High Size Filtering 161 High Voltage safety 10 How the Software Analyzes DNA Data44 HV Current Calibration Test 231 HV Isolation Relay Test 231 HV Kelvin Mode Test 231 HV Voltage Calibration Test 231 Identifying peaks 250 Import 46 165 167 169 data file 46 Excluded Fragments button 167 Expected Peaks button 165 Smear button 169 Inflection Threshold 161 244 Inflection Threshold changing 54 Installation Qualification Window 185 Instrument description 211 Instrument menu 106 Caliper Life Sciences Inc Instrument safety 7 IO TUNNG 46446404 b dead e ee 228 IV Check Failed Warning 227 L LabChip Kit assay description 20 LabChip XT main window 102 Lab on a Chip 246 Ladder 44 246 247 concentration 160 Ladder Analysis 247 Lane Width 131 Laser ns ss BRS AE 215 Laser Safety 9 Laser Test 231 Last Peak Time 243
3. Figure 3 Gel View V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Introduction 22 Principles of Operation Continued Quantitating the concentration and accurately sizing each fragment are achieved by comparing against a sizing ladder An internal standard or marker is added to each sample to adjust for channel to channel variations The internal standard of known concentration is mixed with the sample to aid in quantitation and sizing The marker lies slightly outside the assay range so it does not interfere with analysis The LabChip XT XTe can use either a virtual software ladder or a ladder that runs in one channel of the chip at the same time as the samples for real time sizing of the separated nucleic acids The following ladder options are available in the LabChip XT XTe software e A virtual Caliper software ladder e A Caliper ladder included in the reagent kit e A customer supplied ladder LabChip XT only V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 23 Operation This section includes general instructions for using the LabChip XT or XTe hardware and software to run an assay For assay specific information see the LabChip XT Assay User Guide for the specific assay that you are running The current version of the Assay User Guides can be accessed on the Caliper web site at http www caliperls com support reference library data sheets labchip systems data sheets h
4. 143 CDR Server Utility Window 145 CDR Utility Window 146 Center point 238 Change Password Window 148 Changing sample name 33 Changing the View of the Results 60 Channel End Time 160 Channel Peak Find Settings 161 Channel Table View 133 adding columns 65 PIIAUNG RAAT AE EE EN 71 Chemical Safety 8 D LR SEE SEE KIE RO 216 preparing and loading 33 FUNDING 4 20444 sors Dei HR ER 8 33 Chip Capacity aaa aaa 218 Chip Expiration 109 CBI is RR 109 Caliper Life Sciences Inc Chip View or Chip List 113 Chromatography Data Interchange FOMA REKE ess rate r 77 Cleaning the electrodes 221 COR nes en 112 Clipboard arene tb ewe 44 40 4 240 GOLLECT rra meti 112 Collection 47 105 116 240 adding to workspace 47 Collection Menu 105 Collection pane 116 template 240 Collection well 216 241 COON del si sake bade eho anes 128 Compare results 60 Computer Resources Test 230 Computer Software Lock Ups 233 Concentration 20 160 Contrast ses as Geb GER EDE SR 128 So ARE EET be i SEE 66 Copy Gel 66 Copy Graph 66 Copy Lane 66 data IS 4244544446444 65 4 450 4 30 Create daily
5. 660 g mol bp is the molecular weight of a single base pair Molecular Separation Techniques Processes such as gel electrophoresis liquid chromatography and capillary electrophoresis which can separate biomolecular organic substances from other compounds V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 249 Peak Baseline A local peak baseline is calculated for each peak For isolated peaks the local peak baseline is a straight line connecting the start point with the end point For peaks that are very close together an average baseline is used when the value between the peaks does not drop to the actual baseline The peak baseline for each peak in Figure 97 is shown in a different color Figure 97 Peak Baselines The baseline algorithm starts at the earliest peak and checks whether the end point is within a certain distance from the start of the next peak When a cluster of peaks is detected the baseline is the line joining the first peak s start to the last peak s end The start and end points of adjacent peaks in the cluster are averaged to the same point so that no gaps exist between peaks The peak baseline Start Point and End Point can be moved in the Overlay Electropherograms Tab if Show Peak Baselines is selected in the Graph View Properties Peak Height The value at the apex of the peak minus the local baseline start value V2 1 LabChip XT XTe User Manual Caliper Life
6. Audit Trail Log Opens the Audit Trail Window to view search export and print the audit trail Lock Application Opens the Unlock Application Window to lock the LabChip XT software and prevent other users from using the software until the software is unlocked by the current user or an Administrator The View menu contains the following commands Event Viewer Opens the Event Viewer Window to view events and errors that occur during the current run or during a previous run Run Info Opens the Run Info Window to view information about the run Version Change Details Displays the Data File Version Window to view changed versions of the selected open data file LabChip XT only Validation Menu V2 1 The Validation menu contains the following commands Software IQ Opens the Software Installation Qualification Window to perform the IQ Diagnostics Opens the System Diagnostics Window to run diagnostic tests to verify system operation and performance Reports Opens the Print Validation Reports Window to view or print IQ OQ results LabChip XT XTe User Manual Caliper Life Sciences Inc Window Menu Help Menu V2 1 Software Reference 108 The Window menu contains the following commands Cascade Displays each Collection in a separate cascading window in the Collection Pane Tile Vertical Displays each Collection in separate side by side windows in the Collection Pane LabChip XT only Ti
7. Channel Option Select the channels to be included in the printout either Entire Collection or Selected Channels Add Border Option If selected the Channel Table and Peak Table will print with a border between each column and a border below the column header Add Channel Name as Header If selected a channel header containing the chip name channel name and sample name is printed before each set of peaks in a channel This option is only available if Peak Table is selected Column Header Specifies where to print the column headers which identify each column in the Peak Table This option is only available if Peak Table is selected and Channel Table and Electropherogram are not selected e Per Page the column header is printed only at the top of each page e Per Channel the column header is printed at the top of each page and at the start of each new channel Run Report Generates a one page report of the selected data file The report includes gel and graph views of the data Method Info and the contents of the Channel Table This option is only available in the LabChip XT software e Add Border If selected borders are printed for the tables in the Method Info and Channel Table sections Preview button Displays a preview of the selected options Print to PDF button Prints the selected information from the active collection to a pdf file Print button Prints the selected information from the active
8. For information on changing the view properties in the Electropherograms tab see Viewing Graphs in the Electropherograms Tab on page 64 See Graph View Properties on page 122 for descriptions of the properties that can be set for the Electropherograms tab V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 122 Graph View Properties To view the Properties for the Electropherograms Tab or the Overlay Electropherograms Tab click the Properties tab on the right side of the Graph View Layout Rows x Columns Annotation 1 Text Orientation A button V2 1 Properbes E Properties e mr Er Armotaton1 a Set Fot a Fows X Cama Type Anmctabon MU Sat Font Ponetetion i A Th Hors H Type _ Peak Annotation Legend Amata 9 Channel Annasan lona 7 A 7 Peak Annotation Legend Ve 4 Show Peak Baselines N Shove Seana 50 ng ok kt Sc Time DSe Log Size Gidse 2 JON A Men 5d e o Time Size log Sire Grd Style Na Fite Figure 29 XT Electropherograms Properties and XT Overlay Electropherograms Properties This window contains the following options Specifies the number of rows and columns of graphs displayed on the Electropherograms Tab Only displayed when the Electropherograms tab is selected Labels each peak in the graph with the peak property selected from the drop down list Default is Type The Annotations
9. For problems with assays see the Assay User Guide for the specific assay you are running The Assay User Guides contain common problems that may occur for each type of assay and suggested solutions to resolve the problems The current version of the Assay User Guides can be accessed on the Caliper web site at http www caliperls com support reference library data sheets labchip systems data sheets htm If the problem is not resolved by following the suggestions in the Assay User Guide contact Caliper Technical Support see page 2 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 233 Software Problems If any of the following software problems occur follow the suggestions to correct the problem e Cannot Save a File e Computer Software Lock Ups e Software Display Flashes Cannot Save a File File has been saved as a Read Only file If you editing an existing file verify the file is not Read Only If it is the title bar shows Read Only after the file name Read only files can be edited and saved with a new name or in a new location with the same name but cannot be saved over the original file Hard drive is full Verify there is sufficient free space on the drive to save the file If not clear some space on the hard drive On non 21 CFR Part 11 systems you can archive files that you are not using to another location If you do have sufficient space try closing all op
10. Pause a Run V2 1 The run in progress can be manually paused to remove material from the collection wells or to edit certain extraction parameters While the run is paused the voltage for each channel is set to zero the lasers are turned off and the samples stop moving through the channels The run will automatically pause if the lid is opened during the run but using the software Pause feature ensures that all of the extracted material has entered the collection well before the run is paused To manually pause a run in progress 1 Move the cursor over the instrument icon on the upper left side of the LabChip XT XTe Main Window The Pause Stop button displays as shown in Figure 4 Figure 4 Pause Stop Button 2 Click the Pause Stop button The Modify Run Settings Window opens the voltage in each channel is set to zero and the lasers turn off 3 While the run is paused the settings on the Setup Tab and User Info Tab can be edited On the Setup Tab the Operation mode for a channel cannot be changed only the Search Region Extraction Region and Extraction Mode can be edited It is the operator s responsibility to select valid settings while the run is paused 4 Ifthe lid is opened while the run is paused the chip can be removed and the material can be collected from the appropriate Collection wells The channels in which the extraction is complete display COLLECT in the Run Setup area on the LabChip XT XTe Main Window
11. To electronically sign a data file 1 On the LabChip XT XTe Main Window click Security gt Perform Signature The Perform Signature Window opens on top of the LabChip XT Main Window 2 Select the username of the user that is signing the data file in the Username drop down list 3 Type a comment describing the reason for the signature in the Enter Comment text box 4 If desired select Accepted or Rejected as the Approval State 5 If desired select the Lock check box to lock the data file and prevent any changes Unreviewed data files cannot be locked 6 Type the User Password for the signing user in the User Password text box 7 Click the Sign button The Signature Performed window opens to confirm the signature was performed 8 Click the OK button in the Signature Performed window The Perform Signature window closes Signature information is embedded in the data file and the signature is logged in the Audit Trail LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 87 Automatically Exporting Copies of Data Files The LabChip XT software provides the option of automatically exporting a copy of the data file xtd to a folder outside the CDR when the 21 CFR Part 11 Security option is installed The data file is copied to the specified folder after the run is complete To automatically export a copy of each data file 1 On the Output Tab on the Run File Editor Window select the Copy To chec
12. Use the De Activate User tab on the User Administration Window to Deactivate an active user or to Activate a deactivated user Users cannot be deleted from the database User names that will not be used should be deactivated to prevent unauthorized access to the LabChip XT software cu Lap in ET Leur Adrenamranen A Figure 83 User Administration Window De Activate User The De Activate User Info tab contains Option Button Function Select User Select the username to be activated or deactivated User Info Displays the information associated with the selected username Activate button Click to activate a deactivated username Deactivate button Click to deactivate an active username V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 208 Define Access Use the Define Access Tab on the User Administration Window to assign the desired rights to each access level These rights control the actions each user is permitted to perform in the LabChip XT software The Define Access tab is not available while an assay is running Laban XT Dour Admenarranen mms Tine 3 Lauren Er 7 Vir Lens Ed Saree Eca re Data Fale EE sw lk iris ls EA DE daba n CDR PEN lara COP Folders Le corra Lier Perd Vd Fort Export oral maa Rea uta i Ed 3 Teal Goce laste Fig Figure 84 User Administration Window Define Access The Define Access tab displays a colu
13. of selected tests and a separate progress bar for the test that is currently running After all tests are complete the Test Report Generation section at the bottom of the right side of the window displays the date and time when the test report was created the name of the test report log and the location where the test report was saved Test report files can be opened with a text editor such as Windows Notepad Option Button Run Tests button Runs the selected tests The Test Report Generation section displays Abort button Stops running the diagnostic tests Limits Report Generates a report that contains the limits upper and lower button for each selected test Displays date time File name Imt and location of report file Print Summary Prints the summary of the report to the default Windows button printer This button is disabled after running the Limits Report Print button Prints the details of the tests to the default Windows printer Close button Closes the System Diagnostics window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 201 Unlock Application Window For LabChip XT software with the 21 CFR Part 11 Security option installed use the Unlock Application Window to access the LabChip XT software after it automatically locks This window displays on top of the LabChip XT software when the software is locked The automatic lock option is set in the Set Policies tab on the Us
14. Click the Import Setup button at the bottom of the window The Import Fractionation Setup from XML File window opens Click the name of the run file that contains the settings for the run Click the Open button to display the saved settings in the Start Fractionation Window Edit the settings if required If desired click the Export Setup button to save the modified settings to a run file When the settings are correct go to Start the Run Click the Start button in the Start Fractionation Window to start the run A new workspace opens to display the data See Monitor the Run on page 35 for information about viewing data during the run LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 35 Monitor the Run V2 1 The following occurs after a run is started 1 The Run button on the LabChip XT XTe main window changes to Pause Stop The software performs a Connectivity Test to verify that correct voltage and current is achieved in both separation and collection modes If all four channels are enabled performs a Current Leakage Test to verify there is no current leaking between the channels All four channels are tested at full current then each channel is switched off one at a time and the currents are tested Data collection begins Data is saved to a file with the name shown above the chip diagram The Graph View displays the electropherograms of the channels being read If any channels
15. LabChip XT XTe User Manual na 5 Il rights reserved Y Ca pe r ifeSciences Copyright Trademarks Content Preface 2 Preface This manual is published by Caliper Life Sciences Inc a PerkinElmer company 68 Elm Street Hopkinton MA 01748 USA Copyright 2011 2012 Caliper Life Sciences Inc All rights reserved Reproduction by any means or in any form of this manual or the products it describes is prohibited Caliper Life Sciences Inc LabChip and the LabChip logo are registered trademarks of Caliper Life Sciences Inc The Caliper logo is a trademark of Caliper Life Sciences Inc Microsoft Windows and Windows NT are either registered trademarks or trademarks of Microsoft Corporation in the United States and or other countries All other trademarks and registered trademarks are the property of their respective holders The information in this manual may contain typographical errors or technical inaccuracies and is subject to change without notice Modifications may also be made to the product described in this manual at any time Proper Equipment Operation Contact Us V2 1 WARNINGS To reduce the risk of electric shock do not remove the cover No user serviceable parts inside Refer to qualified service personnel if help is required e Use this product only in the manner described in this manual If the equipment is used in a manner not specified by the manufacturer the protection provided by t
16. Se LO 4 o e AA Figure 59 XT Modify Run Settings Window Only the settings on the Setup Tab and User Info Tab can be edited while the run is paused Some settings cannot be changed while the run is paused The Operation for a channel cannot be changed Multistep Cut settings cannot be changed Steps can be deleted if they have not been executed yet Editing a completed step has no effect and is ignored Editing the running step is blocked with a message indicating that the change was ignored Inserting a new Collect on Click step before a running Collect on Click step does not change running step but the old step becomes the next step and executes after the running step Deleting the last running step is ignored The options available on each tab are the same options available in the Start Fractionation Window See page 186 for details LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 174 New Collection Window The New Collection window is used to create a new collection using either a Template a Blank Collection default or the Current Collection This option is only available in the LabChip XT software To open the New Collection window select Collection gt New Collection on the LabChip XT XTe Main Window New Collection A Create a new colection using Template Current Collection as Figure 60 New Collection Window The following options are available Temp
17. The following buttons are located at the bottom of the Start Fractionation window Start Starts the run using the options specified in the tabs on the Start Fractionation window Test Performs the same chip test that automatically runs at the beginning of Chip every run The chip must be properly filled with buifer but do not load any sample DNA prior to running the test Only run the chip test separately if directed by Caliper Technical Support Review Opens the Fractionation Setup Review window to view the settings for Setup the current run Import Opens the Import Sample Names window to select the desired Sample Names Name File csv LabChip XT only Import Imports the settings from a run file xml into the Start Fractionation Setup window Use the Run File Editor Window or export the desired settings to create a run file Export Exports the settings from the Start Fractionation window into a Run file Setup xml Cancel Closes the Start Fractionation window without saving any changes and without starting the run V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 188 Setup Tab The Setup Tab in the Start Fractionation Window specifies the operation the extraction mode the extraction or search region the threshold and or the collection width for each channel Some Operations allow additional extraction steps to be added to the same channel to support extracting multiple
18. 78 93 9 8 6 46 24 0 73 10 89 3 29 6 91 9 7 46 16 6 9 7 28 4 52 17 47 10 5 46 08 1 23 9 58 17 07 4 94 11 9 45 99 2 92 6 36 14 41 0 73 Figure 19 Exported Raw Data Raw data can also be exported in a Chromatography Data Interchange Format formerly AIA format which is used by some graphical analysis software tools The Include Size Data and Export Single Table options are not available with Chromatography Data Interchange Format LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Gel Exports the selected gel s in the selected image format Options are available to export the entire collection or only the selected Data Analysis 76 gels Gels can be exported into the same image file or into separate files for each gel Figure 20 shows multiple selected gels exported to the same image file LabChip XT XTe User Manual Sizing Ladder Sample 3 Sample 4 Sample 2 1000 nn ss 1000 850 a 850 700 ER 700 500 x s00 400 ms as 400 300 ee ez 300 200 i 7 150 o s Es mms Y Cf 100 mm coms cs cs 100 50 m ns ns 50 25 ms cs cs 25 Figure 20 Exported Gel Caliper Life Sciences Inc Data Analysis 77 Exporting Data Manually V2 1 If the workspace contains multiple collections the data exported is from the active selected collection Exporting data is not supported in the LabChip XTe software 1 2 3 Open the f
19. Button Copy Button Copies the selected data file to another location The copy of the data file will not be part of the CDR and will not be change controlled New Button Creates a new folder in the CDR Rename Renames the selected folder in the CDR Data files Button in the CDR cannot be renamed V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 144 Delete Deletes an empty folder in the CDR If the folder is Button not empty you cannot delete the folder Hide Button Hides the selected folder or data files from view in the CDR Manager window If a folder is selected all files and subfolders in the selected folder are hidden Show Displays all hidden data files and folders in the Button selected folder Top Right Buttons New Button Creates a new folder in the CDR Delete Deletes an empty folder in the CDR If the folder is Button not empty you cannot delete the folder Show Hide Shows or hides the filenames of all files that have Hidden Files been hidden in the CDR Manager window Button Expand All Expands all folders in the CDR to show all data files Button and folders Collapse All Closes all folders in the CDR folder Button V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 145 CDR Server Utility Window Use the CDR Server Utility Window to create a repository the Remote CDR Server Folder on a remote computer to b
20. Use the New Step button to add steps Buffer Utilization Displays an icon that represents the buffer use for the currently selected channel options Operation Specifies the action for each channel as described below Click on the channel icon to choose the desired operation for each channel e Disabled The channel is not used in the run Any channel that has already been used is automatically set to Disabled and cannot be reused e Ladder The channel contains a sizing ladder that is used to calculate the sizes in the samples in the remaining three channels during the run Only one channel in the chip can be designated as a ladder channel e eXtract and Stop The sample in the channel runs until the extraction is complete and then the voltage to the channel turns off After the extraction the run ends if no other channels are busy If channels are busy the run ends as soon as all channels are complete The extracted material is located in the Collection well Only the Flush Sample step can follow this step e eXtract and Continue The sample in the channel runs until the end of the chip range The sample specified by the Extraction Mode is collected in the Collection well In a multistep extraction the next step begins after the extracted region is removed from the collection well the instrument lid must be opened e eXcLuDe Region The sample in the channel is collected in the Waste well except for the sample spec
21. on page 109 e Error Message Area on page 110 e Run Setup on page 111 e Chip View or List View on page 113 e Collection Pane on page 116 e Graph View on page 117 e Graph View Properties on page 122 e Filter View on page 124 LabChip XT only e Gel View on page 128 e Gel View Properties on page 131 e Channel Table View on page 133 e Peak Table View on page 135 LabChip XT only e Peak Table Properties on page 137 LabChip XT only Clicking and dragging the borders between the views changes the size of the views in the collection To change the location of the views see Changing the View of the Results on page 60 LabChip XT XTe User Manual Caliper Life Sciences Inc Menu Bar V2 1 Software Reference 103 The menu bar is directly below the title bar on the LabChip XT XTe Main Window Clicking a menu name displays a list of commands to access software functions The LabChip XT XTe software contains the following menus File Menu on page 104 Workspace Menu on page 104 Collection Menu on page 105 LabChip XT only Analysis Menu on page 105 LabChip XT only Instrument Menu on page 106 Instrument mode only Tools Menu on page 106 Security Menu on page 107 Only displays if the 21 CFR Part 11 option is installed with the LabChip XT software View Menu on page 107 Validation Menu on
22. plato Figure 61 Perform Signature Window The Perform Signature Window contains the following options Data File Name Displays the name of the data file being signed Select the username of the user that is signing the data file Role Displays the Access Level of the selected LabChip XT user Enter Comment Details on why the signature is being performed and what actions have taken place lt is the signer s responsibility to ensure all details required by the company s procedures are included in this comment Approval State Displays the approval state of the data file Unreviewed data files cannot be locked Lock Select the check box to prevent any future changes to the data file Locked data files cannot be saved To unlock the data file a user with the correct permissions can choose Security gt Unlock Data File U The password for the user Sign button Signs the data file and closes the window Cancel button Closes the window without signing the data file V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 176 Print Window V2 1 Use the Print window to print information from the currently open workspace If the workspace contains multiple collections information from the active selected collection is printed To open the Print window select File gt Print on the LabChip XT XTe Main Window Lib hp AT Print A KA WER Page Opisi Table Opor Gad z Portal Ad Eis
23. the size of the fragment to allow for small variations in fragment size e Color Displays the color to use to mark the fragment in the Graph View or the Gel View e Name Specifies a name to display in the Type description for the fragment e Exclude All If selected all fragments in the specified range are excluded from analysis e Apply to Channels Specifies the channels that the excluded fragment is applied to lt All gt specifies that the excluded fragment applies to all channels Clicking on the column opens the Select Channels window to choose the specific channels to apply the excluded fragment to LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 168 Excluded Fragments Tab Continued Export button Opens the Export Excluded Fragments window to create an Expected Fragments File gep from the current settings in the tab Import the gep file into another method to use the same excluded fragments in another method Restore button Restores the settings to the last saved settings for excluded fragments Import button Opens the Import Excluded Peaks window to select an Expected Fragments File gep to import The gep file is created by exporting excluded fragments from another method Clear button Deletes all Excluded Fragments from the table V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 169 Smear Analysis Tab V2 1 Use the Smear Analy
24. 42 Sample 2 C alper Od M 2E CH2 Sample 2 000 Se PO 1500 wi EPS du Erro 100 7 157 EPST 4 pl 7 l 1000 f 1 E MJ Big A L E LU L E Eon f EA Ai he Lower Marker Peaks for DNA Assays For each DNA sample the lower marker peak is assigned first and then the data is aligned so that the channel markers match the ladder markers in time allowing the size and concentration of the sample peaks to be determined For DNA assays the peak in a sample channel that meets the lower marker criteria specified in the method file is assigned to be the lower marker and is then offset to match the lower marker in the ladder The Sample Lower Marker is aligned to the ladder marker by resampling the channel data in a linear stretch or compression using a point to point fit If there are unexpected peaks in the ladder analysis or the markers have been set incorrectly you can manually exclude peaks or seta peak to be used as a lower marker V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 58 Aligning or Unaligning the Marker Peaks Continued V2 1 NOTES e Excluding a peak or manually setting a peak to be an lower marker for a DNA assay can cause errors with analysis e You can move the boundary between the Peak Table and the Graph view up or down to increase or decrease the size of the Peak Table making it possible to see
25. 4microl Sample names containing commas must be enclosed in double quotes The Sample Name file can be created in Microsoft Excel or a similar spreadsheet program and must be saved as a csv file LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 293 Saturation Detection The LabChip XT software can be set to compensate for optics detector saturation on the Advanced Tab on the Method Window The instrument electronics saturate at approximately 3200 RFU optics detector voltage of approximately 3 2 volts When the analog amplifier saturates it switches rapidly to 0 volts output The detection is based on the very high negative slope of the signal as it transits into saturation and very high positive slope when it comes out of saturation The corrected signal is flat over the saturated region with a value equal to the maximum of the largest RFU value detected just before entering saturation and just leaving saturation The well is annotated in the Analysis Error column with the message Signal Saturation Detected Figure 98 shows a signal that saturated the electronics The left graph with the Saturation Detection option disabled shows the true signal with a saturation artifact which would seriously compromise the quantization accuracy The right graph shows the same signal with the Saturation Detection option enabled The saturation is corrected so the signal appears as expected and will quantized fairly cl
26. Filter View 124 Gel VieW 128 Graph View 117 hiding views 62 Peak Table View 135 showing and hiding 62 Voltage safety 10 W Warnings 227 Current Leakage Check Failed VVarniINd ss ske 24404260 227 IV Check Failed Warning 227 Waste disposal 8 Waste well 216 Wavelength 218 Weight 218 Window menu 108 Workspace 47 104 257 adding collection 47 opening a new workspace 45 printing 68 Saving Workspace Files 42 Workspace Menu 104 X KID Eis ss cesse 46 257 KIE Wes enseres ven 258 Z Zero baseline 44 60 258 Zipping log files 200 ZOOM RE ER RE Re rr 62 Zoom OuUt 62 V2 1 LabChip XT XTe User Manual Index 269 Caliper Life Sciences Inc D Y Caliper Caliper Life Sciences Inc 68 Elm Street Hopkinton Massachusetts 01748 TEL 508 435 9500 FAX 508 435 3439 http www caliperLS com
27. Inc Instrument Safety 9 Laser Safety V2 1 WARNING AA e The Red Barcode LED is a Laser Class 1M device safe under reasonably foreseeable conditions of operation with the naked eye Looking directly into the source of radiation by employing optics within the beam such as a magnifying glass telescope or microscope can be potentially hazardous e Caliper LabChip XT XTe Instruments contain Class 3R Excitation laser diodes The LabChip XT XTe is classified as a Class 1M device because the lasers are appropriately enclosed embedded and indicated with Warning labels e Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous radiation exposure e This instrument is not intended to be serviced at the customer site e NEVER remove instrument covers while the laser is powered The laser block assembly is marked with the label shown below Barcode LED Red 625nm wavelength 4 5 mW maximum continuous CW in box Excitation Laser Green 532nm visible green laser source 5 mW maximum continuous CW Complies with FDA performance standards for laser products except for deviations pursuant to Laser Notice No 50 dated 6 24 2007 amp IEC EN60825 1 2007 LabChip XT XTe User Manual Caliper Life Sciences Inc Instrument Safety 10 Electrical Safety The LabChip XT XTe is powered by a UL CSA VDE CE approved 100 240 VAC 50 60 Hz input 24 VDC output extern
28. LabChip XT software and then restore the CFR files Setting the CDR folder as accessible 1 6 7 8 Log in to the computer with a User Name in the Administrator group For Windows 7 Right click on the LabChip XT icon on the Windows desktop and select Run as Administrator For Windows XP Double click on the LabChip XT icon on the Windows desktop Log in to the LabChip XT CFR software as the Administrator user On the LabChip XT main window select Tools gt CDR Utility The CDR Utility Window opens Select the Accessible by Windows Administrator Level Users check box and then click the Apply button Click OK in the Confirmation window Click the Close button on the CDR Utility Window Close the LabChip XT software Restoring the CDR Folder 1 V2 1 In Windows Explorer navigate to C Program Files Caliper Life Sciences Delete the existing CDR folder Copy the backed up CDR folder into the folder See Backing Up CFR Files on page 97 LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Software Security 100 Setting the CDR folder back to not accessible 1 5 6 7 For Windows 7 Right click on the LabChip XT icon on the Windows desktop and select Run as Administrator For Windows XP Double click on the LabChip XT icon on the Windows desktop Log in to the LabChip XT CFR software as the Administrator user On the LabChip XT main window select Tools gt CDR Utility Th
29. Layout Options Window 155 EE OE EE EE 214 Line Voltage 218 Loading a chip 33 Ho les ms too RR 247 Log files dee sie KALE OR rn ee 235 Login Window 156 Lower Marker 247 Quantification 171 M Main window 102 Maintenance and Service 220 Cleaning the electrodes 221 Manual export 77 Manual peak 55 Manually exporting data 17 Marker 44 160 UNI riera hb oa ee eae ae 57 Assigning 44 concentration 160 LM for DNA 57 Not detected 44 EPA EP PS 160 Marker Drift Tolerance 171 Maximum Graphs per Page 122 Menu 103 104 105 106 107 108 Analysis menu 105 Collection Menu 105 File menu 104 V2 1 LabChip XT XTe User Manual Index 266 Help menu 108 Instrument menu 106 Menu Bar 103 Security menu 107 Tools menu 106 Validation menu 107 View menu 107 Window menu 108 Workspace Menu 104 Merging two peaks 56 Method Method file 247 Method Window 157 Microfluidics 247 Migration Time 44 Min P
30. OTHER PROMISES REPRESENTATIONS AND WARRANTIES EXPRESSED OR IMPLIED THIS INCLUDES BUT IS NOT LIMITED TO THE PRODUCTS CONDITION ITS CONFORMITY TO ANY DESCRIPTION OR REPRESENTATION THE EXISTENCE OF ANY LATENT OR PATENT DEFECTS AND IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT WILL CALIPER BE LIABLE WHETHER ARISING IN CONTRACT TORT INCLUDING NEGLIGENCE STRICT LIABILITY OR OTHERWISE FOR ANY LOSS OF PROFIT OR ANY OTHER COMMERCIAL DAMAGES INCLUDING BUT NOT LIMITED TO SPECIAL INCIDENTAL CONSEQUENTIAL OR OTHER AND IN NO EVENT SHALL CALIPER S LIABILITY EXCEED THE PURCHASE PRICE OF THE PRODUCT THERE ARE NO ORAL STATEMENTS PROMISES REPRESENTATIONS OR OTHER WARRANTIES COLLATERAL TO OR AFFECTING THIS WARRANTY THIS WARRANTY EXTENDS TO BUYER ONLY AND NOT TO PURCHASERS OR USERS OF BUYER S PRODUCTS No agent employee or representative of Caliper has any authority to bind Caliper to any affirmation representation or warranty concerning a Caliper product that is not contained in Caliper s printed product literature or this Warranty Any such affirmation representation or warranty made by any agent employee or representative of Caliper will not be binding on Caliper P N 113642 Rev 03 Caliper Life Sciences Inc Caliper Life Sciences Inc Software License Agreement 261 Caliper Life Sciences Inc Software License Agreement Thank you for purchasing our products PLEASE READ THE TERMS AND CONDIT
31. The csv file includes the columns in the order displayed in the Channel Table at export time The csv file can be opened in Microsoft Excel If the workspace contains multiple collections the data is exported from the active selected collection Exporting the Channel table and opening multiple collections are not supported in the LabChip XTe software V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 135 Peak Table View V2 1 The Peak Table view in the Collection Pane is a text based representation of all the information about each peak To view or hide columns in the Peak Table view right click on the column headers in the table The Select Peak Table Columns window displays all available columns and the currently selected channels Show columns in the Peak Table by moving the column name to the Selected Columns list Hide columns by moving the column name to the Available Columns list Tere Table Peak Table Fit Figure 35 Peak Table View To change the order of columns in the table click on a column header and drag the column to the desired position in the table Click a column header to sort the table in ascending descending original order The analysis normally labels the lower marker LM in each sample and in the ladder The labels display in the Type column of the table If the analysis has misidentified the markers the correct marker can be selected manually by right
32. This License Agreement does not convey to you an interest in or to the Program but only a limited right to use it revocable in accordance with the terms of this License Agreement In the event of a breach the Licensor reserves the right to seek eduitable relief License Fees The license fees paid by you in connection with the purchase of the associated product s are paid in consideration of the licenses granted under this License Agreement Term This License Agreement is effective upon your opening of this package and shall continue until terminated You may terminate this License Agreement at any time by returning the Program and all copies thereof and extracts therefrom to Licensor Licensor may terminate this License Agreement upon the breach by you of any term hereof Upon such termination by Licensor you agree to return to Licensor the Program and all copies and portions thereof Limited Warranty Licensor warrants for your benefit alone for a period of 90 days from the date of the commencement of this License Agreement referred to as the Warranty Period that the Software Media in which the Software is contained are free from defects in material and workmanship If during the Warranty Period a defect in the Software Media arises you may return the Program to Licensor for either replacement or if so elected by Licensor refund of amounts paid by you under this License Agreement You agree that the foregoing constitutes your s
33. Threstiold Example ss ainia ia 244 El OE OO N EE Ge AE 246 LAA 246 Ladder Analysis AA og GE EG Ge DE oe EE EE 247 LOWER id 247 LOOG FIGS PR a geee eds a sebseent here a E i 247 Method FiO EE A EE DE GE AO DE EE 247 KCO E a TS 247 Minimum Peak Helfte end de aa 248 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Table of Contents 17 Minimum Peak VVIGUIN 2 055 occa nies as GO ee EE DE 248 A ete DE ce et nd 248 Molecular Separation Techniques eise ee se se se Ee Ee Ee Ee ee ER ee Ee ee ee ee ee ee ee ee ee 248 Peak Basculas EE 249 Peak Field EE EE RE EE EE DE ee EE ER ek De ed 249 PEAK Identification Ese EE DE DE ie De EE AR DE EE DS ad cut 250 PFOIMEtO PON TAL GE ER AS 250 Ono mial Filters O ne 250 POW MORIA OTAG ss dede en en en 251 A ne bed nl dat nan ae te 251 Sample Name File ans re naar ner nn ete 252 Saluraton D tection a 253 SlobeThreshold s ES id 254 SA LA ES Ed RE N OR 254 mear Bas SMO EE EE ND EG GE GG US 255 Standard Curve Wind OW EE ER bode ha Ge De ee EE 256 Sa Pol Ese ed GE ED N Ge GE Ee ee GR ee 256 NS ar A A GE E Ne 256 Tool TEE EE O ne D 257 WOKS EE ES a EE Een RR GE DE OG EE de ne DE ee ce OE 257 KT DS FIGS NSR GE TO 257 TE Elle LR ut de deu he De ge css Se dede 258 FET CEs LE EE GE en Ge a A cos 258 Caliper Life Sciences Inc Product Warranty sees Ekke EER RE REK RE RE ER ER ER ee RE Re 259 Caliper Life Sciences Inc Software License Agreement 261 Vale
34. User Manual Caliper Life Sciences Inc Glossary of Terms 256 Standard Curve Window Only the LabChip XT software supports viewing or changing the Standard Curve The Standard Curve window shows the standard curve used for the selected chip data When you choose Standard Curve from the Analysis menu for a DNA assay a window similar to Figure 101 opens The standard curve is drawn from the values obtained for the DNA ladder lt is a plot of the size of the ladder peaks vs time with a point to point fit For each sample peak the apex is interpolated from the Standard Curve to determine the peak size in base pairs BP kem Copy Fi Figure 101 DNA Assay Standard Curve For more information about the use of the standard curve during analysis see How the Software Analyzes DNA Data on page 44 Start Point The peak find algorithm analyzes the data from time zero looking for a slope greater than the Slope Threshold The point where the slope is greater than the slope threshold specified in the Peak Find Tab is marked as the start point of a peak Start Time This setting determines the time after the start of a run when peaks will be detected Any peaks appearing before this time are ignored V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Tool Tip Glossary of Terms 257 small box containing text that describes the item indicated by the mouse pointer To view a Tool Tip position the cursor over an ite
35. an up arrow 2 Select Add Manual Peak from the shortcut menu new peak of type MP is created 3 If necessary adjust the Peak Baseline Excluding a Peak V2 1 You can exclude any peak or fragment from being used in the analysis To exclude a peak 1 Inthe Peak Table View right click on the peak to be excluded 2 Select Exclude Peak from the shortcut menu The Type for the peak changes to X excluded and the value is not used in the analysis 3 Right click on an Excluded Peak in the peak table and select Include Peak to include the peak in the data analysis OR 1 Inthe Graph View right click near the top of the peak to be excluded 2 Select Exclude Peak from the shortcut menu The Type for the peak changes to X excluded and the value is not used in the analysis 3 Right click on an Excluded Peak in the Graph view and select Include Peak to include the peak in the data analysis LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 56 Merging Two Peaks If the analysis has defined two separate peaks the two distinct adjacent peaks can now be merged into one peak in the LabChip XT or XTe software This will include the area of both peaks in the total concentration and percent purity calculations To merge two adjacent peaks 1 Exclude one of the peaks from the analysis following the procedure Excluding a Peak on page 55 Verify that Show Peak Baselines is selected in the Gra
36. background displays behind the text Displays COLLECT on a green background when the extraction for a channel is complete and the run is paused either automatically or manually Pausing the run and then opening and closing the lid to remove the sample from the Collection well changes the display to the trigger for the next step in the channel or to DONE if the extraction is complete in that channel If the run is paused but the lid is not opened the channel continues to display COLLECT Displays DONE when the extraction is complete in each channel V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 113 Chip View or List View The Chip View or List View displays on the lower left side of the LabChip XT XTe Main Window in the LabChip XT software The List View is not available in the LabChip XTe software The Chip View or List View displays the data files in the open collection and enables you to select specific channels of chip data Click the tabs at the bottom of the view to switch between Chip View and List View Chip View Chip View Right Click Menu Right clicking on the chip name in the Chip view displays the following options in the shortcut menu Save Chip Saves the current data file Copy Chip Saves a copy of the chip data file xtd for LabChip XT or xte for LabChip XTe to the selected folder Rename Chip Renames the chip in the workspace If the Rename File to Match check
37. collection to the default Windows printer Cancel button Closes the Print window without printing V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 178 Print Validation Reports Window Use the Print Validation Reports Window to print the results after performing Installation Qualification IQ or Operational Qualification OQ OQ is performed in the System Diagnostics Window To open the Print Validation Reports Window select Validation gt Reports on the LabChip XT XTe Main Window Print Wabdation Reports A Rept Opbors fel Sra HI Baron Faded Tests Oriy Report Period From Lot And 1 10 hi To Acordar Mey 172010 WM Para By A Ve Pans Figure 63 Print Validation Reports Window The Print Validation Reports Window contains Option Button Diagnostics Report If selected the results of Hardware OQ tests are printed Software IQ Report If selected the results of Software IQ tests are printed Failed Tests Only If selected only tests that have failed are printed If not selected both passed and failed tests are printed Report Period Specifies the dates when the tests were run Tests performed between the From and To dates inclusive are printed Print Preview Displays a preview of the report and enables you to print or button export the results Print button Opens the Print window to print the report Close button Closes the window V2 1 LabC
38. column name to the Available Columns list LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 134 Channel Table View Continued Change the order of columns in the table by clicking on a column header and dragging the column to the desired position in the table Click a column header to sort the table in ascending descending original order Right click in the Chip Name column to open the Rename Chip window to rename the chip The Data file can also be renamed by selecting the Rename File to Match check box if the 21 CFR Security option is not installed Right click in the Sample Name column to edit the channel name or copy the row to the clipboard Right click in the User Comment column to add or edit the User Comment or copy the row to the clipboard Analysis error messages display in the Channel Table View Most are the result of peaks not being located by the analysis algorithms This can be due to a sample or ladder peak not appearing as expected In the LabChip XT software the settings in the Peak Find Tab can also cause peaks to be undetected Manually excluding a peak see page 55 from analysis in the Peak Table View or changing the start or end times for a run can also cause errors with the peak find algorithm in the LabChip XT software The Channel table in the LabChip XT software can be exported to a csv file by choosing Export on the File Menu see Exporting Data on page 74 for details
39. database are searched database Username text Select a specific user name to view only events performed under DOX the specified user name Select All Users to view events performed by any user Filename text Clicking the Browse button opens the Audit Trail CDR DOX Browser window to open the audit trail for a different data file V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 141 Event Category Specifies the Event Category of events to search for Default selects all event categories Green Arrow Displays the Audit Trail Manage Columns Window to select the button columns to view in the Audit Trail window Search button Searches for events matching the search criteria specified Export button Opens the Audit Trail Export Window to export a copy of the selected events out of the audit trail log Displays a preview for printing the Audit Trail Report button Close button Closes the Audit Trail Window Audit Trail Export Window Use the Audit Trail Export Window to export the contents of the Audit Trail Window to either an ASCII text file and XML file or a Microsoft Excel file Only the events displayed in the Audit Trail Window are exported Events filtered out of the view are not exported Only available if the 21 CFR Security option is installed with the LabChip XT software To open the Audit Trail Export Window click the Export button in the Audit Trail Window E AuditTrai
40. ee Re 228 DIAGROSTICS EE IS ie EG haa Se DE ee tn 229 Running the Diagnostics Tests Ee se se se Ee Ee Ee Ee Ee ee ee ee ee ee ee ee ee ee ee ee ee ee 229 Description of Diagnostic Tests ss EE EE chen ee Ee ie PS DS EE GE ER Ed EE DES 230 Troubleshooting Assay Problems is sesse Ee EE ER Ee Ee ER ER RE Re Re Ee be Ee Ee ER ER Ee Ee ee ee 282 SOMWare POD MS ida 233 Cannot Save a Fleur oe Ge Ge Ge E Ge ee 233 Computer Software Lock UpS siese ee ee ee ee ec Ee ee Ee Ee Ee Ee Ee Ee Ee ER ee ee Ee ee ee ee ee ee ee ee ee 233 Software Display Flashes EE SE ds 234 APPO INS Log FIE ren te taa tne ane ee EE Tete EE Ge 00 235 THS ANA VOC UES asia dida 236 Glossary of Tefies ie SE re SE EE GE OE sense ER De etait te ee 231 APOK AE RA ER EE AE ORE OE EE 238 A EA a EE idee 239 D 0 6 MR RTE A ON EED 240 CMD O ANG EE ER EE AI AE EA EED HE ENE ERG 240 COIS CU Olds EE a EE De Ee Ee 240 Collection Template se DA ida 240 Collection Well ii ears 241 WAV ARE WES A Ge N Ee 241 Data POM Sister older 241 Data FINGTING PR e iia EE 242 DNA Assay AnalysIS 0 A Se GE a dead 242 Electrode Cll anemia ER GE Ge De GE oe Ge be Ge Ee 242 Ele irokineti FO COS ee ES GE EG Ge ie De EE IN 243 Elecifoosmotie FOW iia Dee a de ee ee EG Ge ee ee ie be GE 243 Ele lophoies IE ER de ee ae an ER OE ED de ooie 243 Ed PONE SE SE EE DE Re ee eo 243 Eie FINE acia coto N ee 243 PUIG de RE OR EE EE EE N ER 243 Hardware DlAGMOSIICS boe cd de toe do 244 Infl cion
41. existing method and then saving the method with a new name Only the pre defined Caliper method files are available in the LabChip XTe software To create a new method 1 On the LabChip XT XTe Main Window select Tools gt Method Editor The Select Method To Edit window opens 2 Select the name of the Method file that you want to edit and click the OK button The Method Window opens and displays the settings for the open method 3 Modify the settings as necessary for the new method See Modifying Analysis Parameters or Reanalyzing a Data File for information on setting or changing analysis parameters 4 Click the Save Method button at the bottom of the Method window specify the desired name for the new method file and click the Save button NOTE 1 All method files must be saved in the C Program Files Caliper Life Sciences LabChip XT Assay folder Only the methods saved in this folder are available in the Fractionation Method list in the Start Fractionation Window and the Run File Editor Window LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 40 Saving Data Files V2 1 While running a method the raw data received from the instrument is automatically saved to the data file xtd for LabChip XT or xte for LabChip XTe If a run is stopped before it is complete the data that has already been collected for the run is saved in the data file The name of the data file is specified in the Output Tab
42. in each case at Caliper s option Parts replaced during the Warranty Period will be covered for the remaining term of the original Warranty Period or for thirty 30 days from time of replacement whichever is longer Such replacement parts may at Caliper s option be new or remanufactured All parts removed from warranted equipment become the property of Caliper Caliper reserves the right to satisfy its warranty obligations in full by refunding the purchase price of any non conforming product minus any service validation or travel charges B Customer Responsibilities In order for a product to be covered under this Warranty Customer must comply with the following terms e The equipment must be used under normal installation and application conditions as described in the products User Manual e The equipment must be maintained as described in the User Manual e Only water or DMSO at a maximum concentration of 65 may be used as a system fluid in the Sciclone inL10 Any other system fluid must be approved by Caliper before use in the inL10 e When Caliper provides telephone fax or email support Customer is responsible for completing any necessary documentation of the service e If Customer maintains a change control validation logbook as a permanent record then Customer is responsible for entering all service documentation into such logbook e Customer must perform the appropriate level of revalidation required as a result of the mainte
43. in each collection Only the LabChip XT software supports multiple collections in a workspace To add a new collection to an open workspace 1 On the menu bar select Collection gt New Collection The New Collection Window opens Select the desired option for creating the new collection e Template Opens a new collection with the same settings as a saved collection template file e Blank Collection Opens a new template using the default collection settings e Current Collection Opens a new template based on the current settings in the currently open collection If no chips are open in the collection choose the desired Assay Type for the collection DNA Only data files from the selected assay type can be imported into the workspace If desired type a new name for the collection in the Name text box Click the OK button to open the new collection LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 48 Using Expected Fragments You can track expected DNA fragments EFs for the samples in a DNA assay in the LabChip XT software The LabChip XTe software does not support defining Expected Fragments Entering EFs in the Method Window V2 1 Only supported in LabChip XT software 1 10 11 Select Analysis gt Analysis Settings on the Menu Bar The Method Window opens Click on the Expected Fragments Tab Click in the bottom empty row in the table In the column labeled Size ent
44. in minutes at which the center of the peak reaches the detector Size BP The size of the peak based on the ladder sizes specified in the assay Height The height of the peak Aligned Area The area of the peak after the data has been aligned with the ladder Used to calculate the concentration Conc ng uL The concentration calculated relative to the ladder and marker peak concentrations The ladder concentration is displayed in the Analysis Tab of the Method Window This value represents the concentration of each fragment as was present in the sample well To compute the fragment mass multiply by the sample volume in uL Purity The ratio of peak concentration to total concentration above the lower marker in the sample Molarity nmol l Displays the molarity of the peak Peak Table View Shortcut Menus Right click on a peak in the peak table to display a shortcut menu containing the following commands e Exclude Peak e Force Lower Marker e Force Expected Peak NOTE Excluding a peak or manually setting a peak to be a lower marker can cause errors with analysis LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 137 Peak Table Properties To view the Peak Table Properties click the Properties tab on the right side of the Peak Table View Properties hd Hide eocluded praks Expected Feaks Onhy _ Fiterad Peaks Oriy fe Show All Peaks _ Selected in Gel a Entire
45. of the filter and shows what peaks may resemble if the filter application is too strong V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 291 Polynomial Order This setting on the Peak Find Tab in the LabChip XT software determines the order of the polynomial filter used to convolve with the data A polynomial filter is used to filter the data to increase the signal to noise ratio and calculate filter slope information for peak detection The default setting is 6 for 6th order Run Button V2 1 To begin running an assay click the Run button located on the graphic of the LabChip XT XTe instrument at the top left of the LabChip XT XTe Main Window The Start Fractionation Window opens to select the method channels data file name etc After the run has begun this button changes to Pause Stop See Stop a Run on page 38 NOTE u The Run button does not display if the software was installed in Reviewer mode LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 252 Sample Name File V2 1 Use a Sample Name file to import the desired sample names into the Run File Editor Window or the Start Fractionation Window LabChip XT only The entries in the Sample Name file must be formatted as shown below with one pair on each line lt Channel Sample name gt Example CH2 1ug of 2 5k gDNA Smear 1k extraction CH3 2ul library CH4 HL60 500 ng starting
46. other program Choosing Copy Gel copies all of the channels displayed in the Gel View with the labels as part of the graphic To copy a gel right click in the Gel View and choose Copy Gel Choosing Copy Lane copies the selected channel in the Gel View with the labels as part of the graphic To copy a gel right click in the Gel View and choose Copy Lane Right clicking in the Electropherograms Tab and selecting Copy places a graphic of all the channels displayed in the Electropherograms tab on the clipboard Right clicking in the Overlay Electropherograms Tab and selecting Copy places a graphic of the entire Overlay Electropherograms tab on the clipboard Copying rows from the Channel Table View places selected channels on the clipboard To copy a row or multiple rows select the desired rows in the table right click on one of the selected rows and select Copy Rows to Clipboard Copying columns from the Channel Table View is only available for certain columns in the table To copy a column select a single cell in the column right click on the cell and select Copy Column to Clipboard V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 67 Reanalyzing a Data File Occasionally you may need to open and view or reanalyze a data file that was run and saved previously The raw data values are saved in the chip data file along with the original analysis settings that were chosen for the run and any changed a
47. page 107 Window Menu on page 108 Help Menu on page 108 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 104 File Menu The File menu contains the following commands New Workspace Creates a new blank workspace LabChip XT only Open Workspace Opens a saved workspace All data files in a workspace must be the same type LabChip XT only Import Data File Opens a saved LabChip XT XTe data file for a specific chip If the 21 CFR Part 11 option is installed opens the CDR Manager Window graphical representation of the chip displays Data files are file type xtd LabChip XT or xte LabChip XTe Export Opens the Export Window to choose the type of data to export Exports a Peak Table Channel Table Gel Single Graph or all open graphs in the current Collection to a file depending on the options selected LabChip XT only Print Opens the Print Window to choose the data to print Save Workspace Saves the current workspace LabChip XT only Save Workspace As Saves the current workspace with a new filename LabChip XT only Exit Closes the LabChip XT XTe software Workspace Menu The Workspace menu contains the following commands Remove Chip Removes the selected chip data file from the workspace Save Chip Saves the chip data file xtd for LabChip XT or xte for LabChip XTe Changes to the analysis settings in the Method Window are saved at
48. peaks 56 Peak Find Tab 161 Peak integration mode 171 Peak Table View 135 Show Peak Baseline 122 Valley to Valley Baseline 171 Peak Find Tab 161 Peak Table 135 exporting 14 BEIDE e ermano 12 Properties 137 Perform Signature Window 175 Point to point fit 160 250 Pollution Degree 218 Polynomial 44 161 242 250 251 PIE so ode satire ares 250 PR ONE N Ro dei 160 Order 161 242 251 Power cable 213 Power cord selection 10 Power Input Specification 218 Preparing a chip 33 Preparing and Running An Assay 33 Print A 68 Print Validation Reports Window 178 Print Window 176 PRICING amp E D oc RU 68 Channel table 71 electropherogram 69 De in st ser 69 peak table 12 Run Report 13 V2 1 LabChip XT XTe User Manual Index 267 Workspace information 68 Properties Gel View 131 Graph view 122 Peak Table 137 Q Quantification 171 Quantitation 20 44 R Raw Data exporting 15 Reanalyzing data 67 Rename Collection Window 179 Reports printing 68 Restore
49. ranges of material from the same channel For Extraction Modes that are centered on the trigger point for any mode except Size Range or Manual Width for Peak Max and Smear Max the distance on the chip between the detection point and the switch point provides time to divert the sample to the collection well as long as the collection width is not too large Fronton Lattes ET DARA 200 t Channel 1 Tew Sien lA ME ep Cu A a E y 1 of Set Tea De z haat j a tn Carcel Figure 71 Setup Tab The Setup tab contains the following options and settings for each of the four channels on the chip Sample name Displays the name of the sample in the channel To change the name type the desired name in the text box Channel Number Displays the number of the channel on the chip V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 189 Setup Tab Continued V2 1 New Step button Adds another step to the channel to create a multistep extraction Use the up and down arrow buttons to display each step If you want the run to pause after an extraction to enable you to remove the extracted sample from the collection well select the eXtract and Pause operation Click the small gray X button above the step number to delete that step from the channel Step Displays the selected step in a multi step extraction Click the up or down arrows to display the settings for the desired step
50. regions at the beginning and end of the trace During extraction when the end of the signal has not yet been reached the baseline uses a single value averaged over the Baseline region at the beginning of the trace Two Point is the default selection e Peak Baseline The local baseline computed for peaks is used as the smear baseline The baseline is a straight line from the beginning of the smear region to the end of the smear region and follows the local peak baseline The Two Point baseline option is best for traces where both ends of the signal return cleanly to background levels If there are local artifacts before the lower marker after the upper marker when used or at the end of the trace the Two Point baseline may shift above the smear trace resulting in poor quantization of the smear Figure 99 shows a trace with a large sample artifact after the upper marker which elevates the two point baseline a a i Figure 99 Smear with Poor Two Point Baseline Figure 100 shows the same smear using the Peak Baseline option Note that the smear baseline drops to the local baseline at the end of the smear Figure 100 Peak Baseline Option for Smear The Peak Baseline option is not a good choice for very shallow smears which do not rise above the Peak slope threshold The peak baseline will follow up into the smear and the smear baseline will depend strongly on where the smear extends are set LabChip XT XTe
51. se se see ee ee ee ee Ee Ee Ee Ee Ee Ee Ge ee 82 Changing A ce ss RIAMIS SR ee IN MSIE GE GE GE EG GO DE DE Ge 83 PRIME ACCESS RIGE EE OR ela en be ER Ge 84 Setting Policies for User Accounts UV 84 Printind User ONCICS tic o SNS oe ee ED ES RES ie oe nee 89 Electronic Signatures Re a EE EE OGE cn DE ie 86 Automatically Exporting Copies of Data Files ese se see ee Ee Ee ee ee Ee Ee ee ee ee ee 87 Reverting to a Specific Data File Revision 87 AUCIE Ni PP GEES EE ET OK AR AE RA OE EN 88 WICWIIIG ne Audit Trail ss EE nr a Ee 89 Exporting the Audit Trails ke oe ie ee DEE ee sente 89 Central Data Repository CDR HEER ans en en 90 CDR Security suggestions Ee era een ont Race hee a EE 90 Creating New Data Folders ss 91 Moving Data Files into Folders ee Re be Ee ee ee ee 91 Deleting Data FOldelS ista 91 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Table of Contents 14 Hiding Data Files in the CDR Manager Window ee ee se ee Ee se Ee Ee ee Ee Ee ee 92 Showing Hidden Data Files in the CDR Manager Window 92 Remote CDR Server Backup 93 Setting Up the Remote CDR Server 93 Backing Up Data Files to the Remote CDR 95 Restoring Data Files from the Remote CDR 96 Manually Backing Up and Restoring the CFR Files 97 Backing UPEFREIESI SS n ee aa 97 FRESIONING CFR AMOS cid italia adria 99 Software Reterence cu a a hase lO DES 101 LabChip X
52. separations in the chip channels Barcode Reader Reflects the barcode label on the chip so it can be read by the Mirror barcode reader inside the instrument Barcode Reader Window for barcode reader to read the 2D matrix barcode on Window the chip Chip Locator Recessed area to hold the chip in the correct position for the electrodes to contact the electrode pads on the chip and to align the chip with the optical windows Optical Windows Windows for laser to illuminate channels and detector to read fluorescence High Voltage Interface Supplies DC voltage to the separation channels in the chip via pins on the lid that contact electrode pads on the chip HV channels run in constant voltage mode V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Optics LabChip XT XTe Instrument Description 215 The LabChip XT and XTe optics provide fluorescence detection 532nm green excitation and 547 750nm green to red emission for DNA chips and methods Green Laser The LabChip XT and XTe instruments include high intensity 532nm green lasers to excite fluorescence in microfluidic chips Focusing Alignment and Calibration The LabChip XT and XTe instruments are optically focused aligned and calibrated at the factory The optics does not require alignment or focusing An optical test chip is available for instrument performance verification by the customer Photodiode Detector The LabChip XT and XTe use a silicon photod
53. subdirectories 45 Create New User Tab 204 Current Leakage Check Failed Warning 227 Curve fit 250 Customer Support plans 3 D Data Analysis 43 44 How the Software Analyzes DNA DONA a a eee 84 44 Data File 46 60 241 257 258 evaluation 60 opening 46 reanalyzing 67 reverting to revision 59 Data Flle Version Window 149 Data file copying 30 Data filtering 44 242 Data points 241 Data Range 160 De Activate User Tab 207 Define Access Tab 208 V2 1 LabChip XT XTe User Manual Index 264 Detection Wavelength 219 Detector 215 Device Disconnected Error 226 Diagnostics 229 running tests 229 Disconnected Device Error 226 Display problems 234 DNA Assay Analysis 242 DONE 404424444444 EER 40004853 112 DOO Ed PROE TR 4 eee hese ees 212 E Edit Users Tab 205 Electrical safety 10 Electrode Cleaner 242 Electrodes 214 cleaning 221 Electrokinetic Forces 243 Electroosmotic Flow 243 Electropherogram Graph View Properties 122 DNA a gg EE ee er rs 69 Electropherog
54. the LabChip XT software Features that are only available in the LabChip XT software are identified in this manual Chip and Reagent Kits which include the required reagents and consumables are available to run specific assays on the LabChip XT XTe Contact Caliper to order Assay Kits This manual includes general instructions for using the LabChip XT and XTe hardware and software lt includes general procedures for operating the system analyzing the data using software security to comply with 21 CFR Part 11 requirements instrument maintenance and hardware and software troubleshooting V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Introduction 19 Assay User Guides Assay User Guides provide information about the assay Instructions for preparing the chip and the sample are included in the LabChip XT Assay User Guide for the specific assay that you are running Detailed information about the assay including Specifications Safety Warnings Preparation Procedures Expected Results Troubleshooting LabChip Kit Essential Practices and Reordering Information is also located in the LabChip XT Assay User Guide for the assay Assay Quick Guides Assay Quick Guides are included with each Assay Kit and include instructions for preparing the chip to run an assay The current version of the Assay User Guides and Assay Quick Guides can be accessed on the Caliper web site at http www caliperls com support referen
55. the chip where the sample is diverted to either the waste or collection well Barcode Label The 2D Matrix barcode used to identify the chip in the LabChip XT or XTe instrument V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 217 USB Key for 21 CFR Part 11 Option If the 21 CFR Part 11 option is installed in the LabChip XT software the USB Key must be plugged into a USB port on the LabChip XT computer If the USB key is not plugged in the LabChip XT software displays an error message when starting and then shuts down The 21 CFR Part 11 Security option is not available for the LabChip XTe software Figure 90 USB Key for 21 CFR Part 11 Option V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 218 Specifications This section lists the technical specifications for the LabChip XT and XTe instruments Technical specifications are subject to change without notice General Size 7 09 H 180mm H lid closed x 7 09 180mm W x 12 99 330mm D additional 7 178mm required above instrument to open lid Weight 10 Ibs 4 6 kg Chip Capacity one 4 channel chip Ventilation 3 77 mm minimum space required around instrument for proper Cooling air flow Environmental Operating Temperature 65 to 82 F 18 to 28 C Operating Humidity 10 to 70 relative humidity noncondensing Storage Temperature 5
56. to save data files unless the data files in the workspace have been modified LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Data Analysis 43 Data Analysis After a run is complete use the LabChip XT or XTe software to view and analyze the chip data The LabChip XT and XTe software can open multiple data files in the same workspace to compare the data from different chips In the LabChip XT software analysis settings can be changed for single channels entire chips or all chips in the workspace This section contains the following information e How the Software Analyzes DNA Data e Organizing Retrieving and Backing Up Data Files e Opening a New Workspace LabChip XT only e Opening a Data File e Adding a Collection to a Workspace LabChip XT only e Using Expected Fragments LabChip XT only e Modifying Analysis Parameters LabChip XT only e Reverting to a Specific Data File Revision LabChip XT only e Changing the View of the Results e Copying Information e Reanalyzing a Data File LabChip XT only e Printing Workspace Information e Exporting Data LabChip XT only LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 44 How the Software Analyzes DNA Data The LabChip XT and XTe DNA Assay Analysis calculates the size of nucleic acid fragments during the run to provide accurate extraction of the desired fragment sizes Three options are available for calculating the fragment size
57. user can unlock data files Edit Users Use the Edit Users tab on the User Administration Window to edit an existing LabChip XT user account Ed Lakh XT Oder Adminmirabomn Ss Va Ek Le Lee Here User Dne eer in Edit na E a Dos Fi Mars Jobn Hidde Hyrre AE Lover Hiera Doe Penis hochnician a Activado Unes ce Level tt er Car Gaan re if Er Accept Part Look data Me sf Loc data de wf Set Fok bet eer Passe he Figure 81 User Administration Window Edit Users The Edit Users tab contains Option Button Select User to Edit Select the Username for the account to edit The first name of the user Middle Name The middle name or initial of the user The last name of the user If desired the job title of the user The Access Level of the user User Can Perform If selected the user can sign data files using the Perform Signature Signature Window Accept Reject Lock If selected the user can accept reject and lock data files Data File using the Perform Signature Window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 206 Unlock Data File If selected the user can unlock data files Edit User Password If selected the user s password can be changed Password Type the desired password for the user The password must meet the password policies selected on the Set Policies tab Confirm Password Repeat the desired password for the us
58. window 157 turning on off 57 Analysis IAD 12 402515 160 Annotation Annotate expected peaks 122 od ES TREE 122 ADR ne EE ER ETE 44 238 PSSA Er na KA SR 642 EE Ee 20 23 Assay Information Tab 199 Assay User Guides 23 Assay Voltage 219 GEES anses 64 0444 45 4 KO 159 Comments 159 Method window 157 Name 159 Principles 20 Starting a RUN 23 TUE as sd sa as EES 159 Audit Trail Export Window 141 Audit Trail Manage Columns Window 142 V2 1 LabChip XT XTe User Manual Index 263 Audit Trail Window 140 Auto Export selecting settings 31 Auto Export window 151 B Backing up data files 45 DaliodE ss da ns cee ene ee eas 219 Barcode Engine 219 Barcode reader 2719 Supported Barcode Types 219 Baseline 44 160 161 239 249 Algorithm 161 Analysis Tab 160 SL OR 4 655d se RR os 249 Plateau 44 161 Smear 255 Baseline Plateau changing 54 DUDOIC ss sa ir iS demande 6545 240 C Cable connectors 213 Calibration ODUCS es AE 215 Caliper Center for Training and Development 3 Cannot save a file 233 CDR Folder 146 CDR Manager Window
59. 0 to 104 F 10 to 40 C Storage Humidity 20 to 70 relative humidity noncondensing Transient Overvoltages Installation Category II Overvoltage Pollution Pollution Degree 2 Altitude Up to 2000m Electrical Power Input 1 0Arms max at 90Vac 47 63Hz 0 6GArms max at 264Vac 47 63Hz Input Voltage 100 127 200 240V nominal 90 264V maximum operating range Power Consumption 24VDC 1 2A max Fuses No customer replaceable fuses in system Contact Caliper Technical Support see page 2 if blown fuses are suspected Through the power cord Computer Interface USB 2 0 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 219 Assay Voltage Minimum Voltage Current 50V limited by current Maximum Voltage Current 600V limited by current Fluorescence Detection Detection Wavelength Bandpass 547 750nm Light Source Green laser diode Excitation Emission 532 nm Wavelengths Power output 5 mW maximum continuous Barcode Reader Barcode Barcode Engine Motorola id Barcode i Matrix Types V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Maintenance and Service 220 Maintenance and Service Cleaning the electrodes and chip interface prevents current leaks The electrodes should be cleaned daily or more often if dyes or reagents contact the electrodes or the chip locator See Cleaning the LabChip XT XTe The test chip should be cleaned as
60. 0 000 aspirate or dispense movements whichever comes first e The laser component of the LabChip 3000 is warranted for the earlier of one 1 year from the date of installation or 8 000 hours of use e The use in a Sciclone inL10 of DMSO above 65 concentration or any other system fluid not sanctioned for use by Caliper will invalidate this warranty as it relates to the pipetting head assembly 1 LabChip XT and Twister are not eligible for on site service and must be returned to Caliper s Repair Depot for warranty service pursuant to the process set forth in Section E below P N 113642 Rev 03 Caliper Life Sciences Inc Caliper Life Sciences Inc Product Warranty 260 If Caliper performs service on eduipment and determines that any of the exclusions set forth in this Warranty apply then Caliper shall charge Customer its then current current list prices for parts labor and travel D Limited Life Parts Limited Life Parts are any parts that are exposed to solvents reagents or samples Such parts include but are not limited to syringes valves seals and fittings A pre defined list of Limited Life Parts are routinely replaced by Caliper Field Service Engineers during an Extended Warranty or Service Contract Preventative Maintenance visit or during Caliper Repair Depot servicing Otherwise these parts are available from Caliper at current list prices and are designed for replacement by Customer E Equipment Return Policy In serv
61. Caliper by Customer will be free from defects in material and workmanship for a period of sixty 60 days from the date of shipment the Warranty Period A defect for purposes of this Warranty is defined as any failure that occurs during analysis of the first one hundred 100 samples being run on a Chip During the Warranty Period if the Chip fails to comply with this Warranty Caliper will repair or replace the Chip at its option and expense If a Chip becomes damaged or its performance otherwise deteriorates due to solvents and or reagents other than those supplied or expressly recommended by Caliper Caliper will replace the Chip at Customer s request and expense No such replacement will extend the original Warranty Period This Warranty does not extend to any Chip which has been a the subject of an accident misuse or neglect b modified by a party other than Caliper c used in a manner not in accordance with the instructions contained in the product User s Manual or d used for an assay or application which has not been approved by Caliper All claims under this Warranty must be made within thirty 30 days of the discovery of the defect Caliper s obligations under this Warranty are limited to replacement as Caliper deems necessary to correct those failures of the Chip to comply with this Warranty of which Caliper is notified prior to expiration of the Warranty Period lll GENERAL CALIPER SPECIFICALLY DISCLAIMS ANY AND ALL
62. Caliper manufactured instrument s hardware and firmware against defects in material and workmanship for a period of one 1 year from the date of installation but not later than 14 months from shipment subject to the exclusions set forth below and i the warranty for Limited Life Parts as defined below shall be thirty 30 days from the date of installation and ii the warranty for cosmetic surfaces shall be thirty 30 days from the date of installation each a Warranty Period Ongoing service support after the Warranty Period may be available at an additional expense A What is Included during the Warranty Period e unlimited emergency on site repair services parts and software updates that affect original functional design specifications their associated labor and travel expenses e unlimited access to Caliper s Technical Support Center which provides troubleshooting repair instruction service dispatching other than for LabChip XT and Twister replacement part information and shipment e A completed Caliper Field Service Report provides thorough documentation of all maintenance and service work performed by the Caliper Field Service Engineer during an on site visit Documentation is not provided when Caliper provides service via telephone fax or email Any failure of a product to conform to this Warranty shall be corrected by replacing or repairing the affected product or refunding the purchase price as described below
63. Chip button 157 Revision data file 59 RUN KERE EER TE DUS 23 33 38 ADOFUNG errada 38 assay principles 20 lee RE ERA SE 247 monitoring the run 39 running a method 33 starting a run 23 Run button 109 251 Run File Editor Window 180 Run Info Window 181 Run Report printing 13 Run Status 109 S Safety 7 8 9 10 11 chemical 8 electrical 10 USES om c 11 instrument T laser 9 power cord 10 training required T Sample 33 44 122 171 ER TT EE TT 44 Calculating size 44 Ladder 44 Name 122 Sample Color 122 Sample Peak Quantification 171 Sample Name file 252 Caliper Life Sciences Inc SVC aa eke bbe AL RE E E E 40 Saving Data Files 40 Saving Workspace Files 42 Save Workspace As Window 183 Scale Gel Contrast 128 Searching for Events in the Events Tab 224 Security menu 107 Select a Data File Window 184 Selected in Gel 137 SCIVICE 444464 KERE Ok Ek cam 0 220 Service plans 3 Set Policies Tab 209 Setup Tab Sta
64. He ENDER EES cer 33 Select tie Run FS da died 34 Start die e 34 Monitor ie RUN sesse SEE nn MAR nie net een tree BA be tn heat te 39 PAUSE a RUN civic oa ce SS DE is 37 SOPA RU see RS an 38 Create a New Method is 39 Sa VIN Data PES acabo ee 40 SAVING WorkSpace Ple ea elas 42 Data ANAIVSIS iras r 43 How the Software Analyzes DNA Data ese ee see Ee Ee Ee eee ee Ee Ee Ee ee Ee ee Ee ee Ee ee ee 44 Organizing Retrieving and Backing Up Data Files 0 45 Opening a New WorkSDaCe simio 45 opening a Data A oe n ee SE nt Na get 46 Adding a Collection to a Workspace UV Ee Ee Ee ee Ee Ee Ee ee ee ee ee 47 USING Expeet d Fragments sis sn ss cloacas 48 Entering EFs in the Method Window VU 48 EXPO 411016 ER a D ID edito TU 49 IMPONIET SE RS ee ER GE oe Ge EE ee se aed 49 Forcing Expected Peaks ss ie EE N N N cid 50 Viewing the EFs in the Graph View 50 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Table of Contents 13 Viewing the EFs in the Gel VieW ees see ee ee se se Ee ee ER Ee ER ER Ee ee ER ee ee Ee Ee ee ee ee ee ee 51 Viewing the EFs in the Channel Table ie ese se Ee Ee Ee ER Ee Ee Ee Re Ee Ee Ee ee ee ee ee 51 Viewing the EFs in the Peak Table iss se sesse se see ee ee be ee ee Ee ee ER Ee Ee Ee Ee Ee Ge ee 52 Modifying Analysis Parameters sis oe nr SR GE Ee li Ee Re 53 Changing the Peak Find Parameters sees ee se se se ee ee se ee ee ee ee Ee ee ee ee ee ee ee 54 Adding aP A E
65. IONS OF THIS LICENSE AGREEMENT CAREFULLY BEFORE OPENING THE PACKAGE CONTAINING THE SOFTWARE MEDIA THE COMPUTER SOFTWARE CONTAINED THEREIN AND THE ACCOMPANYING USER DOCUMENTATION COLLECTIVELY REFERRED TO HEREIN AS THE PROGRAM THE PROGRAM IS COPYRIGHTED AND LICENSED NOT SOLD BY OPENING THE PACKAGE CONTAINING THE PROGRAM YOU ARE ACCEPTING AND AGREEING TO THE TERMS OF THIS LICENSE AGREEMENT IF YOU ARE NOT WILLING TO BE BOUND BY THE TERMS OF THIS LICENSE AGREEMENT YOU SHOULD PROMPTLY RETURN THE PROGRAM IN UNOPENED FORM AND YOU WILL RECEIVE A REFUND THIS LICENSE AGREEMENT REPRESENTS THE ENTIRE AGREEMENT CONCERNING THE PROGRAM BETWEEN YOU AND CALIPER LIFE SCIENCES INC REFERRED TO AS LICENSOR AND IT SUPERSEDES ANY PRIOR PROPOSAL REPRESENTATION OR UNDERSTANDING BETWEEN YOU AND LICENSOR 1 License Grant Licensor hereby grants to you and you accept a nonexclusive license to use the Program only as authorized in this License Agreement The software included in the Program the Software may be used only on a single computer owned leased or otherwise controlled by you or in the event of the inoperability of that computer on a backup computer selected by you If the Software is an applications package you may use it on a single local system controller Neither concurrent use on two or more computers nor use in a local area network or other network is permitted without written authorization from licensor and the payment of
66. Ladder Analysis ladder is a mix of compounds of known sizes that is used to create a size ruler for the samples Ladder data is used to convert the migration time of each sample peak into a size for the compound responsible for that peak The known sizes of the ladder compounds are supplied in the method file In the LabChip XT software the ladder sizes can be viewed in the Analysis Tab on the Method Window The ladder analysis identifies the most prominent peaks in the ladder channel and associates each peak with the known ladder sizes The ladders provide a table of values relating size to migration time Typically the migration time uses the center of the peak in the ladder and the sample Lower Marker Log Files An internal standard that is added to a sample in a channel to assist in determining size and concentration of the sample The marker is the same as the first peak in the ladder The LabChip XT XTe software log file displays in the Event Viewer Window The log file maintains a running record of all events that occur with the instrument while it is online with the software and records all events that occur in the software Each event specifies the date and time of the event source of the event the event code and a description of the event Method File File created in the LabChip XT software to specify assay and analysis settings such as Ladder and marker sizes and concentrations peak find settings expected peaks
67. Peak Find Tab and select the None check box under Baseline Algorithm Adjust Pane Widths The LabChip XT XTe Main Window displays several different views of the data files open in the workspace You can change the height and width of the views to make the views smaller or larger To adjust panes 1 Place the cursor over the edge of the pane that you want to adjust The cursor changes to a line with arrows on each end 2 Click and drag up down left or right The pane is resized after you release the mouse button The layout setting is saved as part of the collection 3 Inthe LabChip XT software to save the settings save the workspace To create new collections in the LabChip XT software with the same settings the collection can be saved as a collection template see Collection Menu on page 105 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 62 Show or Hide Views The views displayed in the LabChip XT Main Window can be hidden to maximize other views in the main window The Layout of the LabChip XTe Main Window cannot be changed To hide a view 1 Select Collection gt Layout on the LabChip XT Main window The Layout Options Window opens 2 Click on the location that is selected for the view to clear the selection The view is hidden 3 Ifa location Left Right or Bottom does not contain any views the pane closes and the remaining panes enlarge to fill the space Note The Ge
68. Peaks within the range are weighted based on the difference from the ladder time The weight of peaks farther from the marker migration time decreases faster as the marker drift tolerance is made smaller Enable Saturation Detection If selected default the software detects if the optics are saturated with a signal that is too high and approximates the signal with a flat straight line connecting the start of the saturated region to the end the saturated region High Concentration Size Correction A correction factor that can be applied if the sample concentration is higher than the ladder concentration This correction adjusts for higher mobility of sample fragments when the sample concentration is higher than the ladder concentration If selected the correction value is used when computing the collection start and end times V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 173 Modify Run Settings Window Use the Modify Run Settings window to change settings for the method while the run is paused To open the Run Settings click the Pause Stop button on the instrument icon while a method is running V2 1 see Run Status and Chip Info on page 109 PAUSE MODE Modesty Fun Settings Hansen Marsa ampe ry CL Woa om Tagger Pak Start Pem Mar Sarh Regor Mal Park San kers on kk Thread Eu ARs FR oreg ee N ask Mae Saar kar Colector tete 10 H EA e rere bof A Sey
69. REEDE RE AO ne EE N N OD OR EIE 263 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Introduction 18 Introduction The LabChip XTe fractionation system performs fast automated nucleic acid fractionation accurately and reproducibly The resulting sample is tightly sized and is delivered in a seduencing compatible buffer The XTe improves laboratory efficiency and provides sizing that is difficult to obtain using manual methods Data is displayed digitally and non fractionated sample can be recollected and used at another time The LabChip XTe software can be used to run standard Caliper methods to perform extractions and to view the analyzed data after the run The LabChip XT Instrument has all the functionalities of the XTe with added features for sample tracking and data analysis The quantitation feature allows for each sample s total input concentration to be determined Additionally the estimated concentration of the extraction region is automatically calculated using Smear analysis Sample Names can be imported and data can be automatically exported for LIMs compatibility The LabChip XT software includes additional features for data analysis sample tracking data filtering and data export to reports or LIMS The following additional extraction modes are also available in the LabChip XT software Fluorescence Peak Max Smear Max Skip Extraction and Separation Only 21 CFR Part 11 Security option is available for
70. S GE oe ED ee ie DO we 55 EXCUSA Peak sis e O Ge EG GE die 55 Merging Two Peaks se dE tn AS Lo e sn SE ie 56 Changing the Time Window for Analysis ese ee se se Ee ER Ee Ee Ee ee Ee Ee Ee ee ee ee ee 56 Aligning or Unaligning the Marker Peaks sees see ee ee Ee Ee Ee ee Ee Ee Ee Ee Ee ee ee ee of Reverting to a Specific Data File Revision 59 Changing the View of the Results sie same Ee De N EE ER De EO Ee Ee Ee 60 VlewindiSElS ra Ge De ee 60 Viewing Zero Baselines ss 61 AGIUSE Pare VIS EED o aci 61 SLOW OF Hide VIEWS DE ee nes 62 ZOO and ZOOUHOUE SAS DR EE Se ie EO Se Bidar eee sence 62 Viewing Graphs in the Overlay Electropherograms Tab 63 Viewing Graphs in the Electropherograms Tab iese see se se ee Ee ee ee ee ee ee ee ee 64 Viewing Multiple Properties in the Channel Table VIEW ee see se se ee ee ee 65 COpViinGUINTONMANON EE SE AR NN M NN ot in 66 Reanalyzing a Data Fil sisie tese RE SR bes ees bose eks eb SE De ge be be Se id Bk SS ge ED hisa 67 Printing Workspacelnformatiof os EE it dde 68 EXxportindibala ke dias 14 Exporting Data Manual sessies es kes Se EE re Sunde iia Re 17 Software Seun AS EE ita 18 Locking and Unlocking the Software ss 79 Managing User ACCOUNTS DE EE Ee EG ee GE OE ndo 80 Adding New USGS oles EE ER tasado 80 Changing User Information ss ne ie ee DE Re ene 81 Printing User Information sus rene rd a tan 82 Activating and Deactivating User Accounts se
71. Sciences Inc Glossary of Terms 250 Peak Identification From the smoothed data peaks are identified using a hill climbing algorithm running along the smoothed data and its first derivative The slope threshold determines peak start point and end point e The first point with local derivative above the slope threshold indicates the peak start point e The first point where the negative slope on the falling edge of the peak drops below the slope threshold indicates the peak end point The peak baseline is stitched across the peak bottom by taking local averages just outside the peak start and end points The peak height measured from the apex down to the peak baseline must exceed the minimum peak height specified in the Method Window to have a bump tagged as a peak The peak start end and baseline can be viewed in the Graph View by selecting the Show Peak Baselines option in the Graph View Properties The area of each peak is determined by trapezoidal integration of the peak signal between peak boundaries and above the peak baseline Point to Point Fit This curve fit is composed of line segments between each pair of data points that are used to interpolate data between the points Polynomial Filter The first step the software takes in analyzing the raw data is to apply Data Filtering Data filtering is performed by means of a polynomial filter that is applied to the raw data The figure below approximates the shape
72. T XTe Main Window 102 Men Das dia 103 FUN Stats and CNIP MO idad a Ge ee Ge ee 109 Error Message Are di SA e ende ios ee 110 RUSSIE RE D A ias 111 Chip VIEW Or List VIEW se li 113 Collection Panes ol ah ket 116 SIDO MIS np a 117 Graph View PIoperli S is 122 Palle A Ee abacus 124 EP ME N ER EE OE OE EE 128 Gel VIEW Propertie Sta Adame be ee ee re Ee Ge 131 Channel Table VIEW std ie rennes some sonne see cias 133 Peak Table VIEW EER EE NG EE EG GE aci eL oi GE ie 135 Peak Table PODEIS EE EG a EG RE EE were De De rt ions 137 AbolitlabE np XX Te WIRAOW ss da NR SN dea 138 Add New Expected Peak Window 139 AUQIE TEMO Wi Ge ee ee DE ES be Led tt EE ote iia ts 140 Audit Trail EXDOFE WIRAOW as ese a a a 141 Audit Trail Manage Columns Window 142 CDR Manager VWIindOW EE onesies do pal es e RE SG 143 CDR Server Utility WIAAOW ss Es EE IE Se nee ee ts ha 145 CDR UU AR WING OWEN EE IE A ED GR EG ie 146 Change Password VWVING OW os 2 8 edad diia 148 Data File Version WINAOW susse ee Ee Ge EG De 149 Event Viewer Window si Eb se EE GE tea 150 EXPO V VIN GOW si EE EE N GE GE DE a Ge 151 Fush CMD VIRGAOW is ER RE A ceeabaie 154 Layout Options WINdOW se ne de lp ee 155 EOGI ANINA OW is es la iaa 156 Method VIO OW ES SE EE A des 157 Method INTO TaD issie until las 159 Analysis Tab ti o etes 160 Peak Find Tabs EE ER EE AE SR EE EE RE et eee ne RE De 161 Expected Fragments Tab eiii 165 Excluded Fragments Tab ss cadet GER sia 167 Smear Analysis Ta
73. Verify that the Remote CDR Server is set up on an accessible network server 2 Log into the LabChip XT software using the default administrator user name and password 3 Select Tools CDR Utility The CDR Utility Window opens 4 Select the Enable Remote CDR Backup check box NOTE Server name folder name username and password are case sensitive 5 Type the computer name of the Remote CDR server in the Remote Computer Name IP Address text box If the remote computer and the local computer are not in the same Windows workgroup type the IP address of the remote computer 6 Inthe Folder text box type the name of the folder to use in the remote CDR server to store the LabChip XT data The folder must have already been created using the CDR Server Utility on the remote computer 7 Type the folder username in the User Name text box This username is the same username that was used to create the CDR Server folder 8 Type the folder password in the Password text box This is the Same password that was used to create the CDR Server folder 9 Click the Apply button 10 Click the Close button to close the CDR Utility Window LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 96 Restoring Data Files from the Remote CDR V2 1 The last backed up copies of LabChip XT data files can be restored from the backup database on the remote CDR Server if the LabChip XT computer is replaced To restore the data fi
74. When the lid is closed any channels that have finished all of the extractions display DONE Channels that have not completed display information about the next step 5 To stop a run while the run is paused see Stop a Run on page 38 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 38 Stop a Run V2 1 If you need to stop the run before it is complete click the Pause Stop button After a run is stopped it cannot be restarted and the channel cannot be reused The Modify Run Settings Window opens the voltage in each channel is set to zero and the lasers turn off Click the Stop Run button A message box confirms that you want to stop the run in progress al Stop Run d A Do you want to stop the run currently in progress Click Yes to stop the run The Run Status line displays Run stopped by user Run Status a Chip info Chip ID ND160001 00 02 Expirabion Date Jun 6 2011 Available Channels 4 Tire XT DNA 750 Run Status Run stopped by user The data that has been collected up to the time the run was stopped displays in the LabChip XT XTe Main Window Save the workspace see page 42 if desired in the LabChip XT software In the LabChip XTe software the data file is saved automatically LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 39 Create a New Method V2 1 The LabChip XT software enables you to create a new method by opening and editing an
75. XTiData Deiat MA Create daly sub deectory Copy To Fia pretis Calger Computer Name Faad Nara Oe 10 if Date A Time Example Cakper_2011 06 03_124544xtd Aveo Export Stina A Automate Expor Figure 75 Start Fractionation Window Output Tab Data Path Specifies the location where the data files will be saved Click the Default button to reset the text box to the default directory 21 CFR Part 11 option not installed The default location is C Program Files Caliper Life Sciences LabChip XT Data Click the Browse button to choose a different location 21 CFR Part 11 option installed The default location is C Program Files Caliper Life Sciences CDR Click the Browse button to choose a folder in the CDR LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 198 Output Tab Continued V2 1 NOTE Data files should be saved to a local folder on the computer s hard drive Saving data files to a network drive may cause loss of data if the network connection is slow or interrupted Create Daily Sub Directory check box If selected a new directory is created each day in the specified Data Path and all of the data files from that day are saved in the directory The directory name is the current date and the format is YYYY MM DD where YYYY is the year MM is the month and DD is the day Copy To If selected the data file is copied to the specified folder after the run is co
76. abChip XT XTe Main Window Figure 23 shows a barcode reader error at the bottom of the Run Status area See Error Messages on page 226 for a list of errors and tips on preventing or resolving errors LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 111 Run Setup The Run Setup area displays information about the run currently in progress This section only displays during the run C 5 Mode Size Range BP Trigger At 1 Lddr 2 2 XAP 50 1000 10 CLICK 3 2 MEP 625 4 600 BP 4 1 XEC 301 10 DONE Figure 24 Run Setup The Run Setup displays the following information Single step extractions display 1 in this column Displays the Extraction Mode for the current step e Lddr Ladder Off Disabled X amp S eXtract and Stop X amp C eXtract and Continue XId eXcLuDe region XT only Sep Separation XT only X amp P eXtract and Pause e Skip Skip extraction XT only See Setup Tab on page 188 for descriptions of each extraction mode Size Range Displays the Size range or Search region for each BP step V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 112 Trigger At Displays the trigger point for the current step in each channel e For Collect on Click Extraction Mode or Manual Collection Width click on the word CLICK to begin or end the extraction The sample in the channel is within the specified search region when a pink
77. ack up the CDR The repository stores secure backup copies of data files The CDR Server Utility Window is only available if the CDR Server Utility is installed on the remote computer Only used if the 21 CFR Security option is installed with the LabChip XT software To open the CDR Server Utility Window double click the CDR Server Utility icon on the remote computer desktop Create Mea Server Folder arre Faites Cent TH Cage rare oker ns area Een lol ke e Bree Frider here CAT seel EK 1 d Cat Folder det sie Apr A Ler ml add port number 3630 m the monpliona lial in casn of ing non Wndows tve Vere Code Cir Figure 43 CDR Server Utility Window The CDR Server Utility Window contains the following options Confirm The same password as typed in the Password text box Password Get Folder If selected creates a text file containing the URL Folder Name Details Username and Password for the new data folder View Contents Opens the CDR Server Viewer window to view the data files and folders in the remote CDR server Click a folder and enter the user name and password that was used to create the folder to view the contents of the CDR server folders Apply button Creates the specified data folder V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 146 CDR Utility Window Use the CDR Utility Window to view the location of the local CDR folder specify whether the CDR folder is acces
78. additional license fees You agree that you will not assign sublicense transfer pledge lease rent or share your rights under this License Agreement except that you may permanently transfer all of your rights under this License Agreement provided that you retain no copies you transfer all of the Program and the transferee agrees to the terms of this License Agreement You agree that you may not reverse assemble reverse compile or otherwise translate the Software Upon loading the Software into your computer you may retain the Soitware media for backup purposes In addition you may make one Copy of the Soitware on a second medium for the purpose of backup in the event the Software media is damaged or destroyed Any such copies of the Software shall include Licensor s copyright and other proprietary notices Except as authorized under this paragraph no copies of the Program or any portions thereof may be made by you or any person under your authority or control Licensor s Rights Licensor has invested significant time and money in developing the products purchased with the Program The Program contains Licensor s trade secrets which must be used in confidence You acknowledge and agree that the program is proprietary to Licensor and protected under U S copyright law You further acknowledge and agree that all right title and interest in and to the Program including associated intellectual property rights are and shall remain with Licensor
79. ak Hubo Caen rk Cone sae Lar rege Le Laida Tres Advance Figure 58 Method Window Advanced Tab Quantification Determines whether the lower marker or a sample peak is used for quantitation Selecting Sample Peak uses the peak size and concentration of the User Standard instead of the default ladder settings Peak Integration Mode Specifies the mode for determining the baseline e Peak Baseline A global peak baseline is used as the baseline for all peaks This baseline is determined by stitching together regions of low variance across the data signal e Valley to Valley Each peak is assigned a baseline by drawing a line that joins the start and end of the peak at the data signal values Smear Baseline Mode Specifies the Smear Baseline option to use for all smears See Smear Baseline on page 255 for more details on each option This option only displays if smears are defined in the Smear Analysis Tab e Two Point If selected a Two Point baseline from the start of the trace to the end of the trace is used as the baseline e Peak Baseline If selected the local peak baseline is used as the start and end of the smear baseline LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 172 Advanced Tab Continued Marker Find e Marker Drift Tolerance Specifies the time within which to find the marker peak specified as a percent of the marker migration time Range is 1 to 100
80. al Caliper Life Sciences Inc Operation 42 Saving Workspace Files V2 1 When viewing chip data in the LabChip XT XTe main window you view the selected data files in a Workspace When a new run starts a new blank workspace opens which contains the data file for the chip in the run After the run is complete saving the workspace in the LabChip XT software saves the data file with the current analysis settings See Saving Data Files for more information on the contents of the data files The LabChip XTe software does not Support saving workspace files The Data Files are not saved in the Workspace file In the LabChip XT software the saved workspace file contains links to the revision of the data file that was last open in the collection If a Workspace file is moved to another folder or computer the data files must be moved with the Workspace file The data files must be in the same location relative to the Workspace file as they were otherwise you are prompted to find the missing data files when you open the Workspace file It is a good practice to save the workspace files in the same location as the data files that are included in the workspace Saving a Workspace file in the LabChip XT software automatically saves any changes to the data files that are open in the workspace and saves the settings for each collection in the workspace If the 21 CFR Part 11 option is installed saving Workspace files does not require permission
81. al power supply Users should observe the following WARNING AA Do not open the instrument enclosure There are no user serviceable parts inside The wall outlet or the power cable connector on the back of the instrument should be accessible after the system s installation to allow personnel to safely disconnect power from the system The computer supplied with the LabChip XT XTe instrument has Internal lithium batteries Batteries should not be incinerated WARNING AN AN AN Danger of explosion if battery is incorrectly replaced Replace only with the same or eguivalent type recommended by the manufacturer s instructions Power Cord Selection V2 1 The LabChip XT XTe is powered by the same power supply for 100 120 and 230VAC operation Use the correct power supply cord for the region where the instrument will be installed as described below United States and Canada When using the LabChip XT XTe instrument in the United States or Canada use the North American power supply cord shipped with the instrument The cord is intended to be plugged into a standard NEMA 5 15R receptacle in the wall If the power cord needs to be replaced contact Caliper for a replacement cord International All power supply cords must be approved by an acceptable accredited agency responsible for evaluation in the country where the power cords and system will be used Power cords for international use must have an IEC 60320 1 C7 fema
82. all of the results at once Right clicking in the Peak Table View LabChip XT only of a channel opens a shortcut menu with the following commands e Include Peak only for peak type e Exclude Peak e Force Lower Marker e Add Expected Peak NOTE You can also right click on a peak in the Graph View to view the same menu LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 59 Reverting to a Specific Data File Revision Each time a LabChip XT data file is changed a new version of the data file is created and saved The LabChip XT software enables you to revert to a previous version of a data file This option is not supported in the LabChip XTe software V2 1 To revert to a previous data file version 1 On the LabChip XT XTe Main Window select Analysis gt Analysis Settings on the main menu The Method Window opens Click the Restore Chip button at the bottom of the window The Restore Chip Settings to Version window opens Select the data file version that you want to restore to Click the OK button The Method Window displays the settings for the selected data file version Click the OK button to display the data file with the selected settings LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 60 Changind the View of the Results The views in the LabChip XT XTe Main Window can be customized to display data according to the preferences of the user These opti
83. and smears Editing method files and changing analysis settings are only supported in LabChip XT software Microfluidics V2 1 The miniaturization of chemical processes generally pertaining to systems involved in the control of fluid flow This includes pumps valves jets and microchannels LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 248 Minimum Peak Height The Minimum Peak Height value determines the height limit below which a peak will not be detected For each peak the difference between the peak start time and the peak apex must be greater than the Minimum Peak Height value The Minimum Peak Height is specified on the Peak Find Tab on the Method Window in the LabChip XT software The Minimum Peak Height cannot be changed in the LabChip XTe software Minimum Peak Width The Min Peak Width value determines the width in minutes under which a peak will not be detected For each peak the difference between the peak start time and the peak end time must be greater than the Minimum Peak Width value The Minimum Peak Width is specified on the Peak Find Tab on the Method Window in the LabChip XT software The Minimum Peak Height cannot be changed in the LabChip XTe software Molarity Molarity Concentration 10 660 Size nmol l where molarity is measured in nanomoles per liter nmol l Concentration is measured in nanograms per microliter ng pL Size is measured in base pairs bp
84. annel table for each Displayed in expected peak Channel Table Apply to Specifies the channels that the expected peak is applied to lt All gt Channels specifies that the expected peak applies to all channels Clicking on the column opens the Select Channels window to choose the specific channels to apply the expected peak to V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 140 Audit Trail Window The Audit Trail Window enables you to search the Audit Trail Log for specific events to export the events or to print events Only available if the 21 CFR Security option is installed with the LabChip XT software To open the Audit Trail window select Security gt Audit Trail Log on the LabChip XT XTe Main Window al Lab XT Aude Trad AA Cala Fs Aur al El ede Fs EXA 43507 PM Wir 1 760 ais dla Enbpar 2011 Figure 39 Audit Trail Window The Audit Trail Window contains the following options Search most If selected the specified most recent number of entries is recent entries searched for entries matching the selected criteria Number of Specifies the number of most recent entries to search entries Search by dates If selected entries between the specified dates are searched for entries matching the selected criteria From and To Select the dates that contain the events that you want to view text boxes Search entire If selected all entries in the
85. anual Caliper Life Sciences Inc Bubble Clipboard Collection Glossary of Terms 240 If the tip of a pipette is not positioned below the liduid level in the chip well bubbles can result If a large bubble forms at the bottom of a chip well remove the sample from the well pipette the sample back into the chip well and continue with the loading procedure A temporary storage area that contains information you have cut or copied You can paste the contents of the clipboard into other programs provided that program supports that type of information Information remains on the clipboard until you replace it with the information from another cut or copy command Use a collection to view the chip data In the LabChip XT software a workspace can contain multiple collections to supply different views of the same data Each collection specifies e the channels selected for view in each chip data file e the layout of each Collection tab and e the display properties for each view in each collection Collection Template V2 1 In the LabChip XT software a collection template saves the display options for a collection and any defined filters in the collection Collection templates are used to create new collections using the saved display settings and filters Collection templates do not save the list of chips or the channels selected in the chips To save a collection template based on the settings in the open collection selec
86. are set to Collect on Click watch the data and click on the word CLICK in the Run Setup section when the green collection area shown on the graph is near the desired point The Fractionation Pending window opens Click Start Now when the green collection region is over the desired area E CH Fractionanon Pendeng on Channel 2 3 A A l Collection of Green regi n will begin when Start Now is pressed St ra During the run each extracted region is highlighted in the Graph View and in the Gel View The color of the highlight indicates the type of region e Red Normal extraction region e Yellow Exclusion region e Green Target region for Collect on Click Changes to red during collection e Gray Skip extraction region e Red changes to Purple Buffer capacity exceeded during the extraction LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 36 Monitor the Run Continued V2 1 8 10 11 12 13 14 15 The highlighted regions correspond to Smears created automatically by the software The smears are included in the Smear Analysis Tab on the Method Window after the run is complete If any channels are set to eXtract and Pause the run automatically pauses after the extraction is complete the Run Paused window displays and any channels that have completed the extraction display COLLECT in the Run Settings While the run is paused remove the sample from the collection well re
87. arkers and the aligned data displays in real time Graph View Shortcut Menus Right Click Menu not near a peak Right click away from a peak in the graph to display a shortcut menu containing the following commands Synchronize Zoom If checked all open graphs will zoom to the same level when one graph is zoomed Unzoom Zooms out to the previous zoom level Unzoom All Zooms out completely and returns to the standard view Set Scale Opens the Set Graph Scales window to specify the X and Y ranges to show on the graph Scale to Sample Peaks Scale to All Peaks Scales the view to the minimum and maximum X values of the all peaks including marker peaks and system peaks Remove Removes selected graph from the view Copy Copies the selected graph to the clipboard in a bmp format Analysis Settings Opens the Method Window to change the analysis settings LabChip XT only LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 119 Graph View Continued Right Click Menu near a peak Right click above or below a peak in the graph to display a shortcut menu containing the following commands Exclude Peak Excludes the peak from the analysis The Peak Type label displays X Force Lower Marker Defines the selected peak as the Lower Marker The Peak Type label displays LM Add Expected Peak Opens the Add New Expected Peak Window to add a new Expected Peak to the specified chann
88. assword for the current user Password Confirm Retype the new password for the current user Password OK button Saves the new password and closes the window Cancel Closes the window without saving changes to the button password V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 149 Data File Version Window Use the Data File Version Window to view the saved versions of the data file in the LabChip XT software Also displays when the data file was signed whether the file was locked and the current approval state if the 21 CFR Part 11 Security option is installed To open the Data File Version Window select View Version Change Details on the main menu Dass File Verion Change Delta lt Cakper 2011 02 28 02222219 xt A A A v 2010072 14 27 41 by CAUPERL Sade ed OS 150457 by Dela Sino Signature Lio Details tl fin tar eb erelid Signature Parameter Value Date Tone Stamp 112011 112848 AM serna administrator Data Fie Name Cabper 2011 05 28 02 27 59 Role Aciertos Comment Accepted by Adra Ses Type Lockmg Approval State Accepted locked Yes OM Version 1 Selected Version Prri Presses Pi Cina Figure 46 Data File Version Window The Data File Version Window contains the following options List of Displays the list of all saved data file versions and Versions electronic signatures To open a different version of the data file click the Restore Chip button in the Me
89. available depend on the columns selected in the Peak Table View LabChip XT only Specifies the orientation of the text for the annotation horizontal vertical up or vertical down LabChip XT only LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 123 Set Font button Opens the Font window to choose the font style and size of the text for all annotations LabChip XT only Annotation 2 Labels each peak in the graph with a peak property selected from the drop down list Default is None LabChip XT only Peak Annotation If selected the types of the annotations display in the upper left Legend corner of the graph LabChip XT only Channel Displays the selected channel property outside the graph Annotation LabChip XT only The location of the channel annotation Click the button to change to location upper right upper left lower left or lower Channel Annotation Location Button right LabChip XT only arrow Show Data Points If selected displays a dot on the graph at the location of each data point Show Peak If selected displays the baseline for each peak on the graph Baselines Show Smears If selected displays smears as a colored line on the trace and displays the smear baseline This option only displays if smears are defined in the Method Window Only Annotate If selected only the peaks that are labeled as Expected Expected Peaks Fragments display the annotatio
90. b se ls tits alos 169 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Table of Contents 15 Advarited Tab EE EE E EG N tne a e oies 171 Modify Run Settings Window ss 173 New Collection WindoW ee ee ee ee ee ee ee 174 Pertorm Signature WINGOW 22 nice 26 nus MU De Re a RE ds 175 P ELE VIE ON EE D TR RE Ee ee RE be ee 176 Print Validation Reports WINdOW ese see se se Ee Ee Ee ER Ee ER EE ER ER ER RR ER RR Ee Ee Ee ER Ee Ee Ee ee ee 178 Rename Collection VINdOW GEE SG DE GE GE ie dai 179 RUN Ele EQtor VWINAOW EE EDE Se Do eons aetna Ge had 180 RUN INTO VVING OW 22s a 2 in td ke ne SEE Ge ES EE GE De ciel ES EG ed EG id Ee 181 FRU TOS Tab ds de ES EE 182 Save Workspace File As WINdOW ese ee ee ER Ee Ee ER Ee Ee ER Ee EE Ee Ee ee ee ee ee ER ee ee ee ee ee 183 Select a Data File WMiINAOW Es ER io 184 Software Installation Qualification Window ee ee ee ee ee ee ee ee ee ee 185 Start Fractionation Window ee a ee ee ee ee ee ee ee ee ee ee ee ee ee ee ee 186 SOUDE Tarda 188 Buffer Utilization Hab da dol en cn 194 ser linie ab O A a 195 SIZING MAD Ie FI ee N ES as 196 ouput Tab RS De N OE is 197 System DIAGNOSTICS VV ING OW EE EE PG RE ne en tn ee et ee 199 Unlock Applicaton VVINGOW cad 201 Unlock Data File WINdOW sasie soeke been NS Ne nd an d s duch 202 User Administration WindoW ee ee ee ee ee ee ee ee ee ee ee ee ee a 203 create New LEEF EG oir Ge Ee de 204 E d
91. bChip XT software 1 After the EFs are entered in the Expected Fragments Tab click the Export button at the bottom of the window The Export Expected Fragments Window opens Navigate to the desired location for the file type the desired name for the file in the File Name text box and then click the Save button A GEP file is created to save the expected peak settings Only supported in LabChip XT software After an Expected Peak file GEP has been exported you can import the settings into another chip or workspace 1 3 4 With the chip open in a workspace in the Expected Fragments Tab click the Import button at the bottom of the window The Import Expected Fragments Table window opens Navigate to the location of the file select the name of the file to import and then click the Open button The expected peak settings are imported into the tab To apply the EFs to the active chip click the Apply button To apply the EFs to all chips in the workspace click the Apply Global button LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 50 Forcing Expected Peaks Only supported in LabChip XT software If there are multiple peaks in the tolerance range the largest peak is labeled as the expected peak even if it is not the exact size specified If a different nearby peak should have been selected as the expected peak you can specify which peak is labeled the expected peak 1 Inthe Grap
92. before a real time ladder peak of greater size has passed the detector In this scenario the DNA size is calculated from previously observed real time ladder peaks of smaller sizes and the sizing ladder points of greater size After the run is complete additional data analysis can be performed in the LabChip XT software to filter the data change peak find settings or change the view of the data in the software See the procedures in this section for details V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 45 Organizing Retrieving and Backing Up Data Files As you work in the LabChip XT or XTe software it s a good practice to organize the files generated by the software e Create a folder in which to save the data files or use the default Data folder If desired each person can save data files to their own subfolder to organize the data files e Save Workspace files in the LabChip XT software in the same directory as the data files to prevent missing data files in the workspaces e Review the files periodically even if only one person uses the software If you are not using the 21 CFR Part 11 option archive files you are no longer using but want to save to a backup disk and discard unneeded files If you are using the 21 CFR Part 11 option see Software Security on page 78 for backup options Verify there is enough free space on the hard drive to save new chip data files e Each user in t
93. before another IQ test is run Saves the results of the IQ in an xml file Begins running the IQ Closes the Installation Qualification Window LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 186 Start Fractionation Window The Start Fractionation window specifies the method to run the collection settings for each channel the user name auto export settings and import options for sample names and expected peaks freira Wha ET FA 300 de Dn AE A T Ifi i TP mr Ej r EF MES pa ME JE n Sample rare Sarpie d Channel 4 7 ELIS se See Toer Gimin Regen TA is iv tire Siep EG Asa ME Sep Qu 5 EE 315 amp s1 al e LU A i Pi f AE ee incor bood or ET l Le res er mee testa me af eel Figure 70 XTe Start Fractionation Window The Start Fractionation window opens when you click the Run button on the LabChip XT instrument graphic If a workspace is open in the LabChip XT software you are prompted to save the workspace before the Start Fractionation window opens To begin the run select the desired settings on each tab and then click the Start button The Start Fractionation Window contains the following tabs e Setup Tab e Buffer Utilization Tab e User Info Tab e Sizing Table Tab e Output Tab V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 187 Start Fractionation Window Continued
94. blem or directs you to call Caliper Technical Support see page 2 Inflection Threshold Example 1 LIG L 600 V2 1 Inflection Threshol called Peaks that are very close together will be identified as a single peak if the peaks do not have a clear valley between them The Inflection threshold property in the LabChip XT software allows splitting of peaks evidenced by a region of lower slope The figures below llustrate the operation of the Inflection threshold The green line in the figures below shows the signal slope The shoulder peaks have a slope minuma inflection point but the slope doesn t change sign so they are not split into multiple peaks via the slope threshold HA Inflection point inside threshold new peak Figure 93 Slope Threshold 0 The inflection threshold defines the value that the slope minimum must be below to trigger a splitting of the peak As the threshold is increased more peak splitting occurs The figures below show the same data with the slope threshold set to 80 and 200 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 245 soo inflection point inside threshold new peak Inflection Threshold called F 80 sec z 400 A Witch as is un e ii 200 Hoe I BRIE ht N A HT she an ENE Mi a _ 1 in a E 4 Ta 10 0 1 4 4 1 1 ELI 20 2 20 4 Aligned Tira os 1000 Inflection T
95. box is selected the data file is also renamed If the Rename File to Match check box is cleared not selected the data file name remains the same The data file cannot be renamed if the 21 CFR Security option is installed Remove Chip Removes the chip data file from the workspace The data file is not deleted only the workspace view changes Analysis Settings Displays the Method Window to change the analysis settings for the data file This option is not available in the LabChip XTe software Version Change Details Displays the Data File Version Window to change the version of the data file displayed in the workspace This option is not available in the LabChip XTe software Run Info Displays the Run Info Window to view the run information and Event Log V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Software Reference 114 Chip Channel Color Code Green Channels are running Blue Channels are included in the open collection channel 1 above Blue with Black Ring Channels are selected for analysis channel 2 above White Channels are not included in the open collection but have data Grey Channels do not contain any data White with Red Ring An analysis error has occurred in the channel White with Green Ring The channel is not analyzed Any Other Color Channels are selected by a Filter See the Filter View to determine which color represents each filter If a
96. buffer use is estimated based on the current selections in the Start Fractionation window The run can be started even if the run is over the buffer limit but be aware that if the buffer capacity runs out the current will drop and the DNA will not continue to migrate into the collection well Sram Fractionation Fractionation Method XT DNA 750 iH No animala for mamas ending of extraction Bestaan 23 and 6 4 en Between 04 and 1 ran Figure 72 Start Fractionation Window Buffer Utilization Tab The Buffer Utilization tab displays the following information Channel Displays channel numbers 1 through 4 Estimated Extraction Time Displays an estimated range of time required to perform the extraction in each channel Status Displays an icon indicating whether the buffer is estimated to be exhausted during the run Type Description ooo OK Buffer is estimated to be sufficient for the channel Warning Buifer may be exhausted if the extraction occurs at the end of the run Error Extraction may occur after the buffer has been exhausted Unknown An estimate cannot be made whether the buffer is sufficient Usually occurs with a Collect on Click extraction or a manual endpoint V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 195 User Info Tab The User Info Tab in the Start Fractionation Window specifies the operator name and any comments added to the run Operon ca
97. ce library data sheets labchip systems data sheets htm LabChip XT XTe User Manual Caliper Life Sciences Inc Introduction 20 Principles of Operation V2 1 The LabChip XT XTe assays are based on traditional gel electrophoresis principles that have been transferred to a chip format The chip format dramatically reduces separation time and provides automated sizing and quantitation information in a digital format The additional collection well on the chip allows a specified range of nucleic acid sizes to be separated from the rest of the sample Fractionation is the separation of a small range of DNA strand lengths from a sample of DNA containing a broad mixture of DNA strands The LabChip XT XTe uses a microfluidic chip to separate the DNA strands by length in a gel contained in the chip The sample is directed into a waste well on the chip until the specified size range is detected The desired portion of the sample is then diverted into a collection well on the chip At the end of the extraction the run can be paused automatically and the extracted sample can be removed from the collection well Multiple extractions can be performed during the same run to collect multiple sizes from the same sample Options are also available to skip specific sizes or regions The run can stop automatically when all extractions are complete or the run can continue to the end of the supported range and the remainder of the sample is diverted into the
98. channel is selected by multiple filters the colors are combined in the channel LabChip XT XTe User Manual Caliper Life Sciences Inc List View V2 1 Software Reference 115 The List View in the LabChip XT software displays a list of all the channels in the currently open data files Select the List tab at the bottom of the Workspace pane to see the List view The List View is not displayed in the LabChip XTe software e Black channels are not included in the open collection e Dark Blue channels are included in the open collection e Light Blue channels are selected in the Gel View and Channel Table View e Channels outlined in black are selected by a filter e Red channels have an analysis error 1 Calper_04 31 25 Ladder Sir Ladder CHS Sepie CHA Sample 4 Chapa Lal Figure 25 List View LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 116 Collection Pane V2 1 The Collection Pane in the LabChip XT XTe Main Window displays a tab for each collection in the workspace Each collection displays the information from the data files that are open in the Chip View or List View Multiple collections are not supported in the LabChip XTe software The Collection Tabs each contain the following views Graph View Gel View Channel Table View Peak Table View Filter View The views in the Collection pane are synchronized with each other Selecting a graph on the Grap
99. ciences Inc Data Analysis 71 Channel Table Choosing this option prints the columns displayed in the Channel Table View To change the columns that are printed or the order of the columns change the columns in the Channel Table View e Selecting the Add Border check box prints the table with a border around each cell in the table e Selecting both the Channel Table and the Peak Table prints each channel on a separate page with the Channel Table row at the top of the page and the Peak Table for the channel below it N sag eir ro APD Figure 15 Printed Channel Table V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 72 Peak Table LabChip XT only Choosing this option prints the columns displayed in the Peak Table View To change the columns that are printed or the order of the columns change the columns in the Peak Table View V2 1 Selecting the Exclude Marker check box removes all markers from the printout Selecting the Add Border check box prints the table with a border around each cell in the table Selecting the Add Channel Name as Header check box prints a channel header chip name and channel name before the peaks in each channel Selecting the Per Page or Per Channel option for the Column Header specifies whether the Peak Table column headers are printed only at the top of each page default or if the headers are also printed at the beginning of each n
100. clicking on the peak row to open a shortcut menu of possible peak types for the peak This can also be used to label a peak as Excluded X The concentration of an excluded peak is forced to zero so that it does not affect the total channel concentration and the Percent Purity calculation Expected Peaks are indicated by the Expected peak name in the Type column The peak table in the LabChip XT software can be exported to a csv file by choosing Export on the File Menu see Exporting Data on page 74 for details The csv file includes the columns in the order displayed in the Peak Table at export time the csv file can be opened in Microsoft Excel If the workspace contains multiple collections the data is exported from the active selected collection Multiple collections are not supported in the LabChip XTe software LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 136 Peak Table View Continued V2 1 To show only filtered peaks sort within each channel or hide excluded peaks see Peak Table Properties The Peak Table displays the following columns by default Chip Name The name of the chip defined in the workspace Sample Name The sample name defined in the Setup Tab on the Start Fractionation Window The Sample name can also be changed in the Channel Table View or the Gel View Type Displays the type of peak for markers or expected peaks Migration Time min Center The time
101. colection Figure 36 Peak Table Properties This window contains the following options Sort within If selected default sorting occurs only within each channel rather each Channel than across the entire table Click a column header to sort the table rows by the column value If cleared uses conventional sorting which mixes together peaks from all channels Clicking the column header sorts in ascending descending original order Hide excluded If selected excluded peaks and unknown peaks are hidden in the peaks Peak Table view Expected If selected only peaks identified as Expected peaks display in the Peaks only Peak Table Filtered peaks If selected the Peak Table displays only peaks that match the filter only criteria Useful when generating a collection based on a filter whose selection criteria are peak specific such as Area Concentration Purity Expected Peaks and Size Show all Peaks If selected all peaks display in the Peak Table Selected in Gel If selected only the gel lanes selected in the Gel View display To select multiple channels Ctrl click on the lanes in the Gel view Entire If selected all channels in all chips that are included in the Collection collection are displayed Pin icon In the top right corner used to lock in place or unlock the Properties tab If locked in place the Peak Table display panel is resized to accommodate the tab V2 1 LabChip XT XTe User Manual Caliper Life Science
102. ct Analysis gt Analysis Settings to open the Method Window and then click the Peak Find Tab 2 Change the parameters as necessary at the top of the window under Chip Peak Find Settings 3 Click the OK button to save the setting reanalyze the data and close the window Click the Apply button to apply the changes and reanalyze the data but keep the Method window open Click the Apply Global button the apply the settings to all chips in the workspace and reanalyze the data but keep the Method window open To change peak find settings for individual channels 1 Select Analysis gt Analysis Settings to open the Method Window and then click the Peak Find Tab 2 Inthe Channel drop down list select the channel number that you want to change the settings for LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 55 3 Change the settings at the bottom of the window under Channel Peak Find Settings to change the settings for the selected channel 4 Click the OK button to save the setting reanalyze the data and close the window Click the Apply button to apply the changes and reanalyze the data but Keep the Method window open Adding a Peak You can manually add a peak in a region where a peak has not been identified in the LabChip XT software 1 Inthe Graph View right click near the top of the area where the peak is to be added The area must be outside any previously identified peak and the cursor must be
103. d 9 Specify the desired name for each channel e Type the desired name for each channel in the Sample Name text box e Click the Import Names button at the bottom of the window and select the Sample Name File that contains the desired names LabChip XT only 10 To add another step to a channel click the New button The Step text box displays the step number of the new step Repeat steps 2 through 8 to select the settings for the current step e To add a new step between existing steps go to the step before the desired location for the new step and click the New button For example to insert a step between steps 2 and 3 go to step 2 and click New The new step is numbered step 3 and the step that was step 3 is now numbered step 4 11 If desired use the Copy and Paste buttons to copy settings between channels The Copy function selects the source channel not the actual settings If the settings of the copied channel are edited before clicking Paste the edited settings are pasted 12 When the settings on the Setup tab are correct go to Check the Buffer Utilization on page 29 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 29 Check the Buffer Utilization Before the run verify that the buifer will not run out during the run The buffer cannot be refreshed The Buffer capacity is an estimation The run can be started even if the run is over the buffer limit but be aware that if the buffer ca
104. d e Require Signature on File Update If selected an electronic signature is required to save modified data files Signatures can be performed by any user who has the Perform Signature option selected in the User Administration Window 4 Click the Save button Printing User Policies After changing the LabChip XT user policies the user policies can be printed for record keeping purposes To print the user policies 1 On the LabChip XT XTe Main Window select Security User and System Administration The User Administration Window opens 2 Click the Set Policies button 3 To preview the printout click the Print Preview button 4 To print the selected information click the Print button V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 86 Electronic Signatures V2 1 Based on a company s procedural requirements creating and saving LabChip XT data files may require a superior s signature If so a user with signature permissions must enter a valid username password and comment to explain the purpose of the signature The authorized user also has the option to mark the file as Accepted or Rejected and to Lock the data file to prevent changes The data file can be signed approved and locked any time except while the assay is running Electronic signatures are not supported for LabChip XTe NOTE To change user signature permissions see Changing User Information on page 87
105. d or Time to the data file name select or clear the desired check boxes or type the desired project name To automatically export data tables graphs or gels in the LabChip XT software select the Automatic Export check box click the Settings button and then select the desired Auto Export settings see page 31 Auto Export is not supported in the LabChip XTe software See Save the Run File on page 32 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 31 Select the Auto Export Settings The Auto Export settings in the LabChip XT software specify which views to automatically export at the end of each run and specifies the format for each view Click the Settings button located after the Automatic Export check box in the Output Tab on the Run File Editor Window to open the Export Window Auto Export is not supported in the LabChip XTe software To select the desired views to export 1 V2 1 Select the check boxes next to the views to export Selecting Export All selects all check boxes For each selected view to change the location for the files click the Browse button and select the desired location If Raw Data is selected click the AIA Format check box to export in Chromatography Data Interchange Format or clear the check box to export in CSV format If CSV is selected e Select Include Size Data to align the data to the channel s ladder for one file per channel or to the first channe
106. debris or fibers that may scatter light 1 fluoresce or block light during the run 2 Dust can be removed with pressurized and filtered air 3 To clean dyes or reagents from the chip use a lint free wipe dampened with 70 isopropanol solution in Dl water 4 To clean dyes or reagents from the optical windows use only the provided swabs dampened with 70 isopropanol solution in DI water Rinse with swab dampened with DI water NOTE V2 1 Do not apply pressure to the optical windows when using the swabs Lightly press the swab on the windows to prevent scratching or damaging the optical fiber tips Do not touch the optical windows when handling the test chip If necessary the PCB on the Test Chip can be cleaned with a swab dampened with 70 isopropanol solution in Dl water Rinse with swab dampened with DI water Let all parts air dry Run the High Voltage Diagnostics after cleaning the system to verify cleaning is successful If the High Voltage Diagnostic fails repeat the cleaning procedure If a second cleaning does not resolve the error contact Caliper see page 2 LabChip XT XTe User Manual Caliper Life Sciences Inc Maintenance and Service 223 Long Term Shutdown If the LabChip XT XTe will not be used for an extended time more than 10 days the instrument should be shut down as follows V2 1 1 2 Remove the chip from the instrument Turn off the power switch on the back of the instrument and unplug th
107. der To delete a CDR data folder 1 Select File Import Data File The CDR Manager Window opens Verify the folder is empty Click on the folder name Click the Delete button on the left side of the window or at the top of the window Close the CDR Manager Window LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 92 Hiding Data Files in the CDR Manager Window The CDR Manager window enables users to hide or show specific LabChip XT data files or folders in the CDR Manager window This functionality can be used to reduce the number of data files displayed in the CDR Manager window when certain files or folders are not used The user must have Hide Show in CDR rights in the Define Access tab in the User Administration Window Hiding data files or folders does not change the data file or folder they are just not displayed in the CDR Manager Window To hide data files or folders 1 Select File gt Import Data File The CDR Manager Window opens 2 Select the name of the data file or folder that you want to hide If you select a folder name all data files and folders in the selected folder will also be hidden 3 Click the Hide button on the left side of the CDR Manager Window 4 Close the CDR Manager Window Showing Hidden Data Files in the CDR Manager Window V2 1 To set hidden LabChip XT data files back to unhidden show 1 Click the Show Hidden Files button at the top right of th
108. e Creating a Run File on page 24 If the run file exists see Running a Chip on page 33 To analyze data from a previous run see Data Analysis on page 43 Creating a Run File V2 1 Before running a chip you should create a Run File The Run File specifies the extraction or separation settings for the samples on the chip Specifying the settings in a run file enables you to import the desired settings into the Start Fractionation Window after the chip has been prepared to minimize the time between preparing the chip and starting the run To create a run file 1 On the LabChip XT XTe Main Window select Tools Run File Editor The Run File Editor Window opens Select the Method to run from the Fractionation Method drop down list Select the options on the Run File Editor window e Select the Extraction Parameters on the Setup Tab e Check the Buffer Utilization e Enter the User Info e Specify the Ladder Settings e Select the Output File Locations e Select the Auto Export Settings LabChip XT only LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 25 Select the Extraction Parameters on the Setup Tab V2 1 The Setup tab displays the selected options for the run The icon for each channel indicates the Operation mode and the Extraction mode To change the settings for a channel 1 2 Click the Setup Tab in the Run File Editor Window For each channel select the desired Ope
109. e and Description fields are searched The search results appear in the Search Result fields The Search Result tab contains the following fields Time The time the event or error occurred Source The source of the event or error Event Code The event error ID number used by Caliper to troubleshoot problems Description A detailed description of the event or error that occurred V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 225 Viewing Current Events in the Events Tab While a job or batch is running the events and errors that occur during the screening display in the Current Events tab in the Event Viewer Window e On the Event Viewer window click the Current Events tab The Current Events fields display These fields are read only The Current Events tab contains the following fields Time the time the event or error occurred Source The source of the event or error Event Code The event error ID number used by Caliper to troubleshoot problems Description detailed description of the event or error that occurred Viewing Past Events in the Events Tab All events and errors that have occurred during the screening of previous jobs or batches display in fields on the Past Events tab in the Event Viewer Window e On the Event Viewer window click the Past Events tab The Past Events fields display These fields are read only The Past Events tab con
110. e 170 Smear Analysis Tab Continued e Apply to Channels In the Method window specifies the channel in which the extraction took place In the Method Editor window specifies the channels that the smear is applied to lt All gt specifies that the smear applies to all channels Clicking on the column opens the Select Channels window to choose the specific channels to apply the smear to Export button Opens the Export Smear Analysis Table window to create a Smear Analysis Export File sma from the current settings in the tab Import the sma file into another assay to use the same smear in another assay Restore button Restores the settings to the last saved settings for smears Import button Opens the Import Smear Analysis Table window to select an Smear Analysis Import File sma to import The sma file is created by exporting smears from another assay Clear button Deletes all smears from the table V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 171 Advanced Tab V2 1 Use the Advanced tab on the Method Window to view the quantification marker settings or change the Peak Size Calibration point Method XT DNA 750 Method info Anatysa Peak Fraj Expected Fragraris Exoluded Fragments Smear Anaea Vi Fek erger Mode Seem Gane Makes Fd r s r Mate Cerf Page Earle E Two Port Tolerance Fes Lovers Marias _ Wally no Waley _ Peak Espaina Sampie Pe
111. e CDR Manager Window All hidden files and folders show in the CDR Manager window The file or folder icon indicates if the file or folder is hidden 2 Click the name of the file or folder that you want to show and click the Show button on the right side of the CDR Manager Window NOTE Files and folders in a hidden folder do not show in the CDR Manager Window even if the files are not set to hidden To show files the folder cannot be set to hidden 3 Click the Hide Hidden Files button at the top right of the CDR Manager Window 4 Close the CDR Manager Window LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 93 Remote CDR Server Backup The LabChip XT software with the 21 CFR Part 11 option installed supports backing up data files to a remote server using Subversion SVN Subversion is a third party database application used to copy data files to a remote server within the intranet To use remote backup Subversion must be installed on the remote server using the CDRServerUtilitySetup exe included on the LabChip XT Installation CD The LabChip XT software can be set up to automatically back up all new and modified data files to the Remote CDR Server Automatic backup ensures that secure versions of all data files are available and synchronized even in the event of failure of the instrument computer The following procedures are included in this section e Setting Up the Remote CDR Server on pa
112. e CDR Utility Window opens Clear the Accessible by Windows Administrator Level Users check box and then click the Apply button Click OK in the Confirmation window Click the Close button on the CDR Utility Window Close the LabChip XT software Restoring the Audit Trail Database 1 In Windows Explorer navigate to C Program Files Caliper Life Sciences LabChip XT Database Copy the backed up database DBback bak into the folder In Windows Explorer navigate to C Program Files Caliper Life Sciences LabChip XT Double click the RestoreDB bat file The Audit Trail database is restored to the backup point LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Software Reference 101 Software Reference This section describes each of the windows in the LabChip XT and XTe software Each window description describes the options and buttons on the window and how to open the window This section describes the following windows LabChip XT XTe Main Window on page 102 About LabChip XT XTe Window on page 138 Add New Expected Peak Window on page 139 Audit Trail Window on page 140 Audit Trail Export Window on page 141 Audit Trail Manage Columns Window on page 142 CDR Manager Window on page 143 CDR Server Utility Window on page 145 CDR Utility Window on page 146 Change Password Window on page 148 Data File Version Window on page 149 Event Viewe
113. e audit trails can be printed for documentation purposes The audit trail documents can be made available for agency review and copying The audit trail is a log of all of the following events that have occurred in the LabChip XT software e Administration and user management create edit deactivate user policy settings access level modifications login and lock events e Data file run events run started run finished run stopped run aborted e Data file signing events e Data file hide show events e Instrument error events e Data file version changes e IQ events e Application errors related to main database failures In Windows XP the Computer User Role records the Windows role of the user logged in to the LabChip XT software In Windows 7 the Computer User Role records either User or Administrator depending on how the LabChip XT software is Started If the LabChip XT software is started by right clicking on the icon and selecting Run as Administrator the Computer User Role is Administrator If the software is started by double clicking on the icon the Computer User Role is User The Computer User Role reflects the privilege that was used to start the LabChip XT software This section includes the following Audit Trail procedures e Viewing the Audit Trail on page 89 Exporting the Audit Trail on page 89 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 89 Viewin
114. e power cord from the wall outlet Clean the inside of the lid and the chip locator if any reagents or dyes are present Follow the instructions in Cleaning the LabChip XT XTe on page 221 Allow to air dry Close the lid and cover the instrument with a light cloth or dust cover Store the instrument in a location that meets the storage requirements in Specifications on page 218 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 224 Troubleshooting and Diagnostics This section contains the following topics to help troubleshoot problems with the LabChip XT XTe software e Searching for Events in the Events Tab on page 224 e Viewing Current Events in the Events Tab on page 225 e Error Messages on page 226 e Diagnostics on page 229 e Troubleshooting Assay Problems on page 232 e Software Problems on page 233 Cannot Save a File on page 233 Computer Software Lock Ups on page 233 e Zipping the Log Files on page 235 Searching for Events in the Events Tab Events and errors that occurred during the screening of previous jobs are displayed in the Past Events tab in the Event Viewer Window To search for a specific event 1 On the Event Viewer window click the Search Result tab 2 Inthe Events list select Current Past or All 3 Inthe Search Text box type a search query and click the Search button The Source Event Cod
115. e with the laws of the Commonwealth of Massachusetts Any dispute will be resolved in the state and federal courts of the Commonwealth of Massachusetts 9 Severability Should any term of this License Agreement be declared void or unenforceable by any court of competent jurisdiction such declaration shall have no effect on the remaining terms hereof 10 No Waiver The failure of either party to enforce any rights granted hereunder or to take action against the other party in the event of any breach hereunder shall not be deemed a waiver by that party as to subsequent enforcement of rights or subseguent actions in the event of future breaches P N 104954 Rev 3 Caliper Life Sciences Inc Index A Aborting a run 38 About LabChip XT Window 138 AC power cable 213 Add New Expected Peak Window 139 Adding a peak 55 Advanced Tab 171 Method Window 171 AIA format sis 25444348 15 77 Algorithm Baseline 161 Align marker peaks 57 Alignment OPCS 2 fad y 3 ee sede etes 215 turning on off 57 AIU sa is ss sis so 218 Analysis 53 105 242 247 250 Analysis menu 105 Analysis On Off 105 Analysis parameters 94 DNA assays 242 How the Software Analyzes DNA DOTA SKEER SARIE RAL LID oes 44 identifying peakS 250 ladder 247 Method
116. eader of each printout contains the workspace name the collection name and the page number The Footer of each printout contains the LabChip XT XTe software version the date that the workspace was modified and the print date The following information can be printed for the open workspace e Print All e Gel e Electropherogram e Overlay Electropherogram e Channel Table e Peak Table LabChip XT only e Run Report LabChip XT only See below for descriptions of each option Print All This option prints the results of the method in all of the available formats The page layout depends on the options selected in Print Settings LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 69 Gel Choosing this option prints a gel image with the lanes marked by the channel name if n igi 4 Figure 12 Printed Gel Electropherogram Choosing this option prints an individual electropherogram of each of the selected channels with one graph on each page 2 OD 1b gt se er e AT EST ET Page Figure 13 Printed Electropherogram V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Data Analysis 70 Overlay Electropherogram Choosing this option prints one graph with the electropherograms for all of the selected channels overlaid onto a single graph Figure 14 Printed Overlay Electropherogram LabChip XT XTe User Manual Caliper Life S
117. eak Height changing 54 Min Peak Width 44 248 Min Peak Width changing 54 Minimum peak height 161 248 Minimum Peak Width 161 Modifying Analysis Parameters 53 Molarity 44 248 Molecular Separation Techniques 248 Monitoring the Run 35 Mouse shortcuts 236 MOUS exer EE AO bugs tonne 8 N New Collection Window 174 New workspace 45 O Only Annotate Expected Peaks 122 Opening a Data File 46 Opening a New Workspace 45 Operating Humidity 218 Operating Temperature 218 Optical window 214 ODUCOS ai ane MERE EE HEER DRA ERA 215 Optics Test is wee ELE DEER DA 231 OO running 228 Orientation 122 Output Tab Start Fractionation Window 197 Overlay Electropherogram printing 70 Overlay Electropherograms Tab 120 Overlaying channel graphs 60 Caliper Life Sciences Inc P Pane width adjusting 61 Password sis is se 148 Change Password Window 148 Peak 44 55 171 248 249 250 A0GING sirios eee 55 AIRE he ct 135 Baseline 44 161 171 249 changing Peak Find parameters 54 Chip Peak Find Settings 161 count for smears 254 excluding 55 Height 248 249 identifying peakS 250 merging
118. ecified in the Channel Flush Time text box is used Flush button Starts flushing the channels using the times specified Stop button Stops a flush that is in progress Only displays when a Flush operation is in progress Done button Closes the window without starting the Flush operation V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 155 Layout Options Window Use the Layout Options window to change the location of the views in a collection To open the Layout Options window select Collection gt Layout on the LabChip XT XTe Main Window Layout Ouens A Ovetay Bacon Peak Tabie LA i Bectropherograms N Channel Table LA Figure 50 Layout Options Window Viewer Lists the viewers available to display in the Collection Pane Left If selected the view displays on the right side of the Collection pane The view displays at the top if any view is selected to display at the bottom of the pane Right If selected the view displays on the left side of the Collection pane The view displays at the top if any view is selected to display at the bottom of the pane Bottom If selected the view displays at the bottom of the Collection pane The view displays at the top if there are no views displayed at the top left or right in the pane Apply button Applies the selections to the active collection and closes the Layout Options window Reset to Factory Defaults but
119. ectrodes Lid Latch Lift latch to open the lid V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 213 Rear Connectors The rear connectors are used to connect the LabChip XT XTe instrument to the computer and power supply Li TRRNHUTLANTELTTTNNTHT ii lil AL LISE EL ETE SEESEES 4 Power Switch d Power Ai Connector Figure 87 Rear Connectors The following connectors are located on the back of the instrument Power Plug the power supply into this connector and a power outlet Connector WARNING MAA Appliance inlet is disconnecting device Place device or equipment in a manner so that disconnecting device is accessible at all times USB Connects the LabChip XT XTe instrument to the computer Connector Power Turns the LabChip XT XTe instrument On Run or Off Standby Switch Turning the instrument on reads the barcode on the chip if there is a chip in the instrument V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 214 Lid The lid holds the chip in the instrument and provides the voltage to the chip channels to separate the sample and move the sample in the channels Electrodes Barcode Reader Mirror Barcode Reader Window Chip Locator Optical Windows Figure 88 Lid Electrodes Apply voltage to the chip to move fluid through the chip and drive electrophoretic
120. elect the location where you want to display the Overlay Electropherograms tab and click the Apply button The Overlay Electropherograms tab opens o AL Tel E M ER _ pe 1 E l i T J a N 5 a i y I E Fin pan E aa l D a tai E e TT OT TE 5 0 500 PLN LLO ZAR 300 A ad Ti n Is a y Figure 10 Overlay Electropherograms Tab with Multiple Graphs Data from multiple channels can be overlaid in the same graph for visual comparison Each peak graph is shown in a different color and line style with a legend at the top of the window To add samples to the Overlay Electropherograms Tab Ctrl click on the sample that you want to add in the Chip View List View Gel View Channel Table View or Peak Table View Selected channels are identified by dashed outlines around the selected gel lanes in the Gel view black outlines around the selected wells in the Chip view and light blue text in the List view To remove a specific sample from the graph Ctrl click on the sample that you want to remove in the Chip View List View Gel View Channel Table View or Peak Table View Note The list view is not displayed in the LabChip XTe software V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 64 Viewing Graphs in the Electropherograms Tab V2 1 If the Electropherograms Tab is not open select Collection gt Layout on the LabChip XT XTe Main Windo
121. els LabChip XT only V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 120 Overlay Electropherograms Tab Use the Overlay Electropherograms tab on the Graph View to view a single graph or multiple graphs overlaid on top of each other HA Sample 4 EE fi 1000 1500 UL 500 MY Aligned Time ec Figure 27 Overlay Electropherograms Tab The sample list at the upper right displays the name of each sample and the color assigned to the graph for each sample If only one graph is displayed the Gel View Channel Table View and Chip View or List View all show the same selected channel The gel lanes selected in the Gel View are synchronized with the graphs displayed in the Overlay Electropherograms tab For information on changing the view in the Overlay Electropherograms tab see Viewing Graphs in the Overlay Electropherograms Tab on page 63 See Graph View Properties on page 122 for descriptions of the properties that can be set for the Overlay Electropherograms tab V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 121 Electropherograms Tab Use the Electropherograms tab on the Graph View to view a single graph or multiple graphs in the same tab dectropherograms Overlay Electropherogram Sassari id Aar Krag RE Figure 28 Electropherograms Tab Each graph displays the data file name and channel name at the top of the graph
122. en applications and then turning off the power to the computer After a few seconds restart the computer open another file and try resaving it to verify the Save function is working properly LabChip XT XTe software is corrupted Reinstall the software If the problem persists contact Caliper Technical Support see page 2 Computer Software Lock Ups V2 1 If a computer or software lock up occurs 1 Try to exit and then re launch the LabChip XT XTe software 2 If this is not successful exit the application using the Task Manager a Right click in the desktop menu bar and select Task Manager b Click on the Applications tab c While holding down the Shift key select all running applications LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 234 Computer Software Lock Ups Continued d Hold the Ctrl key and click End Task 3 Ifthe Task Manager cannot be accessed try one or all of the following e Press the Ctrl Alt and Delete keys on the keyboard simultaneously e Perform a hard reboot by turning off the computer and then restarting it e Power cycle the LabChip XT XTe instrument 4 If problems persist contact Caliper Technical Support see page 2 Software Display Flashes During a run the views in the LabChip XT XTe software may flash occasionally as the new data is displayed Do not run any other software applications while running the LabChip XT XTe so
123. er Show User Info Use the Show User Information tab on the User Administration Window to view the account information for an existing username EN Latii ET Lau Adrrenmiranen P 4 4 Figure 82 User Administration Window Show User Info The Show User Info tab contains OmionButon Pon o Can Perform Displays Yes if the user has rights to perform signatures using Signature the Perform Signature Window Displays No if the user does not have rights Can Displays Yes if the user has rights to accept reject and lock Accept Reject Lock data files in the Perform Signature Window Displays No if the Data File user does not have rights Can Unlock Data Displays Yes if the user has rights to unlock data files File Displays No if the user does not have rights Account Created Displays the date and time when the account was created On V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 207 Account Last Displays the date and time when the account was last Changed On changed Status Displays Active if the user account is activated Displays Deactivated if the account has been deactivated Print All Users If selected information for all user accounts will be printed check box Print Preview Displays a preview of the printed report The report can be button exported to a rpt file from the Print Preview window Print button Opens the Print window to print the report De Activate User
124. er Area The expected area of the lower marker in a sample Data Range Baseline Specifies the time in minutes after the start of the run when the first peak can appear any peaks appearing before this time are ignored Channel End Specifies the time when peak detection stops The graph ends at this time LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 161 Peak Find Tab V2 1 Use the Peak Find tab on the Method Window to adjust parameters to detect peaks for individual channels or the entire chip specified in the Chip field Method XT DMA 750 Fed peces Fragments Escluded Fragments Smear rats Acranced Channel Mame ae site H Ladder Lisa Chip Wales Less Chip rales Cases Chip ere Regen Ose Ok Pre Preis Pant Cancel Figure 54 Method Window Peak Find Tab To change the options for all channels on the chip change the options in the Chip Peak Find Settings at the top of the window see Table 1 on page 162 To select a single channel right click on a channel in the Gel View or a graph in the Graph View and select the Analysis Settings option The settings for the single channel are displayed in the Channel Peak Find Settings fields at the bottom of the window see Table 2 on page 163 Select other individual channels in the chip by selecting the channel name in the Channel drop down list The chan
125. er A oi E Fede Table EES fe Landesaps Channel Table Channel Orion Sens amp FEE FA Peak Table Eers Colechon Pe Page sasda O i Buse e Per Dhara E ra Print To POF Peri Carmel Figure 62 Print Window The Print window provides the following options for printing e Print All Selects all of the options e Gel Prints a graphic of the gel for either all channels in the collection or all selected channels e Electropherogram Prints a graph of either all channels in the collection or all selected channels e Overlay Electropherogram Prints a graphic of all electropherograms either all selected or all in the collection over laid onto the same graph e Channel Table Prints the channel table for either all channels in the collection or all selected channels The columns selected for view in the Channel Table are printed Changing the columns selected to view in the Channel Table View changes the columns that are printed e Peak Table Prints the peak table for all channels in the collection or all selected channels The columns selected for view in the peak table are printed Changing the columns selected to view in the Peak Table View changes the columns that are printed e Exclude Marker If selected markers are not printed LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 177 Print Window Continued Page Option Select the page orientation either Portrait or Landscape
126. er Administration Window This window only displays if the 21 CFR Part 11 option is installed The 21 CFR Part 11 Security option is not available for the LabChip XTe software LabChip XT Unlock Application LabChip XT has been locked Orly adminestralor or an Administrator can unlock th s application sename EEM streke Password ok Figure 77 Unlock Application Window The Unlock Application Window contains Option Button Function Username Type the user name of the current user or a LabChip XT administrator s user name Type the password for the specified user name OK button Verifies the username and password and opens the LabChip XT software if the username and password are correct V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 202 Unlock Data File Window For LabChip XT software with the 21 CFR Part 11 Security option installed use the Unlock Data File window to unlock a data file The user name must have the appropriate permissions The 21 CFR Part 11 Security option is not available for the LabChip XTe software su Unlock Data file 84 8 You ane curenty unlocking the data fie Calper_20110323 10 14 46 Leman adeinetralor si Role o This Fe a beng unlocked Pame explain reason for his ection Enter Reason Ender your user Figure 78 Unlock Application Window The Unlock Data File Window contains Select the username of the user that is unlockin
127. er information 1 On the LabChip XT XTe Main Window select Security User and System Administration The User Administration Window opens 2 Click the Edit Users button 3 Select the user to edit from the User drop down list 4 Change the User Information as necessary First Name Middle Name Last Name Position Access Level User Can Perform Signature Accept Reject Lock data files Unlock data file User Password 5 Click the Save button to save the updated user information V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 82 Printing User Information After editing a user account in the LabChip XT software the user details can be printed for record keeping purposes To print the user information 1 On the LabChip XT XTe Main Window select Security gt User and System Administration The User Administration Window opens 2 Clickthe Show User Info button 3 To print the information for a single user select the user name in the Select User to Display list box 4 To print the information for all users select the Print All Users check box 5 To preview the printout click the Print Preview button 6 To print the selected information click the Print button Activating and Deactivating User Accounts If a user name is not going to be used the user account can be deactivated in the LabChip XT software The user name is not removed from the system but cannot be used to l
128. er the size of the expected fragment in bp In the Window column if desired change the tolerance value to allow for variations in the expected fragment size This value is specified as a percent of the expected size for that fragment The default is 10 for DNA Note If there are multiple peaks in the tolerance range the largest peak is labeled as the expected peak even if it is not the exact size specified To change the peak identified as an expected peak see Forcing Expected Peaks on page 50 A default color is automatically assigned To change the color click on the color block in the Color column and select the desired color in the Color window If desired change the name shown in the Name column If desired change the Property Displayed in the Channel Table This setting specifies the property that will be displayed in the Expected Peak column for each expected peak listed in the Channel Table View To apply the expected peak only to specific channels double click in the Apply to Channels column The Select Channels window opens Click to select the channels that you want to apply the expected peaks to and then click the OK button To apply the EFs to the active chip click the Apply button To apply the EFs to all chips in the workspace click the Apply Global button LabChip XT XTe User Manual Caliper Life Sciences Inc Exporting EFs Importing EFs V2 1 Data Analysis 49 Only supported in La
129. ereuse risque de blessure par electrocution Crush hazard Risk of body parts hair jewelry or clothing getting caught in a moving part Danger d crasement Faire attention que les parties corporelles les cheveux les bijoux ou les v tements ne soient pas pris dans une piece mobile Risk of puncture injury Risque de blessure par piq re A Risk of exposure to biohazards LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Preface 5 Table 1 Important Symbols Continued Symbol Description Symbole Description Risk of eye injury wear safety glasses Risque de lesion oculaire porter des lunettes de s curite Risk of fire Risque d incendie Risk of poison Risque d empoisonnement Risk of explosion Risque d explosion Hazardous fumes Emanations dangereuses A Laser light avoid exposure Risk of eye injury Rayonnement laser viter toute exposition Risque de l sion oculaire Lifting hazard May result in injury Levage dangereux Peut entra ner des blessures Protective ground symbol Symbole de terre de protection Ground symbol Symbole de terre Fuse Fusible Alternating current Courant alternatif On supply Marche alimentation D Off supply ka Arr t alimentation CE compliance mark Marque de conformit CE Signifies that the unit has passed safety tests for grounding power line transience and current leakage Signifie que l appareil a r ussi les te
130. eview button To print the access rights click the Print button Setting Policies for User Accounts V2 1 User Account Policies specify properties such as password options and whether to require a signature when updating data files in the LabChip XT software 1 On the LabChip XT XTe Main Window select Security User and System Administration The User Administration Window opens Click the Set Policies button Set the options as desired e Password Expires After The number of days until each password expires Range is 1 to 1000 days Number of Retired Passwords to Remember User cannot reuse the specified number of old passwords Range is from O to 5 e Minimum Password Length The minimum length of each password Range is from 5 to 30 characters e Maximum Login Attempts The maximum number of times the user can attempt to log in before being locked out of the LabChip XT software Range is from 3 to 20 This option can be disabled to allow unlimited retries without locking the user out e Minutes to Automatic Lock The number of minutes that the software is inactive until the LabChip XT software locks automatically Range is from 5 to 4320 minutes 3 days To disable this option clear the check box To unlock the software see Locking and Unlocking the Software on page 79 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 85 Setting Policies for User Accounts Continue
131. ew Continued Example Expected Peaks Filter In the example below the sizes 100 10 300 10 and 500 10 are selected with each expected peak size identified by a different color This filter will select any channels that contain all three expected peaks 100 300 AND 500 Note that the filter is selected checked under Available Filters indicating that the filter is being applied to the data EE PE rs m To select channels that contain any of the three peaks create a separate filter for each peak and select OR as shown below V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 126 Filter View Continued When using multiple filters that include peak properties if AND Peak is selected a single peak in the channel must meet all selected filter properties See the examples below which each use two filters e Height gt 100 AND Peak Conc gt 50 selects any channel that contains a single peak that meets both criteria e Height gt 100 OR Conc gt 50 selects any channel that contains a peak that meets either or both criteria e Height gt 100 AND Peak Height lt 50 does not select any channels because a single peak cannot have a height that is both less than 50 and greater than 100 Use OR to select channels that have peaks that match either criteria Use AND Channel to select channels that contain peaks that match both crite
132. ew channel table Selecting both the Channel Table and the Peak Table prints each channel on a separate page with the Channel Table row at the top of the page and the Peak Table for the channel below it pese eir ro EET Caliper_MAWADLEYL_04 31 25 CHA Sampie 4 Figure 16 Printed Peak Table LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Data Analysis 73 Run Report LabChip XT only Choosing this option prints a one page summary of the run which includes the gel for each channel the Electropherogram for each channel Run Information and the columns displayed in the Channel Table View To change the columns that are printed or the order of the columns change the columns in the Channel Table View e Selecting the Add Border check box prints the table with a border around each cell in the table i impir FES LE l l A a I EIER oem Figure 17 Printed Run Report LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 74 Exporting Data V2 1 Data from a Peak Table Channel Table Gel or Graph can be exported automatically and or manually in the LabChip XT software Options selected for automatic export do not affect manual export options and vice versa e To automatically export data during the run select the desired settings in the Start Fractionation Window as described in Select the Auto E
133. extracted material from the Collection well Using a Collect and Stop step ensures that the collected material is not drawn out of the collection well while other channels are completing their extractions The Flush Sample step after a Collect and Stop step moves the remaining sample to the waste well Flush Sample must be the last step in the channel and can be preceded by any of the Extraction operations except the Ladder Separation or Exclude Region steps Extraction Mode Specifies how the range of material to be collected is selected The range of material extracted depends on both the Extraction Mode and the Collection Width Size The size range specified in the Extraction Region text boxes is diverted to the Collection well Size range can be specified as a Size a percent of the size or as a specific start and end size in the Extraction Region text boxes Trigger The software searches for the specified trigger point within the specified Search Region Auto MultiStep Cut If selected an extraction range larger than the assay Maximum Extraction Width can be entered for an extraction The extraction is automatically split into multiple eXtract and Pause steps To view the MultiStep Cut steps click the Review Setup button on the bottom of the Start Fractionation window Only available if Extraction Mode is Size and Operation is eXtract and Stop eXtract and Continue or eXtract and Pause LabChip XT XTe User Manual Caliper L
134. fault on the main window The Collection menu is not available in the LabChip XTe software The Analysis menu in the LabChip XT software contains the following commands Turn On Off Analysis Toggles analysis on and off When analysis is on the data displayed in the main window uses the analysis settings in the Method Window When analysis is off the raw unanalyzed data displays Scale to All Peaks Scales the view to the minimum and maximum X values of the current sample peaks Marker and or system peaks are ignored Analysis Settings Opens the Method Window to choose analysis parameters for the chip Use these settings to change the analysis and peak finding parameters to help resolve hard to decipher data Standard Curve Opens the Standard Curve Window to view the ladder as a curve with a point to point fit The Analysis menu is not available in the LabChip XTe software LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 106 Instrument Menu The Instrument menu contains the following commands Start Run Opens the Start Fractionation Window to begin running a sample chip See the Assay User Guide for chip and sample prep instructions Changes to Stop Run while a chip is running Stop Run Displays a Stop Run window to stop the run Click the Yes button to stop the run Click the No button to continue the run Flush Chip Opens the Flush Chip Window to flush the selected channels on a ch
135. file click the Copy Table from Method button LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 30 Select the Output File Locations V2 1 1 Click the Output Tab in the Run File Editor Window 2 To change the Data Path click the Browse button and select the desired location for the data files Clicking the Default button restores the default data path NOTE Data files should be saved to a local folder on the computer s hard drive Saving data files to a network drive may cause loss of data if the network connection is slow or interrupted 3 If desired select the Create Daily Sub Directory check box to create a new sub directory for data files each day If the 21 CFR Part 11 option is installed and you want to save a copy of the data files to a folder outside of the CDR or if the 21 CFR Part 11 option is not installed and you want to save a second copy of the data files a Select the Copy To check box b Click the Browse button The Browse for Folder Window opens c Navigate to the folder where you want to save the exported copies of the data files d Click the OK button to choose the selected folder The path displays in the Copy To text box on the Output Tab In the File Prefix text box type the desired prefix for all data files The File Name Example text box displays the selected format for the data files To add the Computer Name Project Name Chip ID LabChip XT only Date an
136. ftware especially while a run is in progress The LabChip XT XTe Controller should only be used to run the instrument and should not be used for general computing tasks V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 235 Zipping the Log Files The Caliper Log Zipper is a small software utility that zips the LabChip XT log files and system info files and places the resulting DiagnosticsLog zip file on the computer desktop This utility can be used to package all of the log and diagnostic files together if the files need to be emailed to Caliper Technical Support V2 1 To zip the LabChip XT diagnostics logs 1 On the Windows desktop select Start gt All Programs gt Caliper Life Sciences LabChip XT Caliper Log Zipper The Caliper Log Zipper window opens E caliper Log Zipper I mi This Lit well np al the diagnostics related direclones and files Figure 91 Caliper Log Zipper Window Click the Zip button The DiagnosticsLog zip file is saved to the computer desktop Any existing older file with the same name is over written To save a copy of the file either rename the file or move the file to a different location LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Tips and Shortcuts 236 Tips and Shortcuts This section describes the shortcuts and actions that can be performed in the LabChip XT XTe software by clicking right clicking etc Si
137. g the Audit Trail To view LabChip XT events in the Audit Trail Log 1 7 On the LabChip XT XTe Main Window select Security Audit Trail Log The Audit Trail Window opens Select the desired data range e Select whether to view most recent entries entries between specific dates or the entire database e Select the number of entries or dates to search if Entire Database is not selected To view only events performed by a specific user select a user name To view events for a specific data file select the name of the data file To search only specific types of events select the desired Event Category in the Event Category drop down list Default shows all events To change the columns that are displayed click the green arrow button next to Event Category and select or hide the desired columns Click the Search button to search the database Exporting the Audit Trail The LabChip XT events displayed in the Audit Trail Window can be exported to a file To export the events V2 1 1 On the LabChip XT XTe Main Window select Security Audit Trail Log The Audit Trail Window opens Click the Export button in the Audit Trail Window The Audit Trail Export Window opens Select the desired export file format e Text e XML e Excel Click the Export button The Save As window opens Choose the desired location for the file type the desired file name and click the Save button By default the file name i
138. g the data file Reason Type the reason that the data file is being unlocked Follow laboratory procedures for required information Type the password for the selected user name Unlock button Verifies the username and password and unlocks the data file Locked data files cannot be saved Cancel button Closes the Unlock Data File window without unlocking the data file V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 203 User Administration Window V2 1 For LabChip XT software with the 21 CFR Part 11 Security option installed use the User Administration window to create new LabChip XT users to edit existing users to view user information to activate or deactivate users to set rights for each access level and to set LabChip XT software policies The 21 CFR Part 11 Security option is not available for the LabChip XTe software To open the User Administration window choose Security gt User and System Administration Ls Lap iip ET aar Adrrenatranen LE Figure 79 User Administration window The User Administration window contains the following tabs e Create New User on page 204 e Edit Users on page 205 e Show User Info on page 206 e De Activate User on page 207 e Define Access on page 208 e Set Policies on page 209 Close button Closes the User Administration window without saving changes Save the changes on each tab before closing the
139. ge 82 Changing Access Rights on page 83 Printing Access Rights on page 84 Setting Policies for User Accounts on page 84 Printing User Policies on page 85 Adding New Users V2 1 Each person who uses the LabChip XT software should have a unique LabChip XT user account To add a new user 1 O a BR N On the LabChip XT XTe Main Window select Security gt User and System Administration The User Administration Window opens Click the Create User button Type the desired Username Type the First Middle and Last Name for user Type the user s Position if desired Select the Access Level for the user The Access Level controls which rights the user has The following access levels are avallable Type the desired User Password Restricted User Operator Supervisor Administrator Service LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 81 Adding New Users Continued 8 Type the User Password again 9 Select whether the user can perform a signature 10 Select whether the user can Accept Reject Lock data files 11 Select whether the user can Unlock data Files 12 Click the Save button Passwords must be at least 5 characters long and must contain at least one uppercase letter and at least one number Changing User Information After a user account is created in the LabChip XT software the user details can be edited To change the us
140. ge 93 e Backing Up Data Files to the Remote CDR on page 95 e Restoring Data Files from the Remote CDR on page 96 To back up the Remote CDR Server either back up the entire C drive on the remote server or back up the C RemoteCDR folder The LabChip XT software also contains an option to copy the data files to an unsecured location on the local hard drive These data files do not meet 21 CFR Part 11 security requirements after they are copied out of the CDR To copy data files to a non secure location use the Copy button on the CDR Manager Window Setting Up the Remote CDR Server V2 1 To back up copies of LabChip XT data files on 21 CFR Part 11 compliant systems and keep the copies of the data files secure back up the files to a Remote CDR Server The Remote CDR Server must be running Windows 7 To set up the Remote CDR Server 1 Ifthe CDR Server Utility is not already installed on the remote server see the Readme htm file on the LabChip XT Installation CD for instructions on running CDRServerUtilitySetup exe 2 Onthe Remote computer double click on the CDR Server Utility icon on the Windows desktop The CDR Server Utility Window opens LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 94 Setting Up the Remote CDR Server Continued 3 Ifthe Server has not been created on the computer yet click the Create Server button to create the server The default folder name and location C Rem
141. gnostics Window Use the System Diagnostics window to run the diagnostics tests on the LabChip XT XTe instrument All tests should be run periodically to verify proper operation of the instrument To verify proper operation of a particular function you can select specific tests to run To open the System Diagnostics window select Validation Diagnostics System Diagnosobcs J Laser Lis Aapan Pant Summary Pred Onse Status Idle Overall Progress Test Progress Figure 76 System Diagnostics Window The Barcode Reader test is not shown in Figure 76 The left side of the window displays the tests to run on the instrument Expand each section to view all of the tests in each section Tests selected with a check mark will run To skip a test click on the check box to clear the selection Click on a section check box to select or clear all of the tests in the section See Description of Diagnostic Tests on page 230 for a description of each test V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 200 System Diagnostics Window Continued The right side of the window displays the results of the tests The Icon color indicates the status of each test e Blue The test is in progress e Yellow The test was skipped e Green The test passed e Red The test failed or was aborted The bottom of the window displays a progress bar for the entire set
142. h as disk cleanup after installing antivirus software or after installing Microsoft service packs The Installation Qualification checks LabChip XT XTe software registry settings the directory structure and the integrity of each file specified for the software application To run the IQ 1 On the LabChip XT XTe Main Window select Validation gt Software IQ The Software Installation Qualification Window opens 2 To view the results of the previous IQ before running a new IQ click the Previous Result button The View Installation Qualification Results Window displays the results of the last 1Q that was run 3 To start the IQ click the Start IQ button The Installation Qualification window displays the tests that are run for the IQ the progress of each test and the Pass Fail status of each test as it is completed 4 To save the results of the IQ click the Save As button specify the desired location and name of the file and click the Save button IQ results are saved as xml files Running Operational Qualification OQ V2 1 The System Diagnostics window performs an automated Operational Qualification whenever required by your laboratory procedures The System Diagnostics Window displays the tests that are performed on the left side of the window The test results are displayed on the right side of the window After all tests are complete the test report is generated and saved to a file for review printing and docume
143. h View right click on the peak that should be labeled as the expected peak 2 Onthe shortcut menu select Force Expected Fragment and then select the desired fragment from the menu To clear a forced peak and revert to the default expected peak right click on the forced expected peak and select Clear Forced EP Viewing the EFs in the Graph View Expected Fragments are identified in the electropherogram in the LabChip XT software by solid triangles over the peaks The triangles are the same color as specified in the Expected Fragments Tab To display the expected peak indicators in the Graph view 1 Click the Properties tab on the right side of the Graph view to open the Graph View Properties 2 To view the size of all expected peaks select Expected Fragments in one of the Annotation list boxes L L on Ee L 1500 LM 1000 DO 10 20 30 40 50 Aligned Teme men Figure 5 Expected Fragments in Graph View Ih 10 ad Ju laal LJ Waad y w Fluorescence 500 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 51 Viewing the EFs in the Gel View Expected Fragments are indicated in the Gel View by colored lines in the LabChip XT software The color of the line matches the color specified in the Expected Fragments Tab To display the expected peaks in the Gel View 1 Click the Properties tab o
144. h tab automatically selects the same channel on the Gel tab Selecting a peak in the Peak Table automatically selects the same peak in the Graph tab and the Gel tab Closing a gel on the Gel tab closes the graph for the channel and removes the channel data from the Peak Table and Channel Table tabs LabChip XT XTe User Manual Caliper Life Sciences Inc Graph View V2 1 Software Reference 117 The Graph view in the Collection Pane is a visual representation of the data from each channel as an electropherogram The Graph view contains the Overlay Electropherograms Tab and the Electropherograms Tab to view data while a run is in progress or after the run is complete For information on changing the view in the Overlay Electropherograms tab see Viewing Graphs in the Overlay Electropherograms Tab on page 63 For information on changing the view in the Electropherograms tab see Viewing Graphs in the Electropherograms Tab on page 64 Figure 26 Graph View If Type is selected as an annotation the lower markers are displayed in the graph view with green arrows labeled LM The currently selected peak in the Gel view or Peak Table displays a blue arrow above the peak You can zoom in and zoom out the Graph View of the channels Zoom in by clicking and dragging over a region of an electropherogram Zoom out by right clicking on a graph and selecting either Unzoom or Unzoom All from the shortcut menu Double clicking in
145. he Overlay Electropherograms Tab Thiet on Peak Trigges on Peak a E E qn La ad T 4 5 Y Ll Figure 32 Gel View Moving the cursor over a band in the Gel view displays a tool tip that includes the same information about the peak as the Peak Table View Changing the columns displayed in the Peak Table will change the contents of the tool tip in the Gel view Expected Peaks are indicated on the gel by colored horizontal lines Smears representing the portion of the sample that was routed to the collection well are indicated on the gel by colored regions in the gel For DNA assays the lower markers of all channels are aligned to the lower marker of the first channel in the gel view LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 129 Gel View Continued V2 1 A colored column header indicates that the channel is selected by a filter Click the Filter View to view the color of each filter A red exclamation point under the header indicates an analysis error occurred in the channel A yellow exclamation point under the header indicates an analysis warning occurred in the channel A gray header indicates a normal channel To change the size of the gel header click on the border between the header and the channel and drag the header to the desired size The graphs displayed in the Graph View are synchronized with the lanes selected in the Gel tab You can drag and d
146. he equipment may be impaired AVERTISSEMENTS AA e Pour r duire le risque de choc lectrique ne pas retirer le couvercle Ce produit ne contient aucune pi ce pouvant tre r par e par utilisateur Au besoin confier l appareil a un r parateur qualifi e Ce produit ne doit tre utilis que comme d crit dans ce manuel Si cet appareil est utilis d une mani re autre que celle sp cifi e par le fabricant la protection fournie par l appareil peut tre entrav e If you have a question about a product that is not answered in this manual or online Help or if you need assistance with this product contact the Caliper Technical Support Center from 8 00 A M to 8 00 P M Eastern Time Monday through Friday Phone 508 435 9761 877 LabChip for LabChip products only Fax 508 435 0950 Email technical support caliperLS com Internet www caliperLS com LabChip XT XTe User Manual Caliper Life Sciences Inc Preface 3 For support in Europe contact Caliper Life Sciences LTD Runcorn UK 44 1928 711448 or fax 44 1928 791228 For more information contact your local Caliper representative Before you call have the following information available e Product serial number e Software version found by choosing About from the main Help menu e If applicable the error number shown in the software or in the log file Product Service and Customer Support Plans Caliper offers a full range of services to ensure you
147. he laboratory can specify a particular data file name prefix to easily differentiate data files e A new folder can be created each day to store the data from all runs To automatically create the folders select the Create Daily Sub Directory check box on the Output Tab in the Start Fractionation Window Opening a New Workspace V2 1 A workspace displays data from one or more chip data files from the same type of assay Each workspace can contain one or more Collections to display the data In the LabChip XTe software open a data file to automatically open a new workspace TO open a new workspace 1 On the menu bar select File gt New Workspace If changes have been made to an open workspace you are prompted to save any unsaved changes A blank workspace opens in the LabChip XT XTe Main Window To view data see e Opening a Data File e Adding a Collection to a Workspace e Using Expected Fragments e Modifying Analysis Parameters LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 46 Opening a Data File Open a data file to view the data to compare the data to other data files in the same workspace or to change analysis settings and view the reanalyzed data Data files generated by the LabChip XT software have an xtd file extension Data files generated by the LabChip XTe software have an xte file extension To open a data file 1 V2 1 Open a new workspace see page 45 or a workspace tha
148. hip XT XTe User Manual Caliper Life Sciences Inc Software Reference 147 If selected all new or edited data files are Remote CDR automatically copied to the specified remote database Remote CDR Specifies the path to the remote database Database Folder Name Specifies the name of the folder in the database in which to save copies of the data files User Name Specifies the user name assigned to the folder when the folder was created Password Specifies the password assigned to the folder when the folder was created Apply button Applies the changes and closes the window Cancel Closes the window without saving any changes button V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 148 Change Password Window Use the Change Password Window to change the password for the Current user To change passwords for other users see User Administration Window This window is only available if the 21 CFR Security option is installed with the LabChip XT software To open the Change Password Window select Security gt Change Password on the LabChip XT XTe Main Window E Change Password A Lie adminstraior Curent Passeord onion Password OK Caral Figure 45 Change Password Window The Change Password Window contains the following options Username Displays the user name for the current user Current Type the current password for the current user Password New Type the new p
149. hip XT XTe User Manual Caliper Life Sciences Inc Software Reference 179 Rename Collection Window V2 1 Use the Rename Collection window in the LabChip XT software to rename the currently selected collection The collection name displays on the Collection tab at the top of the LabChip XT XTe Main Window To open the Rename Collection window select Collection gt Rename Collection on the LabChip XT XTe Main Window Rename Collection A Figure 64 Rename Collection Window Name Type the desired name for the selected collection LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 180 Run File Editor Window Use the Run File Editor window to create run files xml to import run settings into the Start Fractionation Window The run file contains all of the run settings that would be specified in the Start Fractionation Window Using a run file enables you to quickly specify the settings for the run after the chip has been prepared To open the Run File Editor window choose Tools gt Run File Editor on the LabChip XT XTe Main Window Stars Fractionation Frectionaten Methed VET DAA NO aH gt x Buster Leke ster j Liam into iang Table Output TR Ed mo import Een i k _ Ta lag Chg A a I 5 at a Sau Figure 65 XTe Run File Editor Window The tabs on the Run File Editor contain the same options as the tabs on the Start Fractionation window See S
150. hreshol Additional inflection points da 200 Iser are inside threshold E f 400 f on E Me H ach L 2 200 1 156 0 14 19 2 iga 19 6 19 6 20 ZO 2 20 4 Sos Time sae Figure 95 Slope Threshold 200 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 246 Lab on a Chip The generic term for a microfluidic product signifying a chemical process or material movement taking place on a microchip In contrast to analysis in a standard laboratory that relies on human intervention at several stages to manipulate or observe samples and record results the self contained lab on a chip represents an almost hands iree technology Ladder A channel on the chip can be designated as a Ladder channel if it is running a Real Time Ladder at the same time the samples are running A default Caliper Ladder is provided if all four channels of the chip are used to run samples The ladder is used to calculate sample sizes and migration times of the sample to accurately determine the collection start time and collection end time for each sample In the LabChip XT software the Peak Table View for the ladder channel shows the peak size and concentration set in the Method Window Caliper_04 31 va Sizing Ladder L L L L Time in Figure 96 Ladder Graph Fluorescence V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 247
151. icing situations requiring the return of equipment to Caliper equipment must be returned to Hopkinton MA USA or another facility designated by Caliper Customer shall prepay shipping charges for equipment returned to Caliper and Caliper will pay for return shipment to Customer Returned Material Authorization RMA must be obtained for any equipment being returned to Caliper Contact the Caliper Technical Support Center by telephone at 508 435 9761 or via the Internet at techsupport caliperls com or by fax at 508 435 0950 before returning any equipment to Caliper Customer must complete a Caliper Chemical Questionnaire prior to the issuance of an RMA All equipment returned to Caliper must first be decontaminated to meet Caliper and United States Department of Transportation procedures and standards for the safety of Caliper personnel F Hazardous Limitation Statement At no time will Caliper personnel perform service on unsafe equipment perform service in unsafe environments or decontaminate equipment to make it safe Prior to performing any service work Caliper personnel will evaluate the condition of the equipment and the environment in which the equipment is located If Caliper determines that the equipment and or the environment could be hazardous to Caliper personnel Caliper reserves the right to refuse to service the equipment Il MICROFLUIDIC CHIPS Caliper warrants that microfluidic chips each a Chip purchased from
152. ife Sciences Inc Data Analysis 53 Modifying Analysis Parameters V2 1 Some analysis parameters can be changed in the software to modify the data evaluation for sample analysis The following procedures are included in this section Changing the Peak Find Parameters Adding a Peak Excluding a Peak Merging Two Peaks Changing the Time Window for Analysis Aligning or Unaligning the Marker Peaks These settings can be changed after the run is complete or when reanalyzing a previously saved data file NOTE Only expert users should change analysis settings while the run is in progress since changes can affect extractions LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 54 Changing the Peak Find Parameters V2 1 After data filtering the peak find algorithm locates the peaks and calculates the local peak baselines The algorithm begins by finding all the peaks above the noise threshold to determine the baseline after which any peaks below the noise threshold are rejected A local baseline is calculated for each peak to allow for baseline drift The following Peak Find parameters can be changed in the LabChip XT software e Min Peak Height e Min Peak Width e Slope Threshold e Inflection Threshold e Start Time e End Time e Filter Width e Baseline Plateau The LabChip XTe software does not support changing analysis parameters To change the Peak Find parameters for all channels 1 Sele
153. ife Sciences Inc Software Reference 191 Setup Tab Continued V2 1 Trigger Extraction Modes Peak Start Specifies a slope Threshold in RFU minute to use to detect the start of a peak within the specified Search Region The trigger point for collection is the point where the slope is greater than the specified threshold Collection ends when the sample specified by the Collection Width has been collected Collect on Click Collects the region displayed in green on the Graph View when you click the Start Now button To start the extraction click on the word CLICK next to the channel number in the LabChip XT XTe Main Window The Fractionation Pending Window opens Click the Start Now button when the desired region is displayed in green Clicking the Cancel button closes the window and allows you to choose a region later in the run The collection region displays in red as the collection is occurring Note that for some width settings the target region may extend beyond the last visible data point on the graph In this case the highlighted region ends at the last visible data point and the dialog box indicates the time when the target region ends When manual mode is selected in the width setting click on the word STOP in the Run Setup section to end the collection or exclusion Fluorescence Specifies an RFU Threshold which must be exceeded within the specified Search Region The trigger point for collection is the point where
154. ified by the Extraction Mode which moves into the Collection well The sample minus the excluded region is located in the Waste well The sample in the channel runs until the end of the chip range In a multistep extraction the next step begins immediately after the excluded region is complete Only available in the LabChip XT software LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 190 Setup Tab Continued V2 1 Separation The entire sample in the channel moves into the Waste well The channel runs until the end of the chip range Only available in the LabChip XT software eXtract and Pause The sample in the channel runs until the extraction is complete When the extraction is complete the run immediately pauses so the desired extracted sample can be removed from the Collection well The method can also be edited while the run is paused In a multistep extraction the next step begins when the run is resumed Skip Extraction Skips over a known region in the sample without extracting any sample to the Collection well Automatically moves to the next step in a multistep extraction immediately after the skipped region is complete Only available in the LabChip XT software Flush Sample The remaining sample in the channel moves into the waste well If preceded by an extraction step execution of this step only begins after the run has been paused and the instrument lid has been opened to remove the
155. il SES ente ee ie a tad lot aa cea 205 Show User INTO Ln Ge ge ee Ge GE ea re ei ecte 206 De ord Vee HE ef EE EE GE EE EE EG EN Te 207 PS TINS CCC SS ra cst sored at Ee NR AE EE EE GR eee es De 208 IS 209 LabChip XT XTe Instrument Description RE RE RE RE RE RE ER ER DR RE RE RE RE Re 211 FOL VIEW ED Os 212 Rear CONMCCIONS rn da ri 213 A EE a ee A O A A A AS 214 High Voltage Interface vesical 214 ODIOS SE Re da 215 EA COU Reader RE ER DE SG e ata Lic tdi OE RE ee ie i 215 TE HIDE vt Dee EED Se ES ER GE aa 216 USB Key for 21 CFR Part 11 Option 217 Spectator a A 218 Maintenance and Service soni a ta 220 Cleaning the LabCnip XT X Te acc ER RD GE GE Be Ee ER OEE 221 Cleaning the estoi dit 222 ONG Term SKULdOWD tica dadas 223 Troubleshooting and Diagnostics RE RE ER ER ER ER ER ER RE Re Rek ERG Re Re RE Re ER ER EE 224 Searching for Events in the Events Tab 224 Viewing Current Events in the Events Tab 225 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Table of Contents 16 Viewing Past Events in the Events Tab ie se se se se se se se se se Ee Ee ee ee ee ee ke ee ee ee ee 220 ENORMES SO CG od DE AD ED ca 226 Device lt Name gt is Disconnected 4 226 IT Festraled ida iia 227 Current Leakage Check Failed UV 227 Running Installation Qualification IQ ocoococconconocncnconocnnncononnncnononnnnnnncnnos 228 Running Operational Qualification OQ ee Ee EA AR ER AA ek
156. ile that you want to export the data from Select File Export The Export Window opens Select the check boxes next to the views to export Selecting Export All selects all check boxes For each selected view to change the location for the files click the Browse button and select the desired location If Raw Data is selected choose the desired export options e Select AIA Format to export in Chromatography Data Interchange Format used by some graphical analysis software The Include Size Data and Export Single Table options are not available with AIA Format e Select Include Size Data to align the data to the channel s ladder for one file per channel or to the first channel for a single data file and include the size data in the exported data e Select Export Single Table to export the data for all channels in the chip to one CSV file If not selected the data from each channel is exported to a separate CSV file lf Electropherogram is selected select either Entire Collection to export a graph for each channel in the collection or select Selected Channels to export a graph for each selected channel If Gel is selected choose the desired export options e Select Entire Collection to export all of the channels in the collection or select Selected Channels to export only the channels that are selected in the Gel view e Select Single File to include gels for all channels in the same image file or select Separa
157. ill be extracted from the collection well To compute the mass of the collected DNA multiply by the sample volume in uL For example for a typical sample volume of 10 uL the collected mass will be 10 times the reported concentration To estimate the concentration in the collection well divide the mass by the buffer volume in the collection well 20 uL The Conc of Collections column is not shown by default but can be viewed by right clicking on the column headers in the Channel table and move the column to the Selected columns list As the run progresses in the LabChip XT software the concentration for each extraction is calculated and displays in columns named Concentration of Collection Region lt gt ng uL These concentrations are reported as was present in the sample well The LabChip XTe software does not display the quantitation values Chip ID Barcode or Molarity in the Channel Table The following values are calculated for each extraction step as the run progresses Molarity of Collection Region lt gt nMol l LabChip XT only Fractionation Start lt gt min and Fractionation End lt gt min To view or hide columns in the Channel Table view right click on any column header in the table The Select Channel Table Columns window displays all available columns and the currently selected columns Show columns in the Channel Table by moving the column name to the Selected Columns list Hide columns by moving the
158. indows must be removed before starting a run 1 Inspect the chip locator especially the optical windows and the inside of the lid for debris or fibers that may scatter light or fluoresce during the run 2 Dust can be removed with pressurized and filtered air 3 To remove liquid spills from the lid and chip locator soak up the spilled liquids with a lint free wipe Remove any liquid on the optical windows only with the swabs provided Lightly press the swab on the optical window to or remove the liquid NOTE Do not apply pressure to the optical windows when using the swabs Lightly press the swab on the windows to prevent scratching or damaging the optical fiber tips 4 After the spilled liquid is removed use a lint free wipe dampened with DI water to rinse the lid and chip locator 5 After the spilled liquid is removed clean the optical windows with DI water using ONLY the swabs provided Lightly press the swab on the optical window to apply or remove the DI water 6 Use a lint free swab dampened with 70 isopropanol solution in DI water to clean the electrodes 7 Use a lint free swab dampened with DI water to rinse the electrodes 8 Let all parts air dry Do not use detergents or other cleaners as they may contain fluorescent dyes that interfere with the run V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Maintenance and Service 222 Cleaning the Test Chip Optical Windows Inspect the chip for
159. iode detector for fluorescence detection Fluorescence signal from each channel is acquired at a rate of BOHz Optical Train The fluorescence excitation and detection optical trains contain lenses fiber optics and a high efficiency interference filter Barcode Reader V2 1 The LabChip XT and XTe instruments are equipped with an internal Barcode Reader The Barcode Reader reads the Caliper applied barcode on the edge of the chip The barcode reader is internal to the system and cannot be viewed from the outside LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 216 XT Chips The figure below show the parts of the microfluidic chips used in the LabChip XT and XTe instruments to perform DNA collection sizing and quantitation sample Waste Collection Wells Wells Wells Figure 89 Top of Chip Sample Well Add the sample to this well using the instructions in the LabChip XT Assay User Guide The Assay User Guide is included with the assay kit Waste Well After the run contains the part of the sample that was not extracted during the run For Separation channels contains the entire sample up to the assay kit range Collection Well After the run contains the portion of the sample that was extracted Detection Point The location on the chip where the fluorescence excitation and detection optics align with the channels on the chip Switch Point The location on
160. ion installed supports backing up data files to a remote server see Remote CDR Server Backup on page 93 The CDR data files and the Audit Trail database can also be backed up manually to another secure location Manual backup does not update the backup copies with any changes to the files The backup copies can be stored on another computer or on a removable storage drive The data files and Audit Trail database can only be restored to the point when the files were backed up Backing Up CFR Files V2 1 To manually back up the CFR Files in the LabChip XT software you must back up both the CDR data files and the Audit Trail database Setting the CDR folder as accessible 1 Log in to the computer with a User Name in the Administrator group 2 For Windows 7 Right click on the LabChip XT icon on the Windows desktop and select Run as Administrator For Windows XP Double click on the LabChip XT icon on the Windows desktop 3 Log into the LabChip XT CFR software as the Administrator user 4 On the LabChip XT XTe Main Window select Tools CDR Utility The CDR Utility Window opens 5 Select the Accessible by Windows Administrator Level Users check box and then click the Apply button 6 Click OK in the Confirmation window 7 Click the Close button on the CDR Utility Window 8 Close the LabChip XT software Copying the CDR Folder 1 In Windows Explorer navigate to C Program Files Caliper Life Sciences 2 Copy the en
161. ion will trigger at the end of the search region if the signal threshold value has been exceeded but the signal has yet to start decreasing Collection ends when the sample specified by the Collection Width has been collected This option is only available in the LabChip XT software Collection Width Specifies the range that will be collected based on the trigger point specified by the Extraction Mode e Specifies the Collection Width as a percent of the size at which the extraction is triggered The extracted range is centered at the trigger point and the collection width is from size to size Half of the collection range occurs before the trigger point so depending upon the migration time of the fragment it is possible that the specified start of the collection range may have already passed the point at which the sample is diverted into the collection well If this occurs the extraction is started immediately and the extraction range shifts forward to meet the specified collection width e BP Specifies the number of base pairs BP to collect For Fluorescence Peak Start and Collect on Click the collection starts at the specified trigger point in the Extraction Mode and collects the specified number of base pairs from the trigger point forward For Peak Max and Smear Max the collection range collects the specified number of base pairs centered on the trigger point e Manual For Peak Start Collect on Click and F
162. ip NOTE The Instrument menu does not display if the software was installed in Reviewer mode Tools Menu The Tools menu contains the following commands Run File Editor Opens the Run File Editor Window to create Run files Run files contain all of the settings in the Start Fractionation Window Method Editor Opens the Select Method To Edit window to select the name of the method to edit The selected method opens for editing in the Method Window LabChip XT only CDR Utility Opens the CDR Utility Window to set or change the CDR options or Remote CDR Backup options This command is only available when the 21 CFR Part 11 option is installed and the default Administrator is logged into the LabChip XT software V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Security Menu View Menu Software Reference 107 The Security menu only displays if the 21 CFR Support option is installed with the LabChip XT software User and System Administration Opens the User Administration Window to create edit and view user login information activate or deactivate users define user access and set user policies Change Password Opens the Change Password Window to change the Login Password for the current user Perform Signature Opens the Perform Signature Window to sign a data file change the approval state or lock the data file Unlock Data File Opens the Unlock Data File Window to unlock a locked data file
163. ip Interlock ontinued oe Contact Caliper Technical Support see page 2 Barcode XT Test Verify barcode Barcode reader hardware or Chip reader software not functioning Contact Caliper Technical Support see page 2 Laser XT Test Channel 1 4 Laser Laser power read back is not Chip Power Readback within 0 2mW of tested power levels 3 0 4 0 and 5 0 mW Contact Caliper Technical Support see page 2 Optics XT Test Channel 1 4 A channel s gain is not Chip Detector Response adedguate or background is too high Contact Caliper Technical Support see page 2 HV Voltage XT Test HV Supply at Voltage out of calibration Calibration Chip 450V 250V Contact Caliper Technical Support see page 2 Interlock Switch is defective Channel 1 4 Hi Lo Pin not connected to power Voltage supply Contact Caliper Technical Support see page 2 HV Current XT Test Channel 1 4 Current out of calibration Pin Calibration Chip Hi Lo Zero Currents not connected to power supply Contact Caliper Technical Support see page 2 HV Kelvin Mode XT Test Channel 1 4 Contact Caliper Technical Chip Kelvin Mode Hi Lo Support see page 2 Voltages HV Isolation XT Test Channel 1 4 Faulty isolation relay Contact Relay Chip Isolation Relay Caliper Technical Support see page 2 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 232 Troubleshooting Assay Problems
164. ip XT only Edit Sample Name Opens the Edit Sample Name window to change the channel name or add a comment to the channel The comment displays in the Channel Table View and in printed reports Rename Chip Opens the Rename Chip window to specify a new name for the chip Also enables you to rename the data file to match the name of the chip by selecting the Rename File to Match check box The data file cannot be renamed if the 21 CFR Security option is installed LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 131 Gel View Properties To view the Gel View Properties click the Properties tab on the right side of the Gel View Properties E if ute fe TEE TE Baciorpund Set Lane Label Font Show EP Smeaar Leger Figure 33 Gel View Properties The following properties can be set for the Gel view Lane Width Sets the width of the Gel column Select Auto Fit to have the software automatically fit all the data or use the slider to manually set the width Gel Contrast Sets the minimum and maximum Gel Band Range Contrast for the bands in each channel Use the sliders to change the Min and Max values Gel Color Click on the Foreground color or the Background color to open the Color window to choose the desired colors for the gel Set Lane Label Opens the Font window to change the font or font Font button size of the labels in the gel headers Show Peak If selected displays pea
165. is applied the bulk solution moves towards one of the electrodes This phenomenon can be used to move fluids through microfabricated channels Electrophoresis technique of separating molecules on the basis of their mobility An electrical potential is applied across a capillary containing a sample in a fluid medium Positive molecules migrate towards the cathode and negative molecules migrate towards the anode at different speeds depending on their electrophoretic mobility End Point The peak find algorithm looks for a leveling off when the value of the slope is less than the value set for the slope threshold This is marked as the end point of the peak End Time This setting determines the time after the start of a run before which the last peak or fragment will be located any peaks appearing after this time are ignored Filter Width This setting on the Peak Find Tab determines the width of the polynomial in minutes to be applied to the data for filtering noise reduction The default depends on the method selected V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 244 Hardware Diagnostics Whenever a run begins the instrument checks for errors e g defective high voltage supplies missing conductivity between channels etc If an error is detected a message box displays and the run stops The message box describes the problem and either contains information on how to resolve the pro
166. isplays the events that occurred during the run The Run Info window contains the following buttons Print Opens the Print Preview window to view the run information before Preview printing Opens the Print window to print the run information Closes the Run Info window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 182 Run Info Tab The Run Info tab on the Run Info Window displays information about the method and the run The Channel Info table at the bottom of the window contains the following information gt creates one row in the table Start The start of the Size Range or Search Region set in the method End The end of the Size Range or Search Region set in the method Size The actual center size of the extracted or excluded region Displays 0 until the step is complete Range The actual range of the extracted or excluded region Displays 0 until the step is complete Threshold The Threshold set in the method for Fluorescence Peak Start Peak Max and Smear Max Width The collection width set in the method for Fluorescence Peak Start Peak Max Collect on Click and Smear Max V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 183 Save Workspace File As Window The Save Workspace File As window saves the currently open workspace with the specified name in the specified location This window is only available in the LabChip XT
167. ists the test names descriptions potential failures and the chip required to run the test Chip Test Name Potential Failures Computer Check for CFR SQL server not started Start Resources database connection SQL Server Express Database has not been installed properly Contact Caliper Technical Support see page 2 Check for CDR Service exited unexpectedly Service or not started Check for Remote Remote server is down CDR Connection Network is down Run only if Remote CDR is set up Memory Check Available memory below 500 MB System may function with lower memory but there is risk of failure if analyzing many chips Disk Space Check Available disk space below 4 GB Risk of losing data as disk space is used Free space on local hard drive System Components Verify Fan operation Damaged fan Contact Caliper Technical Support see page 2 Board Temperature Board temperature is not between 18 and 39 C Verify room temperature is between 65 to 78 F 18 to 26 C Contact Caliper Technical Support see page 2 Low Voltage Supply Low voltage supplies are not delivering 3 3 0 15V 5 0 0 25V and 3 440 15V Contact Caliper Technical Support see page 2 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 231 Chip Test Name reduired Description Potential Failures System XT Test Check Instrument Lid Lid is open Close lid Components Ch
168. k box Click the Browse button The Browse for Folder Window opens Navigate to the folder where you want to save the exported copies of the data files Click the OK button to choose the selected folder The path displays in the Copy To text box on the Output Tab To continue setting the assay options in the Run File Editor Window see Select the Output File Locations on page 30 Reverting to a Specific Data File Revision Each time a LabChip XT data file is changed a new version of the data file is created and saved The LabChip XT software enables you to revert to a previous version of a data file V2 1 To revert to a previous LabChip XT data file version 1 On the LabChip XT XTe Main Window select Analysis gt Analysis Settings on the main menu The Method Window opens Click the Restore Chip button at the bottom of the window The Restore Chip Settings to Version window opens Select the data file version that you want to restore to Click the OK button The Method Window displays the settings for the selected data file version Click the OK button to display the data file with the selected settings LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 88 Audit Trail LabChip XT software uses secured computer generated time stamped audit trails to independently record the date and time of operator entries and actions that create modify or delete electronic records Th
169. k information in a tool tip Information when the cursor moves over a peak If not selected the tool tip does not display when the cursor is over a peak Show EPs and If selected EPs are indicated by a solid color Smears triangle above the peak and smears are indicated by bands of translucent color in the Gel view Expected Peaks are only supported in LabChip XT V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 132 Show Displays a legend of the colors of the Expected EP Smear Peaks and Smears in the Gel view Click and Legend drag to move the legend Expected Peaks are only supported in LabChip XT Pin icon In the top right corner this is used to lock in place or unlock the Properties tab If locked in place the Gel display panel is resized to accommodate the tab V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 133 Channel Table View V2 1 The Channel Table view in the Collection Pane contains a summary of analysis results for the channels selected from the chips in the collection Figure 34 Channel Table View In the LabChip XT software the Total Conc ng uL reports the concentration of all DNA as was present in the sample well The Conc of Collections ng uL column reports the total extracted concentration over all fractionation steps diverted to the Collection well as was present in the sample well not the concentration that w
170. l for a single data file and include the size data in the exported data e Select Export Single Table to export the data for all channels in the chip to one CSV file If not selected the data from each channel is exported to a separate CSV file If Gel is selected a Select either Single File to include gels for all channels in the run in the same image file or select Separate Files to export each gel to a separate image file b If desired change the height in pixels of the exported gel graphics in the Height text box If either Electropherogram or Gel is selected choose the desired format for the image files Click OK to save the Export settings The specified files will be exported at the end of the run LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 32 Save the Run File V2 1 After the desired settings are entered in the Run File Editor Window save the Run File so it can be imported into the Start Fractionation Window To save the run file 1 Click the Save button at the bottom of the Run File Editor Window The Export Fractionation Setup to XML File window opens Navigate to the desired location to save the run file xml You should save the run file in the default location if it will be used to run chips Type the desired name for the run file in the File Name text box Click the Save button to save the run file Click the Close button on the Run File Editor window to close
171. l Export OAB Select file fom select Hie formal sr ASCII tent file f XML file lose MS Excel Number of events included 7 Figure 40 Audit Trail Export Window The Audit Trail Export Window contains the following options File Formats Select the desired format for the exported file e ASCII Text File If selected the file is saved as a txt file e XML File If selected the file is saved as an xmi file e MS Excel If selected the file is saved as an xls file Number of Events Included Displays the number of events that will be exported V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 142 Audit Trail Manage Columns Window Use the Audit Trail Manage Columns Window to select the columns to view at the bottom of the Audit Trail Window Only available if the 21 CFR Security option is installed with the LabChip XT software To open the Audit Trail Manage Columns Window click the Green Arrow button next to the Event Category text box in the Audit Trail Window 3 Audit Trail Manage Columns E Show Al A Event Category Event Detad R Lissmiame f Al Application Access Level T i Dea Tima Stamp q _ Source Computer Name ComputerLser Domper Laser Fiis Data Fle Mame Severity fi Comment Figure 41 Audit Trail Manage Columns Window The Audit Trail Manage Columns window contains the following parts Show All check Selecting the check box selec
172. l IPERLS UserName Comment Figure 73 User Info Tab The User Info tab contains the following settings Operator Type the name of the operator performing the run If the 21 CFR Security option is installed the user name of the logged in user is automatically entered and cannot be edited Comment Type comments that are saved in the data file for the run V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 196 Sizing Table Tab V2 1 The Sizing Table Tab in the Start Fractionation Window specifies the ladder to use when aligning all the sample channels on the chip This tab ts not available in the LabChip XTe software fe Method Ladder Figure 74 Sizing Table Tab The Sizing Table Tab contains the following settings Method Ladder If selected the default Caliper supplied ladder is used to align the samples during the run Custom Ladder If selected the custom ladder sizes in the Size Table are used to align the samples with a custom ladder during the run instead of the ladder supplied by Caliper This option can be used to improve sizing in the fragment size range of interest Select the Custom Ladder option and specify the fragment sizes for the custom ladder in the Size Table Since the custom ladder fragments will also be used to establish the relationship between area and concentration each fragment should be supplied at the same concentration nominally 2 ng ul t
173. l View is always displayed and cannot be hidden To display a hidden view 1 Select Collection gt Layout on the LabChip XT Main window The Layout Options Window opens 2 Click on the desired location for the hidden view Left Right or Bottom If multiple views are displayed in the same location use the tabs at the top of the location to switch between views Zoom In and Zoom Out V2 1 You can zoom in and out on data displayed in the Gel View and the Graph View The Graph View and the Gel view both zoom to the same levels when either view is zoomed in If Synchronized Zoom is selected all graphs zoom to the same level To zoom in e Click and drag to enclose the region of interest When you release the mouse button the selected area enlarges to fill the view In the Gel view all lanes in the collection zoom to the same level e You can continue zooming in until you reach the maximum magnification the graph will not zoom in any closer To zoom out e Right click in the Graph view or Gel view and select Unzoom to go to the previous zoom setting or select Unzoom All to zoom out to the default view For more information see Viewing Graphs in the Overlay Electropherograms Tab LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 63 Viewing Graphs in the Overlay Electropherograms Tab If the Overlay Electropherograms Tab is not open select Collection gt Layout on the LabChip XT XTe Main Window s
174. late Opens a blank collection and then applies the selected collection template Blank Collection Opens a blank collection that does not contain any data The new collection will use the same settings as the last saved collection of the same assay type The current collection settings are automatically saved in a blank collection template in the current user s Documents and Settings folder on the local computer These preferences are applied when a blank collection is created Current Collection Opens a blank collection and applies the settings from the currently open collection as a template Assay Type The LabChip XT XTe only supports DNA assays Name Specifies the name of the new collection V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 175 Perform Signature Window Use the Perform Signature Window to add an electronic signature to a data file Signatures can be added as required by the company s standard operating procedures Data files cannot be signed while the assay is running If multiple data files are open in the workspace only one data file can be signed at a time Only available if the 21 CFR Part 11 Security option is installed To open the Perform Signature Window select Security gt Perform Signature on the LabChip XT XTe Main Window j Eu Perom Signature A A A You ae qumrenihy ra Fa Gate die Cap MAW ADS RA MIT Una EE Hel Enter Comment Ereer pour Lk
175. lay in the Channel Table is specified in the Property Displayed in Channel Table column To display multiple properties for the same Expected Peak or Smear in the Channel Table 1 In the Expected Fragments tab or the Smear Analysis tab enter the properties for the expected peak or smear selecting one of the desired properties in the Property Displayed in Channel Table column Click in the next row and type the same name as an existing EP or smear in the Name field of the table The row will automatically update with the same entries as the original row The only field that can be changed is the Property Displayed in Channel Table column Change the Property to the desired selection Repeat until all desired properties have been added to the table Click the Apply button to display the new columns in the Channel Table Duplicate properties in the table will be removed when the settings are applied to the chip LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 66 Copying Information Some of the right click pop up menus offer the following choices for copying information from the LabChip XT XTe software for use with other applications depending on the selection e Copy Gel e Copy Lane e Copy e Copy Rows to Clipboard e Copy Column to Clipboard Choosing any of these commands places a copy of the selected item on the computer s clipboard You can then paste the item into a word processing graphics or
176. le Horizontal Displays each Collection in separate top to bottom windows in the Collection Pane LabChip XT only Tabbed Displays each Collection in a separate tab in the Collection Pane The Help menu contains the following commands LabChip XT XTe Help Opens the Contents Index page for the LabChip XT XTe Help file About LabChip XT XTe Opens the About LabChip XT XTe Window showing the software and firmware version numbers LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 109 Run Status and Chip Info V2 1 The Run Status and Chip Info areas on the LabChip XT XTe Main Window display the instrument status chip status chip information and information about the current run If the software was installed in Reviewer mode this status area does not display Run Status a Chip ID ND160001 00 02 Expirabon Date An 7 2011 Available Channels 4 Type XT DNA 750 Run Status le Run Button Opens the Start Fractionation Window to begin a run The Run button only displays when the cursor is positioned over the instrument image See the LabChip XT Assay User Guide for chip preparation instructions While an assay is running the Run button changes to a Pause Stop button Pause Stop Button Opens the Modify Run Settings Window to edit the method resume the run or stop the run The Pause Stop button only displays when the cursor is positioned over the instrument image while a method is r
177. le Table If selected the data for all channels in the chip is exported to one CSV file If not selected the data from each channel is exported to a separate CSV file Electropherogram If selected the graph displayed in the Graph View is exported to the specified folder in the selected image format Click the Browse button to specify the desired path for the image file The file name format is lt sample name gt _ lt chip name gt _Egram_ lt channel number gt The following options are available on the Export window These options are not available on the Auto Export window e Entire Collection If selected a separate graph is exported for each channel in the collection e Selected Channels If selected a separate graph is exported for each of the channels selected in the Gel View or Chip View or List View V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 153 Export Window Continued V2 1 Gel If selected the gels selected in the Gel View are exported to the specified folder in the selected image format Click the Browse button to specify the desired path for the image file The file name format is lt sample name gt _ lt chip name Gel schannel number The following options are available on the Export window Entire Collection If selected a gel is exported for each channel in the collection This option is not available on the Auto Export window Selected Channel
178. le connector to be compatible with the power supply For additional information contact your local Caliper representative LabChip XT XTe User Manual Caliper Life Sciences Inc Instrument Safety 11 Fuses The LabChip XT XTe instrument does not contain any user replaceable fuses Contact Caliper Technical Support see Contact Us on page 2 if blown fuses are suspected V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Table of Contents 12 Table of Contents Preface ati 2 NStuments ateo r ae eu 7 REQUIS MEANS ZAR carbs ies EE a T CMG TIGA diese ER suet eds ate E E RE EE 8 aserto ae ne RE ER EE OE EA pe 9 Ele lrieal safety a tone ER ee De cle 10 Power COP Selec vist as 10 FUESE ii 11 INTOdUCHION RE AE OE N ER AE EE EE IE 18 PRIACIDISS af OberatiOn ESE N ee DE ED een ie SN EE ie EE 20 Ope eke AE EE AE EE E EE 23 Opening the LabChip XT or XTe Software 24 Creating a RUM E edo e endo 24 Select the Extraction Parameters on the Setup Tab see ee se ee se se se se ee 25 Check the Buffer Utilization ER EER Ee Ee ER RR Re ee Ee Ee ee ee ee ee 29 Enter die SOR NAL ss SR DE BO E GE ee 29 Specify the Ladder Settings VU 29 Select the Output File Locations iese see see ee ee Ee ER ER ER ee Ee Ee Ee ee ee Ee Ee Ee ee Re ee ee 30 Select the Auto Export Settings 4 31 Save ne RUN ts EE RS N EE GE aa 32 RERIG EE DID es A ds ds Se Ee ee Ee oe nm ie 33 Prepare and koad T
179. lect Workspace Save Chip or right click on the chip name above the chip diagram on the left side of the window and choose Save Chip In the LabChip XT software changes to the analysis settings are saved at the end of the chip data file without overwriting previous settings in the file The Restore Chip button can be used to return to previous analysis settings Data Points V2 1 Data points are determined by the data collection rate set in the method properties Show Data Points is an option in the Graph View Properties that displays the data points used to generate the graph LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 242 Data Filtering Before identification of peaks in the fluorescence data can proceed the raw data must be smoothed to prevent the detection of signal noise as peaks To smooth the data the LabChip XT XTe software 1 Eliminates any narrow spikes from the data and replaces the spike with a local average of surrounding points 2 Applies Baseline correction if selected in the Method Window to the data 3 Smooths the data using a Savitzky Golay filter using the Filter Width and Transition Time specified in the Peak Find Tab ofthe Method Window DNA Assay Analysis DNA samples contain a lower marker peak below the limit of the DNA fragment sizes the method is designed to detect The ladder contains the same lower marker peak The sample data is aligned to the ladder da
180. les from the backup database 1 Verify that the Remote CDR Server is accessible on the network 2 Log into the LabChip XT software using the default administrator user name and password 3 Select Tools CDR Utility The CDR Utility Window opens 4 Select the Enable Remote CDR Backup check box NOTE Server name folder name username and password are case sensitive 5 Type the computer name of the Remote CDR server in the Remote Computer Name IP Address text box If the remote computer and the local computer are not in the same Windows workgroup type the IP address of the remote computer In the Folder text box type the name of the folder in the remote CDR server that you want to restore the LabChip XT data from Make sure to select the same folder to which the data was backed up Type the folder username in the User Name text box This username is the same username that was used to create the CDR Server folder Type the folder password in the Password text box This is the same password that was used to create the CDR Server folder Click the Apply button The progress bar display the status of the restoration process and a confirmation displays when the restore is complete 10 Click the Close button to close the CDR Utility Window LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 97 Manually Backing Up and Restoring the CFR Files The LabChip XT software with the 21 CFR Part 11 opt
181. luorescence the collection begins at the trigger point and ends when the user clicks STOP in the Run Setup For Peak Max and Smear Max collection begins at the specified percent before the trigger point size and immediately ends when the user clicks STOP in the Run Setup The collection stops at the end of the red smear region on the Graph View not where the graph ends If the user has not stopped the extraction when the end of the search region has been reached the extraction will end automatically there The size collected is displayed in the Run Setup area Channel Table View and the red smear region on the Graph View V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 193 Setup Tab Continued V2 1 Slider If the Extraction Mode is Size the blue marker indicates the size of DNA to collect in the collection well of the chip Move the slider left or right to select the desired size to collect The setting in the Size text box changes to reflect the position of the slider Copy button Copies the current settings of a channel so the settings can be pasted into another channel Paste button Pastes the last copied channel settings to a channel LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 194 Buffer Utilization Tab Use the Buffer Utilization tab on the Start Fractionation Window to view estimates of the buffer use for each channel during the run The
182. m on the window Leave the cursor stationary for a moment and a Tool Tip if one exists for that item displays Workspace XTD Files V2 1 Use a workspace file to view the chip data from a run In the LabChip XT software workspace files can be saved and opened In the LabChip XTe software a new workspace opens automatically when importing a data file Multiple chip data files can be opened in the same workspace to enable comparison between data from different chips or different runs In the LabChip XT software each workspace can contain multiple Collections for viewing the same data in different layouts The LabChip XTe software only supports one collection in each workspace A Workspace file includes e the links to the chip data files in each collection e the selected channels and arrangement of the channels in the views and e the layout selected for each collection The file extension for data files created in the LabChip XT software The data file contains the data from the read method information analysis settings and Run Information for the run Data is saved to the file during the run If a run is stopped before the run is complete the collected data for all channels is saved in the data file The file name is specified in the Start Fractionation Window LabChip XT XTe User Manual Caliper Life Sciences Inc XTE Files Glossary of Terms 298 The file extension for data files created in the LabChip XTe
183. mn for each access level Administrator Supervisor Operator Restricted User and Service Select Enabled for each right to be allowed for an access level or select Disabled for each right not allowed for an access level The table below describes the function of each Access ae ELE Access Access Right ad MEN Administration EE EE EE enabled allows access to the User Administration Window to add and edit users set access rights and set policies Run Method If enabled allows users to run methods and save the new data files that are created by the run Users are not permitted to save changes to existing data files Save Existing Data If enabled allows users to save changes to existing data File files Save Workspace If enabled allows users to save new and existing workspaces If Save Existing Data Files is not selected users can only save workspaces where the data files have not changed Hide Show in CDR If enabled allows users to hide and show data files in the CDR Manager Window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 209 Manage CDR If enabled allows users to create rename and delete folders Folders in the CDR Manager window This permission is not required for automatically creating daily subdirectories or to move data files in the CDR Perform Validation If enabled allows users to perform IQ Installation Qualifications and OQ Operation Qualifications Print Exp
184. mplete File Prefix Specifies the text for the first characters of the data file name Computer Name If selected adds the name of the LabChip XT computer to the data file names Project Name The text is added to the data file names Chip ID If selected adds the Chip ID to the data file names The Chip ID is read from the barcode on the chip LabChip XT only Date check box If selected the current date is included in the data file name The date format is YYYY MM DD where YYYY is the year MM is the month and DD is the day The date is automatically added to the data file name when the 21 CFR Part 11 option is installed Time check box If selected the time that the run was started is included in the data file name The time format is HH MM SS where HH is the hour 0 to 24 MM is the minutes and SS is the seconds The time is automatically added to the data file name when the 21 CFR Part 11 option is installed File Name Example text box Read Only text box that displays the selected format for the data file name Automatic Export If selected data is automatically exported at the end of each run Select the type of data to export by clicking the Settings button and choosing the desired settings in the Export Window For more information see Exporting Data This option is not available in the LabChip XTe software LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 199 System Dia
185. n Users are not permitted to save changes to existing data files Save Existing Data File Allows users to save changes to existing data files Save Workspace Allows users to save new and existing workspaces If Save Existing Data Files is not selected users can only save workspaces where the data files have not changed Hide Show in CDR Allows users to hide and show data files in the CDR Manage CDR Folders Allows users to create rename and delete folders in the CDR Manager window This permission is not required for automatically creating daily subdirectories or to move data files in the CDR Perform Validation Allows users to perform IQ Installation Qualifications and OQ Operation Qualifications Print Export Analysis Results Allows users to print or export analysis results Audit Trail Access Allows users to view the Audit Trail in the Audit Trail Window Method Editor Allows users to edit and save methods 4 Click the Save button LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 84 Printing Access Rights After changing the user rights in the LabChip XT software the access rights can be printed for record keeping purposes To print the access rights 1 2 3 4 On the LabChip XT XTe Main Window select Security User and System Administration The User Administration Window opens Click the Define Access button To preview the printout click the Print Pr
186. n Well Data Files Data Points Data Filtering DNA Assay Analysis Electrode Cleaner Electrokinetic Forces Electroosmotic Flow Electrophoresis End Point End Time Filter Width Hardware Diagnostics Inflection Threshold Example Lab on a Chip Ladder Ladder Analysis Lower Marker Log Files Method File Microfluidics Minimum Peak Height LabChip XT XTe User Manual Glossary of Terms 237 Caliper Life Sciences Inc Apex V2 1 Glossary of Terms Minimum Peak Width Molarity Molecular Separation Techniques Peak Baseline Peak Height Peak Identification Point to Point Fit Polynomial Filter Polynomial Order Run Button Sample Name File Saturation Detection Slope Threshold Smear Smear Baseline Standard Curve Window Start Point Start Time Tool Tip Workspace XTD Files Zero Baseline 238 After locating a start point the peak find algorithm looks for the first negative slope value and saves the previous point as the apex If the value of the apex is less than the minimum peak height limit the algorithm starts looking for a new peak LabChip XT XTe User Manual Caliper Life Sciences Inc Baseline V2 1 Glossary of Terms 239 A baseline is established just after the start time setting The Baseline Start time can be changed on the Analysis Tab in the LabChip XT software After the overall baseline is established a local Peak Baseline is calculated for each peak to compensate for baseline d
187. n the manner described in this manual If the equipment is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired LabChip XT XTe User Manual Caliper Life Sciences Inc Instrument Safety 8 Chemical Safety V2 1 WARNING AAAA A Some chemicals used with the LabChip XT XTe are potentially hazardous and can cause illness e Read and understand the material safety data sheet MSDS provided by the chemical manufacturer before you store handle or work with any chemical or hazardous material e Minimize contact with and inhalation of chemicals and chemical wastes Wear appropriate personal protective equipment when handling chemicals e g safety glasses gloves or clothing For additional safety guidelines consult the MSDS e Do not leave chemical containers open Use only with adequate ventilation including a fume hood if necessary e Check regularly for chemical leaks or spills If a leak or spill occurs follow the chemical manufacturer s cleanup procedures as recommended on the MSDS e Dispose of waste in accordance with good laboratory practices and local state provincial or national environmental and health regulations e After emptying waste containers seal them appropriately e Comply with all local state provincial or national laws and regulations related to chemical storage handling and disposal LabChip XT XTe User Manual Caliper Life Sciences
188. n the right side of the Gel View to open the Gel View Properties 2 Selectthe Show EPs and Smears check box To display the legend that identifies the colors and sizes of the expected peaks and smears 1 Click the Properties tab on the right side of the Gel View to open the Gel View Properties 2 Select the Show EP Smear Legend check box EFS EPIO EFE EP mms EF Ciampi 3 E E Sraa ALH b Figure 6 Expected Peaks Legend Viewing the EFs in the Channel Table BE ma am imd dus Mid imi lai bima ad dos el bai liami A column is added to the Channel Table in the LabChip XT software for each Expected Peak entered in the Expected Fragments Tab The column displays the property selected in the Property Displayed in Channel Table list in the Method Window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Viewing the EFs in the Peak Table V2 1 Data Analysis 52 Expected Fragments are identified in the Peak Table in the LabChip XT software with the peak name displayed in the Type column Caliper 04 31 25 Capes 04 31 25 Calper_04 31 25 Calper_04 31 25 E Cape D4 31 25 Caiper_04 31 25 Calper_04 31 25 Calper 04 31 25 Calpei_04 31 25 Sample 2 Sample 2 Sample 2 Sample 2 Sample 2 Sample 2 Sample 2 Sample 2 Sample 2 EP25 EPS EP200 EF300 EP400 EPS00 Figure 7 DNA Assay Peak Table LabChip XT XTe User Manual Caliper L
189. nalysis settings This enables you to reanalyze the data with new settings or to view previously saved settings The following analysis parameters can be changed e Chip peak find settings and channel peak find settings see Changing the Peak Find Parameters on page 54 e Add a Peak see Adding a Peak on page 55 e Exclude peaks from analysis see Excluding a Peak on page 55 e Reassign lower markers see Lower Marker Peaks for DNA Assays on page 57 e Alignment or no alignment with ladder peaks see Aligning or Unaligning the Marker Peaks on page 57 To reanalyze a data file 1 Open the workspace that contains the chip data see page 45 2 Change the analysis parameters see list above as needed 3 When you click the Apply Apply Global or OK buttons in the Method Window the data is automatically re analyzed and the updated information is displayed 4 To view previous analysis settings click the Restore Chip button at the bottom of the Method window and select the version to view V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 68 Printing Workspace Information V2 1 Choosing File gt Print opens the Print Window to select the information to print from the open workspace The selected information can be printed to a printer or to a PDF file If the workspace contains multiple collections information from the active selected collection is printed The h
190. nance or service provided C Exclusions e Failure to comply with any of the Customer Responsibilities listed above will void this Warranty e Any alteration of hardware or software on products covered under this Warranty that are not performed by Caliper or an approved Caliper vendor will void this Warranty e A product that has been subject to misuse accident negligence or improper transportation handling installation storage use or maintenance is not covered under this Warranty e Many Caliper products require the use of Caliper Automation Certified Disposables for proper operation These may include but are not limited to pipet tips seals labels and filters Use of a Caliper product with any disposables other than the specified Caliper Automation Certified Disposables will void this Warranty e This Warranty covers equipment manufactured by Caliper Equipment purchased from other vendors is not covered by this Warranty e Damage to Limited Life Parts caused by insufficient maintenance or cleaning practices or unauthorized applications are not covered under this Warranty e This Warranty applies only to the original buyer and delivery location It is not transferable to other buyers or locations without Caliper s prior written approval e The Sciclone 384 channel low volume head is warranted for one 1 year or 750 000 aspirate or dispense movements whichever comes first e The Sciclone 100nL head is warranted for one 1 year or 60
191. nc Preface 4 NOTE Changes or modifications to this equipment not expressly approved by the party responsible for compliance could void the user s authority to operate the equipment REMARQUE Tout changement ou modification apport cet instrument non express ment approuv par l entit responsable de la conformit peut annuler l autorisation d op rer l appareil accord e utilisateur Table of Symbols V2 1 Table 1 contains symbols that identify particularly important information and alert you to the presence of hazards These symbols may appear in this manual and or on the product it describes Table 1 Important Symbols Symbol Description Symbole Description DANGER An imminently hazardous situation which if not avoided will result in death or serious injury DANGER Situation pr sentant un danger imminent qui s il n est pas limin peut entra ner des blessures graves voire la mort WARNING Caution risk of danger Refer to the User s documentation AVERTISSEMENT Attention danger potentiel Se reporter la documentation de l utilisateur NOTE cautionary statement an operating tip or maintenance suggestion may result in instrument damage if not followed REMARQUE nonc indiquant une pr caution prendre un conseil de fonctionnement ou une suggestion d entretien son non respect peut provoquer des dommages l instrument Hazardous voltage risk of shock injury Tension dang
192. needed before testing the instrument See Cleaning the Test Chip If the instrument will not be used for an extended period of time see Long Term Shutdown The LabChip XT Assay User Guides contain LabChip Kit Essential Practices and instructions for preparing samples and chips Make sure to follow the instructions to ensure the optimum performance of your instrument The current version of the Assay User Guides can be accessed on the Caliper web site at http www caliperls com support reference library data sheets labchip systems data sheets htm If you have any questions concerning maintenance or require additional assistance please contact Caliper Technical Support see page 2 WARNING A Laser maintenance and service should be performed only by a gualified Caliper representative WARNING MAMA A Some chemicals or samples used with the LabChip XT XTe are potentially hazardous and can cause illness Follow the precautions in Chemical Safety on page 8 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Maintenance and Service 221 Cleaning the LabChip XT XTe Make sure the chip locator and inside of the lid are clean before beginning a run Leave the instrument lid closed when not using the instrument to prevent dust or fibers from settling in the chip locator Any potentially fluorescent material such as lint paper dust dyes or reagents or materials that may block the light in the optical w
193. nel list includes all the channels on the currently selected chip The Channel Name field is read only and cannot be changed from the Peak Find Tab LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 162 Peak Find Tab Continued This window contains the following options Table 1 Chip Peak Find Settings Chip Settings Minimum Specifies the height limit below which a peak is not detected For Peak Height each peak the difference between the peak start time and the peak apex must be greater than the Min Peak Height value Minimum Specifies the limit in minutes for the peak width Peaks narrower in Peak Width time than this value are not detected Slope Represents the amount of change in absorbance units over time Threshold required to indicate that a peak has occurred This setting is used to detect the leading and trailing edges of a peak Increasing this setting may cause broad rolling bumps to be ignored or merge multiple bumps into a single peak Decreasing this setting will broaden the peaks width and potentially pick up broad bumps as peaks See Peak Identification on page 250 for more information Inflection Represents the value that the slope minimum must be below to Threshold trigger a splitting of the peak As the threshold is increased more peak splitting occurs See Inflection Threshold Example on page 244 for more information Start Time Specifies the time after the sta
194. ngle Click e In Chip View Selects a channel e In Gel View Selects a channel and displays the graph in the Graph view e In Channel Table View Selects a channel displays the graph in the Graph view and selects the channel in the Gel view e In Peak Table View Selects a peak displays the graph in the Graph view and selects the channel in the Gel view Ctrl Click e In Gel View Overlays second and subsequent channel data over original channel data in the Graph view for each Ctrl click on a channel in the gel Each channel in the graph is shown in a different color e In Channel Table view Overlays second and subsequent channel data over original channel data in the Graph view for each Ctrl click on a row in the Channel Table Each channel in the graph is shown in a different color Ctrl Shift Click e In Gel View Highlights corresponding channel data trace in Overlay Electropherogram view adds trace to overlay if not already included This trace becomes the foreground trace for peak selection Repeat click to undo highlighting Right Click e Right click in any view to display a shortcut menu with available options In the Graph View different shortcut menus display depending on whether the cursor is near a peak or not near a peak LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Glossary of Terms Apex Baseline Bubble Clipboard Collection Collection Template Collectio
195. ns If not selected all peaks display the annotations LabChip XT only Graph Selected If selected only the channels selected in the Gel View or Gels Only Channel Table View are displayed in the Electropherograms tab If not selected all channels in the collection are displayed Only displayed when the Electropherograms tab is selected Sample Displays the names of the samples channel names on the Name Color graph and the color associated with each sample channel Table Click on the color to choose a different color for a sample LabChip XT only X Axis Scale Specifies the units displayed on the X Axis either Time Size or Log Size Log Size displays the size on a logaritmic scale Grid Style Displays grid lines on the graph vertical horizontal both or none Click the button to cycle through the grid options Data Legend If multiple channels are displayed specifies the location where Location the legend displays on the graph The legend shows the color used for each channel LabChip XT only Pin icon In the top right corner locks in place or unlocks the Properties tab If locked the Graph resizes to fit the tab V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Filter View V2 1 Software Reference 124 The Filter view in the Collection Pane is used to define criteria to automatically select the channels to display in the Collection tab The filter types available depend on the method
196. nt or error occurred The system component that generated the event or error Event Code The event error ID number used by Caliper to troubleshoot errors Text describing the event or error Click the OK button to close the Event Viewer window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 151 Export Window V2 1 Use the Export window to export data manually To open the Export window select File gt Export on the main Menu Bar The Auto Export window contains the same options and is used to automatically export data at the end of each run To automatically export data click the Settings button next to Automatic Export in the Output Tab on the Start Fractionation Window Manual and Auto Export are only available in the LabChip XT software Peak Tables and Channel Tables are exported to CSV files which can be imported into a spreadsheet program such as Microsoft Excel Raw Data can be exported to either a CSV file or toa Chromatography Data Interchange Format file formerly AIA which is used by some graphical analysis software tools Electropherogram and Gel data are exported to the selected image format See Exporting Data on page 74 for instructions LabChio XT Export A Pad Tobie GM sege Faan Caliper Lie ES Channel Table n Der Cata Demo Fractionation ChannelTable cav fees Daia Opti A lt KA lt lt A lt lt KA lt gt Eos the data e CSV forma wich can be r
197. ntation purposes See Diagnostics on page 229 for details on running the Diagnostics LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 229 Diagnostics The LabChip XT XTe software contains a set of diagnostic tests to verify proper operation of the LabChip XT XTe instrument These tests are not dependant on assay chemistry All tests must pass to ensure the instrument is functioning properly To open the System Diagnostics Window select Validation gt Diagnostics The following procedures are included in this section e Running the Diagnostics Tests e Description of Diagnostic Tests on page 230 Running the Diagnostics Tests V2 1 Before running the Diagnostics tests turn on the instrument and allow the instrument to run for at least 30 minutes before starting the Diagnostics tests To begin running the Diagnostics tests click the Run Tests button on the System Diagnostics Window The tests run from top to bottom displaying prompts for any actions necessary during the tests Follow the prompts As each test is completed the results display on the right side of the window Supplies required to run diagnostics tests e XT Test Chip Caliper P N 127872 To order the XT Test Chip contact Caliper Technical Support see page 2 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 230 Description of Diagnostic Tests The table below l
198. o match the Caliper ladder If an alternate concentration is used enter the concentration in the Ladder Concentration parameter in the Analysis properties of the method Using custom ladder fragments of unequal concentration is not currently supported A ladder with unequal concentrations can be used but the displayed sample concentrations will be inaccurate Copy Table from Method Imports the ladder from the selected method in the currently open workspace LabChip XT XTe User Manual Caliper Life Sciences Inc Output Tab V2 1 Software Reference 197 The Output tab on the Start Fractionation Window specifies the location name and export settings for chip data files created during the run LabChip XT software data files are xtd LabChip XTe data files are xte LabChip XTe software does not support exporting analyzed data The data file name can include a specific prefix the computer name a project name the Chip ID LabChip XT only the date and the time For example including the prefix LabChip_ XT the date and the time would create file names such as LabChip XT 2011 04 24 10 23 48 If you choose not to use the time of the run as part of the data file name the LabChip XT and XTe software automatically appends 1 _2 etc for each subsequent run on the same day Setup Bufer Ubizaton User info Sang Table Ouma Fin Leman Data Pah Program FilesiCaliper Lie SciencesiLabChip
199. og into the LabChip XT software User names cannot be deleted A deactivated user name can be activated to continue to be used 1 On the LabChip XT XTe Main Window select Security gt User and System Administration The User Administration Window opens 2 Click the De Activate User button 3 Select the Username in the Select User drop down list 4 Click the Deactivate button To reactivate a user name select the deactivated user and click the Activate button to return the user to active status The user name can now log into the LabChip XT software V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 83 Changing Access Rights V2 1 The rights assigned to each Access Level control the actions that a user is allowed to perform in the LabChip XT software The rights apply to any user name assigned to the access level Rights cannot be assigned to an individual user name The Define Access tab is not available while an assay is running To change the rights for an Access Level 1 On the LabChip XT XTe Main Window select Security gt User and System Administration The User Administration Window opens 2 Click the Define Access button 3 Enable or Disable the desired rights for each Access Level User Administration Allows users to create edit activate and deactivate users or to change policies Run Method Allows users to run methods and save the new data files that are created by the ru
200. ole and exclusive remedy for breach by Licensor of any warranties made under this License Agreement EXCEPT FOR THE WARRANTIES SET FORTH ABOVE THE PROGRAM IS LICENSED AS IS AND THE LICENSOR DISCLAIMS ANY AND ALL OTHER WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE Limitation of Liability Licensor s cumulative liability to you or any other party for any loss or damages resulting from any claims demands or actions arising out of or relating to this License Agreement shall not exceed the license fee paid to Licensor for the use of the Program In no event shall Licensor be liable for any indirect incidental consequential special or exemplary damages or lost profits even if Licensor has been advised of the possibility of such damages SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES SO THE ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU P N 104954 Rev 3 Caliper Life Sciences Inc Caliper Life Sciences Inc Software License Agreement 262 7 Software Updates Licensor periodically creates Software updates which will be made available to you at no charge Thereafter Licensor shall not be responsible for your use of and shall not warrant or repair superseded or outdated versions of Software 8 Governing Law This License Agreement shall be construed and governed in accordanc
201. on The Unlock Application Window opens on top of the LabChip XT Main Window and displays the Username of the current user LabChip XT Unlock Application Lab Chip XT has been locked Oniy acimnestretor or am Administrator can unlock this application Lsemame EET Passwort OK Figure 21 Unlock Application Window To unlock the LabChip XT software 1 On the Unlock Application Window type the user password for the logged in user in the Password text box and click the OK button 2 If the password for the current user is not available type a LabChip XT Administrator username and password in the Unlock Application Window and click the OK button The Administrator is logged into the LabChip XT software 3 To change the user to a non administrator user close and restart the LabChip XT software and then log in as the desired user V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Managing User Accounts Software Security 80 Access to the LabChip XT software is controlled by user names when the 21 CFR Part 11 Security option is installed Each user must sign into the LabChip XT software The user s Access Level controls which options are available for each user name The following procedures are included in this section Adding New Users on page 80 Changing User Information on page 81 Printing User Information on page 82 Activating and Deactivating User Accounts on pa
202. on the Start Fractionation Window The analysis settings for a chip are saved at the end of the data file If analysis settings are changed in the Method Window in the LabChip XT software and the data file is saved the new settings are added to the end of the data file but the previous settings are not overwritten This enables a chip to be restored to previous analysis settings using the Restore Chip button in the Method window in the LabChip XT software Changing analysis settings is not supported in the LabChip XTe software If the 21 CFR Part 11 option is installed with the LabChip XT software data files are saved in the Centralized Data Repository CDR The CDR is a secure folder that can only be accessed by the LabChip XT software The location of the CDR is specified in the CDR Utility Window Updated analysis settings are saved when the chip data file is saved To save the data file either e select Workspace gt Save Chip on the Menu Bar e right click on the chip name in the Chip View and select Save Chip or e select File gt Save Workspace or File gt Save Workspace As on the Menu Bar See Saving Workspace Files for more information LabChip XT software only If the 21 CFR Part 11 option is installed with the LabChip XT software and Require Signature on File Update is selected in the Set Policies tab on the User Administration Window the user must have signature rights to save an updated data file To save the da
203. ons do not change the raw data but provide different means of displaying the data To change the view in the main window see e Viewing Gels on page 60 e Viewing Zero Baselines on page 61 e Adjust Pane Widths on page 61 e Show or Hide Views on page 62 e Zoom In and Zoom Out on page 62 e Viewing Graphs in the Overlay Electropherograms Tab on page 63 e Viewing Graphs in the Electropherograms Tab on page 64 e Viewing Multiple Properties in the Channel Table View on page 65 Viewing Gels To compare the gels generated by the instrument view the gels in the Gel View z ml o 5 Le The color width and contrast of the gels can be changed using the Gel View Properties V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 61 To rearrange gels click on the column header channel name and drag the channel to the desired location To hide a channel select the channel and then click the X button on the column header or right click on the channel in the Chip View or List View and select Remove Channel Viewing Zero Baselines All electropherograms produced with the instrument show some amount of background fluorescence By default the LabChip XT and XTe software enables the Zero Baseline function see page 258 In the LabChip XT software to remove the zeroing select Analysis gt Analysis Settings to open the Method Window click the
204. ooted dicii ints Borge share Ona ls par Orrel Data mil be skaad to hs Channa lanis AJA Foral Fl helde San Data Expos Sege Table El Bedrae GT Der De Demo Frecionation bmp Figure 48 Export Window Peak Table If selected the data in the Peak Table View is exported to a CSV file Click the Browse button to specify the desired path and file name for the CSV file LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 152 Export Window Continued Channel Table If selected the data in the Channel Table View is exported to a CSV file Click the Browse button to specify the desired path and file name for the CSV file Raw Data If selected the raw unanalyzed data from the run is exported e If the AIA Format check box is selected the raw data is exported to a file in the Chromatography Data Interchange Format formerly AIA Include Size Data and Export Single Table are not available e If the AIA Format check box is NOT selected the raw data is exported to a CSV file Click the Browse button to specify the desired path and file name for the CSV file The following options are available Include Size Data If selected the data is aligned to the channel s ladder for one file per channel or to the first channel for a single data file and the size data is included in the exported data If not selected the data is not aligned to a ladder Export Sing
205. or exclusion Note that for some width settings the target region may extend beyond the last visible data point on the graph In this case the highlighted region ends at the last visible data point and the dialog box indicates the time when the target region ends When manual mode is selected in the width setting click on the word STOP in the Run Setup section to end the collection or exclusion V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 27 Select the Extraction Parameters on the Setup Tab Continued V2 1 Smear Max The signal must exceed the Threshold value RFU within the search region to arm this trigger The extraction triggers at the point when the signal decreases after averaging over three consecutive data points If the trigger is armed but the signal decrease has not been detected by the end of the search region the extraction triggers at this endpoint LabChip XT only See Setup Tab on page 188 for details on each option If Fluorescence Peak Start Peak Max Collect on Click or Smear Max is selected select the desired Collection Width Percent Specifies the Collection Width as a percent of the size at which the extraction is triggered The extracted range is centered at the trigger point and the collection width is from size to size BP Specifies the number of base pairs BP to collect starting at the specified trigger point For Smear Max or Peak Max
206. ort Analysis If enabled allows users to print or export analysis results Results Audit Trail Access If enabled allows users to view the Audit Trail in the Audit Trail Window Set Policies Use the Set Policies tab on the User Administration Window to specify password login automatic lock and signature policies for the LabChip XT software cu Latin EI Luar Adrmararansn Figure 85 User Administration Window Set Policies The Set Policies tab contains Access Right Function Password Expires After Specifies the number of days until each password expires Range is 1 to 1000 days Number of Retired User cannot reuse the specified number of old Passwords to Remember passwords V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 210 Specifies the minimum length of each password Length Maximum Login Attempts Specifies the maximum number of times the user can attempt to log in before being locked out of the LabChip XT software Range is from 3 to 20 This option can be disabled to allow unlimited retries without locking the user out This setting does not apply to Administrator level users Minutes to Automatic Specifies the number of minutes that the software is Lock inactive until the LabChip XT software locks automatically Range is from 5 to 4320 minutes 3 days To disable this option clear the check box Require Signature on File If selected an electronic signature is req
207. osely to a value that would have been attained if no saturation had occurred Figure 98 Correction by Saturation Detection V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 254 Slope Threshold Smear V2 1 The Slope Threshold setting represents the amount of change in response over time required to differentiate between an eluting peak and baseline noise Changing this setting may cause certain peaks that were previously detected to be ignored or to interpret noise as peaks The Slope Threshold setting is one of the user definable parameters in the Peak Find Tab in the LabChip XT software Specifies a size range in which to detect the region of the fluorescence signal instead of specifying a specific size for a peak Use a smear to detect a broad mix of molecules of similar but distinct sizes in a sample The concentration or fractional presence within a specified range of molecule sizes is measured Specify the Start Size and End Size of a smear in the Method Window on the Smear Analysis Tab Smears are also used to display the region of extraction The extraction smears are created automatically during an extraction run The Smear Properties can be viewed in table form in the Channel Table View To view the Smear Properties in the table add the desired property to the Channel Table View The properties extracted from the smear match those of a peak having extends area concentration etc Pu
208. oteCDR cannot be changed Wait for the Create Server button to be disabled and the text boxes to be active NOTE Server name folder name username and password are case sensitive 4 A folder must be created on the server to store the database To create a new folder on the remote server e Type the desired folder name in the Folder Name text box e Type a Username for the folder in the Username text box This is a separate username from the user names created in the LabChip XT software This username is only used to access the data folder on the Remote CDR Server e Type the desired password in the Password and Confirm Password text boxes e If Get Folder Details is checked a text file specifying the folder details is created and saved in C Program Files Caliper Life Sciences LabChip XT CDRServen ServerDetails e Click the Apply button to create the folder 5 Close the CDR Server Utility Window after the desired folders have been created V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 95 Backing Up Data Files to the Remote CDR V2 1 Remote CDR Backup copies each data file in the LabChip XT software to the Remote CDR server and stores a copy of the data file in a database Each time a data file is created or modified the changes are copied into the remote database Remote CDR Backup can only be enabled by the LabChip XT default Administrator To set up Remote CDR Backup 1
209. ox and enter the desired extraction region in the text boxes Click the Review Setup button to see the actual steps that will be executed 7 Ifthe Mode is Trigger select the desired extraction mode e Fluorescence The extraction trigger point is the point where the RFU exceeds the specified Threshold LabChip XT only e Peak Start The extraction trigger point is the point where the signal slope meets or exceeds the specified Threshold value e Peak Max The signal slope within the search region must exceed the specified slope threshold RFU min to arm this trigger The extraction is triggered when the signal has switched to a negative slope which meets or exceeds the specified threshold in magnitude If the end of the search region is reached after the trigger has been armed but before the negative slope threshold has been achieved the extraction will trigger at the end of the search region LabChip XT only e Collect On Click Collection is triggered by the user The target region displays in green on the graph Click on the word CLICK in the Run Setup section on the left side of the LabChip XT XTe Main Window to open the Fractionation Pending window The target region continues to update until the extraction is triggered Click the Start Now button when the green region is over the region to be extracted When manual mode is selected in the width setting click on the word STOP in the Run Setup section to end the collection
210. p XT XTe User Manual Caliper Life Sciences Inc Software Reference 157 Method Window The Method window specifies the analysis parameters for the channels in the collection Use the analysis settings to analyze the data after the fractionation is complete To view the method for the selected data file select Analysis gt Analysis Settings Methods cannot be edited in the LabChip XTe software The Method Editor window contains the same options as the Method window To open the Method Editor window to view or edit a saved method file select Tools gt Method Editor on the main menu The Method window contains the following tabs e Method Info Tab e Analysis Tab e Peak Find Tab e Expected Fragments Tab e Excluded Fragments Tab e Smear Analysis Tab e Advanced Tab The following buttons at the bottom of the Method window are used to save apply or cancel changes Buttons Function OOOO Apply Applies setting changes and re analyzes the chip but keeps the Method window open Apply Applies the selected analysis settings to all chips in the open Global workspace Restore Restores the analysis settings for the chip to the version of the data file Chip selected in the Restore Chip Settings to Version window If the 21 CFR Security option is installed opens the Restore Chip Settings To Version window to choose which version of a data file to restore OK Applies the changes in the Method window and re analyzes the chip with
211. pacity runs out the current will drop and the DNA will not continue to migrate into the collection well Exceeding the buffer capacity will cause undesired results 1 Check the buffer icons on the Setup Tab and verify all the icons are green indicating the buffer is sufficient for the run If the icons are not green click the Buffer Utilization Tab to view the estimated extraction time and buffer limit 2 Using the estimated extraction time select extraction parameters on the Setup Tab that either complete the extraction before the buffer time limit is exceeded or select the manual collection width and end the collection before the buffer runs out Enter the User Info 1 Click the User Info Tab in the Run File Editor Window 2 Type the operator s name and a comment if desired If the 21 CFR Part 11 Security option is installed in the LabChip XT software the current logged in user name is automatically displayed Specify the Ladder Settings V2 1 Custom Ladder settings are only supported in the LabChip XT software To change the ladder settings 1 Click the Sizing Table Tab in the Run File Editor Window 2 To use the default Caliper ladder select the Method Ladder option 3 To use a custom ladder by specifying the sizes of the peaks in the ladder select the Custom Ladder option and type the ladder peak sizes into the Size column of the ladder table 4 To reset the ladder table back to the settings saved in the method
212. ph View Properties Click and drag the baseline of the remaining peak to include the area under the excluded peak Changing the Time Window for Analysis The Start Time and End Time parameters in the Peak Find tab define the time window within which peaks are found These settings can only be changed in the LabChip XT software To change the Start Time and End Time parameters for all channels in the open assay 1 V2 1 Select Analysis gt Analysis Settings to open the Method Window and then click the Peak Find Tab Change the Start Time and End Time parameters as necessary Click the OK button to save the setting reanalyze the data and close the window OR Click the Apply button to apply the changes and reanalyze the data but keep the Method window open LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 57 Aligning or Unaligning the Marker Peaks To perform data analysis for DNA assays the LabChip XT software aligns marker peaks included in the sample channels with markers from the ladder LabChip XT only e To view the raw data without analysis choose Analysis gt Turn Off Analysis LabChip XT only e To re enable analysis choose Analysis gt Turn On Analysis LabChip XT only The default setting for this function is enabled Turning off the analysis displays the data without aligning the markers in the channels and without displaying peak labels or smears Calne 04 31 25 0
213. place the chip in the instrument close the lid and resume the run by clicking the Resume button on the Run Paused window See the Assay Guide and Run File Guide for important information about using Extract and Pause While the run is paused you can also edit or stop the run To select a single channel as data is acquired or after the run is finished click a channel in the Chip View or List View LabChip XT only a sample name in the Channel Table View or a lane in the Gel View To manually pause a run in progress see Pause a Run on page 37 To stop the run before it is complete see Stop a Run on page 38 When the assay is complete Run Successful displays in the Status line For information on data analysis see Data Analysis on page 43 If desired remove the chip To save the Workspace in the LabChip XT software 1 Select File Save Workspace The Save Workspace File As Window opens with the data file name as the default name of the workspace If desired change the location and or the name of the workspace file and click the Save button Workspace files have an xtw file extension The workspace file should be saved in the default location which is the same directory that contains the data file The data file is automatically saved at the end of the run To view or re analyze the data see Data Analysis on page 43 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 37
214. r Window on page 150 Export Window on page 151 Flush Chip Window on page 154 Layout Options Window on page 155 Login Window on page 156 Method Window on page 157 Modify Run Settings Window on page 173 New Collection Window on page 174 Perform Signature Window on page 175 Print Window on page 176 Print Validation Reports Window on page 1 8 Rename Collection Window on page 179 Run File Editor Window on page 180 Run Info Window on page 181 Save Workspace File As Window on page 183 Select a Data File Window on page 184 Software Installation Qualification Window on page 185 Start Fractionation Window on page 186 System Diagnostics Window on page 199 Unlock Application Window on page 201 Unlock Data File Window on page 202 User Administration Window on page 203 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 102 LabChip XT XTe Main Window V2 1 eo ps ne n rs sas ek asked din aa A vaar le l AA x n Bo Vie sos Tees a ad hy med ee i ia I qe La mi CCE ST L L a IA T ES ns _ Le Figure 22 LabChip XT Main Window The main window of the LabChip XT XTe software includes e Menu Bar on page 103 e Run Status and Chip Info
215. r loss Switch the Power switch on the LabChip XT XTe to the 3 Computer went into Abena ON position See page 213 Restart the LabChip XT XTe software If the problem is not resolved contact Caliper Technical Support see page 2 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 22 Pin Test Failed Warning Message Pin test failed Possible Causes Recommended Actions 1 Not enough liquid in the 1 Prepare the chip as described in the LabChip XT chip wells Assay User Guide 2 If the problem is not resolved contact Caliper Technical Support see page 2 Current Leakage Check Failed Warning Message Current leakage check failed Possible Causes Recommended Actions Dirty electrode block Clean the electrodes see page 221 Run the Current Leak Diagnostic Test see page 229 If the problem is not resolved contact Caliper Technical Support see page 2 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 228 Running Installation Qualification IQ The Installation Qualification 1Q verifies proper installation of the LabChip XT XTe software and verifies no unauthorized changes have been made to the software The 1Q can be run whenever required by your laboratory procedures The Installation Qualification can be used to check software installation qualification after routine computer maintenance suc
216. r success From our original factory warranty through a comprehensive line of customer support plans Caliper offers you Field Service Engineers and in house Specialists who are dedicated to supporting your hardware software and application development needs Call 508 435 9761 877 LabChip for LabChip products only Fax 508 435 0950 Email technical support caliperLS com Our programs can include such useful services as e Preventive maintenance e Diagnostic servicing performed on site by Caliper field service engineers or remotely via Technical Support e Validation performed on site by Caliper field service engineers e Extended use of the Caliper Technical Support Center e Software updates e Parts labor and travel expense coverage e Other customized services upon request Training For Your Product FCC CE V2 1 Contact the Caliper Center for Training and Development for information about the availability of training courses for your product Call 508 497 2634 Fax 508 435 3439 This device complies with part 15 of the FCC United States Federal Communications Commission Rules Operation is subject to the following two conditions e This device may not cause harmful interference and e This device must accept any interference received including interference that may cause undesired operation This device complies with all CE rules and requirements LabChip XT XTe User Manual Caliper Life Sciences I
217. rams tab 64 121 Electrophoresis 20 243 Enable Remote CDR Backup 146 End POlites 4 sde 544440804 243 End Time 44 161 243 changing 54 56 Entire collection 137 Error Messages 226 227 Current Leakage Check Failed Warming sis de ee oe ER ee ee 227 Device Disconnected Error 226 Error Message Area 110 IV Check Failed Warning 227 Event Viewer Window 150 Searching for Events in the Events LE REP TE E EEE od 224 Viewing Current Events in the Events E TE ns ass 225 Viewing Past Events in the Events LEE DT EE N HE NE 225 Excluded fragments 167 Excluded Fragments Tab 167 Excluded peaks 167 Excluding a peak 44 55 Expected fragments 48 Caliper Life Sciences Inc Expected Fragments Tab 165 Expected Peaks creating 48 exporting 49 e ys ne eee sun ge ee 50 IMpOTrtiIng ET e268 RT 49 viewing in Channel Table View 51 viewing in Gel View 51 viewing in Peak Table View 52 Expected Peaks only 137 EXPO Vs 74 141 151 165 169 Audit Trail Export Window 141 Auto Export window 151 Automatically 31 Excluded Fragments button 167 Expected fragments 165 Expected peaks 165 Export window 151 Manually
218. ration for the channel by clicking the down arrow next to the channel icon e Disabled e Ladder e eXtract and Stop e eXtract and Continue e eXcLuDe Region LabChip XT only e Separation LabChip XT only e eXtract and Pause e Skip Extraction LabChip XT only e Flush Sample For descriptions of each option see Setup Tab on page 188 For each channel where eXtract and Stop eXtract and Continue eXcLuDe Region eXtract and Pause or Skip Extraction is selected go to step 4 to select the desired extraction mode Select the desired Mode e Size The extraction is specified by the size of the fragments e Trigger The extraction is specified by searching for the specified trigger in the search region If the Mode is Size select the desired Extraction Region Either e Click and drag the slider to the desired range e Type the desired values in the Extraction Region text boxes e Type the size in BP of the fragments to be collected in the Size text box and type the desired percent of size before and after to collect in the Percent text box Collection will start at the specified size minus the percent and will stop at the specified size plus the percent LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 26 Select the Extraction Parameters on the Setup Tab Continued 6 Ifthe desired extraction region is larger than the assay Maximum Extraction Width select the Auto MultiStep Cut check b
219. rd in a safe place This password cannot be reset if forgotten To change the administrator password e Log into the LabChip XT software as the administrator e Select Security gt Change Password e Type the current password e Type the new password in both the New Password and Confirm Password text boxes e Click the OK button 2 To enable remote CDR install and set up the Remote CDR Server see page 93 then start the CDR Utility and enable remote CDR Backup see page 95 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 91 Creating New Data Folders To create a new CDR data folder for LabChip XT data files 1 9 Select File gt Import Data File The CDR Manager Window opens Click on the upper level CDR folder Click the New Folder button on the left side of the window A new folder named New Folder is created and the name is selected for update Type the desired name for the folder and then press the Enter key Close the CDR Manager Window Moving Data Files into Folders To move a LabChip XT data file into a CDR data folder 1 2 3 4 Select File gt Import Data File The CDR Manager Window opens Click on the name of the data file Drag and drop the file into the desired folder Close the CDR Manager Window Deleting Data Folders V2 1 Only CDR Data folders that are empty can be deleted Move the LabChip XT data files out of the folder before deleting the fol
220. ria Expected Peak Filters can contain multiple size peaks in the same filter as shown above Expected Peak filters with multiple peak sizes in the same filter always select only channels that contain all the peaks listed Figure 31 Filter Applied Example V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 127 Filter View Continued In the chip diagram in Figure 31 on page 126 the orange channels are the channels that meet the filter criteria To see the graph for each channel click on the channel in the chip diagram and view the graph in the Graph view The gel in Figure 31 on page 126 shows the expected peaks marked with colored lines on the Gel view The channel header is orange if the channel meets the filter criteria If a channel meets the criteria of multiple filters the header color is a combination of the filter colors V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Gel View V2 1 Software Reference 128 The Gel view in the Collection Pane is a visual representation of the data formatted to look like the Gel slabs that were originally used to provide DNA data The data is shown in Time vs Fluorescence or digital form Click on a gel lane channel to select the channel Ctrl click to select multiple channels Selected channels are outlined with a dotted gray line Channels selected in the Gel view are also selected in the Channel Table View and are displayed in t
221. rift For isolated peaks the local peak baseline is a straight line connecting the start point of the peak with the end point For peaks that are very close together an average baseline is used when the value between the peaks does not drop to the actual baseline In the LabChip XT software you can select the desired baseline algorithm for all of the samples in the chip Choose the desired option on the Peak Find Tab No baseline Zero Baseline or Baseline Subtraction e For the Zero Baseline option a single value of baseline shift is determined by averaging over a 1 second region just before the Data Range Baseline time This shift is subtracted from all of the data e The Baseline Subtraction option uses a spline fit or rolling ball fit to the data to determine a smooth baseline that is subtracted from the data The percentage of data points used in the spline fit is specified by the Threshold value in the Method window The collection of points with the lowest variance up to this percentage is used for the spline fit The Rolling Ball algorithm uses the Time Diameter to specify the size of the ball in the X direction and the Signal Diameter to specify the size of the ball in the Y direction Figure 92 shows baselines established for DNA assay peaks based on the settings in the Peak Find Tab DNA peak baselines are determined on a peak by peak basis Ig TE i a a Figure 92 Baselines LabChip XT XTe User M
222. rity is the ratio of smear concentration to total sample peak concentration exclusive of markers system peaks and excluded peaks Excluded peaks are not excluded from analysis calculations such as concentration or area within the smear region so the limits must avoid excluded peaks An additional Peak Count property is available for smears Peak Count is the number of non excluded sample peaks in the region where the center of the peak is inside the smear limits In the Graph View the smear regions display with the integration extends drawn at the base of the smear in the chosen color and the trace highlighted with the smear color Override the smear base by dragging with the mouse in the Graph view Only the vertical position of the base corners can be adjusted in the graph since the size limits are specified and should not be altered In the Gel View the smear region is shown on the gel as a colorized region The color is a transparent version of the color selected for the region so the fluorescence intensity still shows through LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 295 Smear Baseline V2 1 A Smear baseline is calculated for each smear Choose the desired Smear Baseline option on the Advanced Tab on the Method Window in the LabChip XT software The following options are available to calculate the smear baseline e Two Point The baseline is a single straight line between the flat baseline
223. rop the gel lanes to change the order of the channels for comparing two or more gel channels To drag and drop a gel lane click in the header of the lane to be moved and drag the gel lane to the desired location Double click in the Gel view to zoom out to the previous zoom level Gel data in the LabChip XT software can be exported to a graphic file by choosing Export on the File Menu see Exporting Data on page 74 for details If the workspace contains multiple collections data is exported from the active selected collection To change the Lane Width or Gel Contrast Range see Gel View Properties Right Click Menu Right click anywhere in a gel to display a shortcut menu containing the following commands Unzoom Zooms out to the previous zoom level Unzoom All Zooms out completely and returns to the standard view Scale Gel Contrast to this Lane If selected for a lane the minimum and maximum RFU values for all lanes in the collection are set to the minimum and maximum RFU values in the selected lane Remove Removes the sample from the collection Copy Gel Copies all of the open lanes channels to the clipboard in a bmp format Copy Lane Copies the selected lane channel to the clipboard in a bmp format LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 130 Gel View Continued V2 1 Analysis Settings Opens the Method Window to change the analysis settings LabCh
224. rt Fractionation Window 187 Shortcuts 236 Show all peaks 137 Show Data Points 122 Show EP Legend 131 Show Expected Peaks 131 Show Legend in Gel 131 Show Peak Baselines 122 Show User Info Tab 206 Showing views 62 oa RE IE TR eae AE EE N 218 Sizing Table Tab Start Fractionation Window 196 Slope Threshold 161 Slope threshold 254 Slope Threshold changing 54 IMC reee Ur REE 254 Smear Analysis Tab 169 Smear Baseline 255 Smear color 169 Smear Name 169 Smear SIE PP TT TT 169 Software display flashing 234 Software IQ Window 185 Software Reference 101 Sort within each channel 137 Specifications 218 instrument 218 Standard curve 44 160 256 Standard Curve fit 160 Sl 2445 noria noni 23 33 256 Monitoring the Run 35 Running a Chip 33 V2 1 LabChip XT XTe User Manual Index 268 Running the assay 33 Start button 33 Stan POIE 3 44 256 Start Fractionation Window 186 opening 34 Stat INE sie ce ee a 161 changing 54 56 Stop Button 33 38 109 Storage Temperat
225. rt of a run when the first peak will be detected any peaks appearing before this time are ignored The Gel and Graph views will not plot data earlier than this time End Time Specifies the time after which peak detection stops The Gel and Graph views will not plot data beyond this time Filter Width Specifies the width in minutes of the low pass filter to be convolved with the data The width of this filter should be about 6 samples wide If this setting is too large peaks will develop spurious side lodes ringing due to over filtering Baseline Specifies a baseline selection parameter for peak finding The signal Plateau is at baseline whenever the slope of the data is less than the slope threshold setting positive or negative for longer than the Baseline Plateau This rejects brief low slope areas such as in between non baseline resolved peaks Polynomial A filter algorithm is used to filter the data increasing the signal to Order noise ratio The data is convolved with a polynomial of this order to produce filter data and a filter slope and decrease the background or baseline noise and or spikes in the signal This value is read only V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 163 Table 1 Chip Peak Find Settings Chip Settings Baseline e None No correction Algorithm e Zero Baseline Offsets all graphs to zero baseline but does not affect analysis Baseline Subtrac
226. s e using the default Caliper Sizing Ladder while running up to four samples in the chip e using the default Caliper ladder while running one ladder and up to three samples in the chip or e using a custom ladder while running up to four samples in the chip LabChip XT only In its simplest form the sizing is performed with only the sizing ladder A generic ladder is provided by Caliper as part of the fractionation method designed for the chip and size range The ladder times of the sizing ladder are used to map migration time to size The collection start time and collection end times are determined at the start of the run and do not change as the run progresses It is essential for each sample to include a lower marker The ladder and sample markers are aligned resulting in an adjustment of the sample migration times relative to the ladder The collection times are corrected using the aligned sample migration times after the sample lower marker passes the detector To improve sizing accuracy a ladder can run in one of the channels and the channel can be designated as the real time ladder The real time ladder runs parallel to the samples The ladder peaks that are smaller than the extraction region pass the detector before the collection time The software uses the sizing lookups from the sizing ladder to estimate the times for sizes larger than the collection region Often the sample DNA of the desired size reaches the switch point
227. s ATexport_ lt date gt _ lt time gt where lt date gt and lt time gt are the current date and time LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 90 Central Data Repository CDR The Central Data Repository CDR is a protected folder located on the local computer All LabChip XT data files xtd are saved in the default CDR folder on the local computer The CDR folder is protected from changes by unauthorized users The CDR is only used when the 21 CFR Part 11 option is installed with the LabChip XT software The CDR Manager Window enables you to organize data files into virtual folders The folders are not actually created in the CDR folder on the local computer but are displayed in the CDR Manager Window to organize the data files The CDR Manager Window enables you to create new folders rename existing folder and delete empty folders The following procedures are included in this section CDR Security Suggestions on page 90 e Creating New Data Folders on page 91 e Moving Data Files into Folders on page 91 e Deleting Data Folders on page 91 e Hiding Data Files in the CDR Manager Window on page 92 e Showing Hidden Data Files in the CDR Manager Window on page 92 CDR Security Suggestions V2 1 To ensure proper security of data files the LabChip XT Administrator should 1 Change the LabChip XT Administrator password Make sure to keep a copy of the passwo
228. s If selected a gel is exported for each of the channels selected in the Gel View or Chip View or List View This option is not available on the Auto Export window Single File If selected the selected gels are all included in the same image file Separate Files If selected the selected gels are each exported to a separate image file Height Specifies the desired height in pixels of the gel graphic Image Format for Gel and Electropherogram Select the desired format for the exported image files LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 154 Flush Chip Window Use the Flush Chip window to flush used channels on a chip for the specified times Individual times can be specified for each channel on a chip To open the Flush Chip Window insert the chip in the instrument and then select Instrument 2 Flush Chip 1 ag Flush Chip A Sal flush lira for sach used channel Flush Time fran Chame stopped by user Channel 2 aborted during extraction Channel 3 UNUSED Do nat flush Channel 4 UNUSED Do not fush AQ Used Chants Qt Fush Cora Figure 49 Flush Chip Window Channel Flush Time Specifies the desired time in minutes to flush each channel Unused channels should not normally be flushed but can be flushed if necessary All Used Channels Time Sets the Flush time for all used channels to the specified time If the time for any channel is changed the time sp
229. s Inc Software Reference 138 About LabChip XT XTe Window The About LabChip XT XTe window displays the software and firmware versions Selecting About LabChip XT or About LabChip XTe on the Help Menu opens this window About LabChip XT Aa LabChip XT Software Verson 2 0 10060 Farmvere Verson 1 04 0 17710 4 Com 2010 2011 Caliper Life Sciences inc Al ghia reserved Mo pat of ihis often mary ba A or in an mem wilhoui the writen person of the copyright owner Fo Figure 37 About LabChip XT Window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 139 Add New Expected Peak Window Use the Add New Expected Peak Window to add an expected peak to specific channels To open this window right click near a peak in the Graph View and select Add Expected Peak Expected Peaks are only supported in the LabChip XT software a Add Mew Expected Peak A A A f ee LES Figure 38 Add New Expected Peak Window Size BP Specifies the expected size of the peak in BP The default size is the size of the peak that was selected Window Specifies the tolerance window as a percent of the expected size for the fragment to allow for small variations in expected peak size Color Displays the color to use to mark the peak in the Graph View or the Gel View Specifies a name to display in the Type description for the peak Property Specifies the content of a column added to the ch
230. se the specific Channels to apply the expected fragment to Export button Opens the Export Expected Fragments window to create an Expected Fragments File gep from the current settings in the tab Import the gep file into another method to use the same expected fragments in another method Restore button Restores the settings to the last saved settings for expected peaks Import button Opens the Import Expected Fragments Table window to select an Expected Fragments File gep to import The gep file is created by exporting expected fragments from another method Clear button Deletes all Expected Fragments from the table V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 167 Excluded Fragments Tab V2 1 Use the Excluded Fragments tab on the Method Window to enter Excluded Fragments for DNA assays After the data is analyzed any peaks matching the excluded fragments are excluded from the analysis Meibod XT DNA 300 a r ze re _ _ _ Pr Method Info Anaya Fem Fra 12 aaa Fragments CO Seren mear Ar rare erry ET mi Export Fesiors i ro i Clear Figure 56 Method Window Excluded Peaks Tab The Excluded Fragments tab contains the following options and buttons Excluded Fragments Table Lists the excluded fragments for the method e Size Specifies the size of the excluded fragments in BP e Window Specifies the tolerance window as a percent of
231. sible by Windows Administrators and to enable Remote CDR Backup Before enabling remote CDR Backup the remote CDR server and folder must be set up see page 93 V2 1 To open the CDR Utility Window select Tools gt CDR Utility on the LabChip XT XTe Main Window The CDR Utility command is only available if the 21 CFR Part 11 Security option is installed with the LabChip XT software Figure 44 CDR Utility Window COR Utility BB Local COR Foder EE COR Folder C Program Fies Calper Lie Sciences COR To enable the above checkbox in Windows 7 pease stad the ecitware by doing rightchexk on the LabChe XT desktop icon and selecting Run as administrator cobor 7 Enable Remote COR Backup Remote COR Database must be rralable and configured before enabling this feature Remote Computer Mama IP Address Lisername Password The CDR Window contains the following options CDR Folder Accessible by Windows Administrator Displays the location of the CDR folder where the LabChip XT data files will be saved This location cannot be changed To access the check box right click on the LabChip XT icon on the Windows desktop and select Run as Administrator If selected Windows Administrators who are logged into the computer can access the CDR folder If not selected Windows Administrators are prompted to set full permission when opening the folder LabC
232. sis tab on the Method Window to view the portion of the sample that was routed to the collection well on the chip as a Smear Use the Smear Analysis tab on the Method Editor window to define smears before the method runs Defining a smear does not cause the region to be extracted it is only marked on the display After the run the area matching the smear is shown in the Channel Table View Gel View if Show EPs and Smears is selected in the Gel View Properties and Graph View if Show Smears is selected in the Graph View Properties To view the smears for the open chip data file select Analysis gt Analysis Settings on the main menu Mead XT DONA 750 Expected Fragments Exdiuded Fr Export Pas ove ro Gear Figure 57 Method Window Smear Tab The Smear Analysis tab contains the following options and buttons Smear Table Lists the smears for the chip e Start Size Specifies the starting size of the area to be included in the smear End Size Specifies the ending size of the area to be included in the smear e Color Displays the color to use to mark the smear in the Graph View or the Gel View e Name Specifies a name to display in the Channel Table View The smear name corresponds to the smear range and channel number e Property Displayed in Channel Table Specifies the content of a column added to the Channel Table for each smear LabChip XT XTe User Manual Caliper Life Sciences Inc Software Referenc
233. software The LabChip X Te software does not support saving workspace files To open this window choose File gt Save Workspace As This window also opens the first time you save a new workspace hane arpa lis Ak A sl Figure 67 Save Workspace As Window Tip You may want to save the workspace file in the same location as the chip data files to prevent missing chip data files when moving workspace files V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 184 Select a Data File Window When you choose Import Data File from the File Menu the Select a Data File window opens as shown in Figure 68 If the 21 CFR Part 11 option is installed the CDR Manager Window opens Data files generated by the LabChip XT software have an xtd file extension Data files generated by the LabChip XTe software have an xte file extension The LabChip XT software can only open XT data files and LabChip XTe software can only open XTe data files alert a Dans Pie Figure 68 Select A Data File Window Select a data file name in the list box and click the Open button or double click a file name to open the data file To select multiple files press and hold CTRL then click each file name To select a continuous block of files click the first file press and hold SHIFT and then click the last file To select all files press CTRL A V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Soft
234. software The data file contains the data from the read method information and Run Information for the run Data is saved to the file during the run If a run is stopped before the run is complete the collected data for all channels is saved in the data file The file name is specified in the Start Fractionation Window Zero Baseline V2 1 Changes to Analysis Settings are only supported for LabChip XT Selecting this setting in the Peak Find Tab offsets the graphs shown for the individual channels but does not affect analysis The mean of 100 points before the baseline time derived when calculating channel noise is used as the zero baseline value All electropherograms produced with the instrument show some amount of background fluorescence By default the LabChip XT software enables the Zero Baseline function To change the Baseline Algorithm select None Zero Baseline or Baseline Subtraction on the Peak Find Tab fl LL ALL nos MECO Re lo ed 1000 1500 2000 500 Ale ned Tues de acj Figure 102 Zero Baseline On CL LU H raniji all NL hdl MI AA hal ln a Serna SN LCR EEE FM 2500 Aligned Time Iser Figure 103 Zero Baseline Off LabChip XT XTe User Manual Caliper Life Sciences Inc Caliper Life Sciences Inc Product Warranty 259 Caliper Life Sciences Inc Product Warranty l INSTRUMENTS Caliper Life Sciences Inc Caliper warrants your
235. ss than the Channel End time Table 2 Channel Peak Find Settings Channel Settings Displays the channel being edited Select any channel or ladder on the chip Read only Displays the ladder used for aligning this channel Minimum Specifies an override to the Peak Find Settings for Minimum Peak Peak Height Height for the entire chip Specify a valid numeric value to override or Clear the field to reset to the Global setting V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 164 Table 2 Channel Peak Find Settings Channel Settings Minimum Specifies an override to the Peak Find Setting for Minimum Peak Peak Width Width for the entire chip Specify a valid numeric value to override or clear the field to reset to the Global setting Slope Specifies an override to the Peak Find Setting for Slope threshold for Threshold the entire chip Specify a valid numeric value to override or clear the field to reset to the Global setting Use Chip Sets Min Peak Height Min Peak Width and Slope Threshold text Value button boxes to lt Uses chip value gt settings Apply Apply channel specific peak find settings only to the channel or Channel ladder showing in the Channel field Ladder button Apply Chip Apply channel specific peak find settings to all channels on the same button chip V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 165 Expected Fragmen
236. sts de s curit pour la mise la terre le courant transitoire de ligne d alimentation et la perte de courant Input ol Entr e LabChip XT XTe User Manual Caliper Life Sciences Inc Preface 6 Table 1 Important Symbols Continued Symbol Description Symbole Description Output io Sortie Equipment Yellow Caution risk of danger labels are color Red Stop coded Blue Mandatory action Les tiquettes Green Safe condition or information de l appareil Jaune Attention danger potentiel sont cod es Rouge Arr ter couleur Bleu Intervention obligatoire Vert Condition s re ou informations de s curit Helpful hints additional information Conseils utiles informations suppl mentaires V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Instrument Safety T Instrument Safety The following safety information about the LabChip XT XTe is included in this documentation Read and review all safety information before operating the LabChip XT XTe e Required Training e Chemical Safety on page 8 e Laser Safety on page 9 e Electrical Safety on page 10 Required Training V2 1 Ensure that all personnel involved with the operation of the instrument have e Received instruction in general safety practices for laboratories e Received instruction in specific safety practices for the instrument e Read and understood all related MSDSs WARNING AA Use this product only i
237. t already contains compatible data files In the LabChip XTe software the workspace opens automatically when the data file is imported On the menu bar select File gt Import Data File If the 21 CFR Part 11 option is not installed the Select a Data File Window opens If the 21 CFR Part 11 option is installed the CDR Manager Window opens Select the name of the data file to open and click the Open button The selected data file is imported into the open workspace Use Ctrl click or Shift click to select multiple files If desired right click on the Chip Name in the Chip View see Chip View or List View and select Rename Chip to change the name of the chip in the display If the Rename File to Match check box is selected the data file is also renamed to the same name as the chip The data file cannot be renamed if the 21 CFR Security option is installed Select the desired channels to view in each collection in the workspace The LabChip XTe software does not support multiple collections in one workspace See Modifying Analysis Parameters on page 53 for information about changing analysis parameters in the LabChip XT software LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 47 Adding a Collection to a Workspace V2 1 Collections are used to specify the channels selected for view in each chip data file the layout of the views in the Collection tab and the display properties for each view
238. t Collection gt Save Template on the main Menu Bar To apply a collection template to a new collection select the Template option in the New Collection Window To apply a collection template to an existing collection select the tab for the desired collection and then select Collection gt Apply Template on the main Menu Bar Collection Templates are not supported in the LabChip XTe software LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 241 Collection Well Data Files The wells on the chip that will contain the fractionated samples at the end of the run There is one waste well and one collection well per channel There are four channels on each LabChip XT chip While running an assay the raw data received from the instrument is automatically saved to the chip data file xtd or xte As the data is received it is saved to the data file The name of the data file is specified in the Start Fractionation Window After a run is complete the data is analyzed using the analysis settings in the method The analysis settings are saved in the data file xtd or xte After the run in the LabChip XT software you can change the analysis settings using the Method Window When the new settings are applied the data is reanalyzed and the updated results are displayed Changes to the analysis settings are not saved until the workspace is saved To save analysis settings without saving the workspace se
239. ta by matching the peak time of the marker in the sample data with the same marker in the ladder data The size of each sample peak is calculated by linear interpolation between the known ladder peak migration time and size using the peak aligned migration time In the LabChip XT software the analysis settings can be changed to perform the interpolation using a local third order polynomial fit to the time instead of the size relationship provided by the ladder The concentration of the sample peaks is calculated using the known area and concentration of the ladder peaks The molarity of each sample peak is calculated using the sample concentration the DNA fragment size in base pairs attributed to the peak and the known molecular weight of the DNA base pair Electrode Cleaner The electrode cleaner looks like a chip except that it is clear Use the electrode cleaner in place of a chip when cleaning electrodes V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Glossary of Terms 243 Electrokinetic Forces Electrokinetic forces are used to move switch mix and separate the nucleic acid samples Active control over voltage gradients directs the movement of materials using the phenomenon of electroosmotic flow or electromigration Electroosmotic Flow A phenomenon that results from an electrical double layer formed by ions in the fluid and surface electrical charges immobilized on the capillary walls When an electric field
240. ta file when the 21 CFR Part 11 option is installed and Require Signature on File Update is selected 1 The Perform Signature Window opens when you save a data file 2 Select the name of the user who is signing the data file in the Username drop down list 3 Type a Comment that meets the requirements of the compliance policies LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 41 Saving Data Files Continued 4 lf desired or required by compliance policies select the Approval State of the data file 5 If desired or required by compliance policies select the Lock check box to lock the data file and prevent any changes until the data file is unlocked To lock a data file the Approval State must be either Accepted or Rejected 6 Type the User Password for the signing user 7 Click the Sign button The Signature Performed window confirms that the signature has been performed 8 Click the OK button The signature is recorded in the data file NOTE Changing the analysis settings in the LabChip XT software and saving the chip data file does not change the raw data from the run Only the display of the data is changed If you change the analysis settings in the LabChip XT software without saving the new settings and then try to close the workspace exit the software or acquire new data you are prompted to save the changes Selecting Yes opens the Save Workspace File As Window V2 1 LabChip XT XTe User Manu
241. tains the following fields Time The time the event or error occurred Source The source of the event or error Event Code The event error ID number used by Caliper to troubleshoot problems Description A detailed description of the event or error that occurred V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 226 Error Messages Before a run is started and while an assay is running the instrument firmware and software checks for errors e g disconnected devices bad parameters bad data etc If an error is detected an error or warning message displays on the LabChip XT XTe Main Window Depending on the error the run may continue or be aborted The error or warning message describes the problem and either contains information on how to resolve the problem or directs you to call Caliper Technical Support see page 2 For specific information about an error or warning message click one of the links below General Errors e Device Name is Disconnected LabChip XT XTe Warnings e Pin Test Failed e Current Leakage Check Failed Device lt Name gt is Disconnected This error message indicates that there is no communication between the software and the specified device Possible Causes Recommended Actions 1 Cable between computer Verify that the USB communication cable is secure and instrument unplugged pgs Verify the power cord is plugged in 2 Instrument powe
242. tart Fractionation Window for definitions of specific options or settings The following buttons are located at the bottom of the Run File Editor window me A Saves the selected settings in a run file with the specified name xml Review Opens the Fractionation Setup Review window to view the settings for the Setup current run Name File csv LabChip XT only Import Imports the settings from an existing run file xml into the Run File Setup Editor window Closes the Run File Editor window without saving the settings Opens the Import Sample Names window to select the desired Sample Names V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 181 Run Info Window Use the Run Info window to view information about the run options for the selected chip data file To open the Run Info window select View gt Run Info on the LabChip XT XTe Main Window or right click on the name of the data file above the chip diagram and select Run Info Aus lefa Orma Fraznsnarsn CAL ABC PEER hd EA RLAR SPENE ET Uber C Peer Fan Cakes Lie Gor Les XT Deo Daa Dee brew ol LETE AR TEIWETETETETETETE TER Mi rages TIM 20111 EE II CUT Pii Lier LAS CHA A er SEP 533 EF SSR WEP anpi DES EP TEN EF MUEP tas Fia ksa Figure 66 Run Info Window The information in this window is view only and cannot be changed The Run Info Tab displays method and run information The Event Log tab d
243. te Files to export each gel to a separate image file e If desired change the height of the exported graphic in the Height text box If either Electropherogram or Gel is selected choose the desired format for the image files Click OK to export the data to the specified location LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Software Security 78 Software Security 21 CFR Part 11 Compliance option is available for the LabChip XT software This option ensures that methods output data analysis settings event data and backup data files are not available for editing or tampering Data is stored in a secure folder on the local computer To create and maintain the Audit Log and LabChip XT user accounts Microsoft SQL Server 2005 Express is provided with the LabChip XT 21 CFR Part 11 option The following procedures are included in this section e Locking and Unlocking the Software on page 79 e Managing User Accounts on page 80 Adding New Users on page 80 Changing User Information on page 81 Changing User Information on page 81 Printing User Information on page 82 Activating and Deactivating User Accounts on page 82 Changing Access Rights on page 83 Printing Access Rights on page 84 Setting Policies for User Accounts on page 84 Printing User Policies on page 85 e Electronic Signatures on page 86 e A
244. the RFU value exceeds the specified threshold Collection ends when the sample specified by the Collection Width has been collected This option is only available in the LabChip XT software Peak Max Specifies that the trigger point for the extraction is the first point found within the specified Search Region where the signal slope is at or above the specified threshold RFU min and the signal has switched to a negative slope that is above the specified threshold If no local maximum is found by the end of the specified search region and the signal is increasing the extraction trigger point is at the end of the search region If the signal has a large negative slope at the beginning of the search region the extraction will not trigger until after the slope has again turned positive and exceeded the slope threshold When the software detects the peak maximum in the search region the collection start size is calculated based on the collection width The actual collection range achieved is reported in the Channel Table This option is only available in the LabChip XT software LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 192 Setup Tab Continued e Smear Max Specifies that the trigger point for the extraction is the first point found in the specified Search Region where the signal is at or above the specified Threshold RFU and the signal decreases after averaging over three consecutive data points Collect
245. the collection is centered on the peak or smear maximum If the extraction size is too large or exceeds the assay range limit the extraction size is automatically adjusted to a valid range For example if the collection width is set to 400 BP triggered by Smear Max starting at 100 BP then the extraction of 100 to 500 would be too large beyond 20 which is the assay limit of XT DNA 750 assay Theextraction range will be automatically adjusted and limited to 100 to 150 For Collect on Click the Fractionation Pending dialog will show that the collection is limited to 150 BP to meet the assay limit constraint Manual For Peak Start Collect on Click and Fluorescence the collection begins at the trigger point and ends when the user clicks STOP in the Run Setup For Peak Max and Smear Max collection begins at the specified percent before the trigger point size and ends when the user clicks STOP If the user has not stopped the extraction when the end of the search region has been reached the extraction ends there automatically If the start point of the collection width has already passed the switch point when the trigger point is detected collection begins immediately and continues for the entire collection width Fluorescence Peak Max and Smear Max are not supported in the LabChip XTe software LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 28 Select the Extraction Parameters on the Setup Tab Continue
246. the end of the chip data file Previous analysis settings are not overwritten enabling you to use the Restore Chip button on the Method Window to go back to any previously saved settings Chip data files are automatically saved when the Workspace is saved The LabChip XTe software does not support changing analysis settings or saving workspaces V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 105 Collection Menu Analysis Menu V2 1 The Collection menu in the LabChip XT software contains the following commands Undo Undoes changes to the collection view settings and filter settings Changes made in pop up windows such as analysis settings export settings etc are not affected by this Undo New Collection Opens the New Collection Window where you choose whether to create a new Collection from a saved Collection Template a Blank Collection or the Current Collection Rename Collection Opens the Rename Collection Window to rename the currently selected Collection Delete Collection Deletes the current Collection Save As Template Opens the Save Template As window to save the display and filter settings currently displayed in the Collection tab as a collection template Apply Template Opens the Apply Template window to open a saved collection template and apply the settings to the current Collection Layout Opens the Layout Options Window to change where tabs are displayed by de
247. the graph will zoom out to the previous zoom level Graph data in the LabChip XT software can be exported to a graphic file by choosing Export on the File menu See Exporting Data on page 74 for details If the workspace contains multiple collections the data exported is from the active selected collection LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 118 Graph View Continued V2 1 To show or change the labels on the peaks in the graph show the data points on the graph show peak baselines or change the graph colors see Graph View Properties on page 122 To select a peak on the graph move the cursor near the peak A blue arrow above the peak shows that the peak is selected and the cursor changes to an arrow that points straight up The Gel View and Peak Table View also select the corresponding entry You can adjust the peak baselines from the graph view after the run is complete if desired Select Show Peak Baselines in the Graph View Properties to display the baseline for each peak To change the baseline click at either end of the peak baseline and drag to the desired location To reset the baseline back to the original position right click near the baseline end point and choose Reset to Defaults While a run is in progress the graphs initially display the raw unanalyzed data as it is being read from the chip As data is acquired the analysis aligns the baselines and lower m
248. the new settings Print Opens the Print Preview window to view the analysis settings before Preview printing Print Opens the Print window to print the default ladder Analysis and Chip Peak Find Settings Analysis Parameters Expected Fragments Excluded Fragments and Smear Analysis Cancel Restores the settings that were selected when the window was opened or when the last Apply was performed No re analysis is performed because the settings were used for the last analysis performed V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 158 Method Window Continued The following buttons at the bottom of the Method Editor window are used to save or cancel changes Buttons Function OOOO Save Opens the Save Method to File window to specify a name for the Method modified method If the specified name is the same as an existing method you are prompted to overwrite the existing method Restore Restores the analysis settings to the last saved settings All changes are Method discarded Close Closes the Method Editor window If the method contains unsaved analysis changes you are prompted to discard the changes V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 159 Method Info Tab V2 1 The Method Info tab on the Method Window displays the header information for the current method Figure 52 Method Window Method Info Tab The following informa
249. the window or modify the settings to create another run file LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 33 Running a Chip Before starting a run make sure the desired run settings have been selected in the Run File Editor Window and saved as a run file see page 24 To start a run to read a chip 1 Prepare and Load the Chip 2 Select the Run File 3 Start the Run 4 Monitor the Run Prepare and Load the Chip 1 Prepare the chip as directed in the LabChip XT Assay Quick Guide or Assay User Guide WARNING AAAAA Some chemicals or samples used with the LabChip XT XTe are potentially hazardous and can cause iliness Follow the precautions in Chemical Safety on page 8 and the precautions in the Assay User Guide 2 Liftthe latch on the front of the instrument to open the lid 3 Place the prepared chip in the instrument with the notched corner of the chip aligned with the notch in the chip locator 4 Close the lid 5 See Select the Run File on page 34 V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 34 Select the Run File After the chip is prepared open the run file that contains the settings for the run 1 6 Start the Run V2 1 1 On the LabChip XT XTe Main Window move the cursor over the image of the LabChip XT instrument to display the Run button Click the Run button or select Instrument Start Run to open the Start Fractionation Window
250. thod Window Details Displays the details of the changes or signature Signature details include approving and locking unlocking the data file Print All Versions If selected version information and Options details for all data versions is printed Selected Version If selected version information and details for only the selected version is printed Print Opens the Print Preview window to preview the Preview printed version information button Print button Opens the Print window to print the data file version information Close button Closes the Data File Version window V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 150 Event Viewer Window Use the Event Viewer window to view events and errors that occur during the current run or during a previous run To open the Event Viewer window select View gt Event Viewer on the LabChip XT XTe Main Window HICAPRDLTAGE SCRET LEMESCLIRCE SYSTEM SYSTEM DEVE DEWLE Em Figure 47 Event Viewer Window The Event Viewer window contains the following tabs Current Events tab Displays the events that occurred during the current session Past Events tab Displays all events from previous sessions Search Results tab Enables you to search for specified text in past events current events or all events The tabs on the Event Viewer window contain the following columns Column Title Description The data and time the eve
251. tion A dynamic subtraction of the baseline that corrects for drifting Baseline Spline This algorithm creates a smooth line fit to the baseline data points and subtracts this smooth fit from the data The threshold specifies how much the baseline fit tries to follow changes in the data Lowering the Threshold below the default value of 20 allows the baseline fit to ignore regions that are slow changes of real signal peaks and not baseline drift Rolling Ball This algorithm simulates rolling a ball under the valleys of the signal The ball size determines how closely the baseline follows the signal A larger ball size creates a smoother baseline Time Diameter specifies the size of the ball in the X direction Signal Diameter specifies the size of the ball in the Y direction High Size If selected a second larger filter is applied to the data after the Filtering specified time This is useful for assays where the peaks are narrow at the start of the assay and become broad and noisy for larger sizes of DNA If not selected the same size filter is used for all data e Filter Width min The width of the second filter to be applied after the specified transition time Filter Width must be greater than the Sample Channel Filter width and less than or equal to 3 0 minutes Transition Time min The time at which to transition to the larger filter size Transition time must be greater than the Baseline Time on the Analysis tab and le
252. tion is displayed Method Class All methods on the LabChip XT XTe are XT DNA 750 XT DNA 750 Ver2 or XT DNA 300 method class DNA Name The name of the method Title The title of the method This field can be changed in the Method Editor window Comments An optional comment that can be used to identify the method Version The current version of the method that was run Format The format of the data file LabChip XT XTe User Manual Caliper Life Sciences Inc Analysis Tab V2 1 Software Reference 160 Use the Analysis tab on the Method Window to view the Lower Marker peak designation Ladder Sizes Ladder Concentration Standard Curve Data Range and Marker Concentration Methead XT OHA 750 Figure 53 Method Window Analysis Tab Default Ladder A table showing the sizes in base pairs of the ladder peaks Ladder Concentration The concentration in ng uL for the ladder peaks Standard Curve Determines whether the fit for the standard curve used to calibrate migration time to size will be done on a point to point or Polynomial fit of the ladder DNA methods are set to point to point curve fits but can be changed to Polynomial Lower Marker Conc ng uL The concentration of the lower marker in ng uL Size BP The size of the lower marker Time min The expected time when the lower marker will be detected in the sample Height The expected height of the lower mark
253. tire CDR folder to the desired location for the backup files LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Software Security 98 Setting the CDR folder back to not accessible 1 5 6 7 For Windows 7 Right click on the LabChip XT icon on the Windows desktop and select Run as Administrator For Windows XP Double click on the LabChip XT icon on the Windows desktop Log in to the LabChip XT CFR software as the Administrator user On the LabChip XT XTe Main Window select Tools CDR Utility The CDR Utility Window opens Clear the Accessible by Windows Administrator Level Users check box and then click the Apply button Click OK in the Confirmation window Click the Close button on the CDR Utility Window Close the LabChip XT software Backing up the Audit Trail Database 1 In Windows Explorer navigate to C Program Files Caliper Life Sciences LabChip XT Double click the BackupDB bat file A backup copy of the database named DBback bak is created In Windows Explorer navigate to C Program Files Caliper Life Sciences LabChip XT Database Copy the DBback bak file to the desired location for the backup files LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 99 Restoring CFR Files To restore the CFR files from a manual backup point you must restore both the CDR data files and the Audit Trail database If restoring the files to a new computer install the
254. tm To run a chip in the LabChip XT or XTe 1 Open the LabChip XT or XTe software see page 24 2 Create a Run File see page 24 3 If necessary clean the electrodes see page 221 4 Prepare the chip for the method as directed in the LabChip XT Assay Quick Guide or Assay User Guide al Run the chip see page 33 6 Monitor the run see page 35 7 If Extract and Pause is selected for any channels remove the extracted material from the collection well when the run pauses and then continue the run see page 35 8 To manually pause a run see page 37 9 To stop a run before it ends see page 38 This section also includes the following procedures e Creating a new method See page 39 e Saving data files See page 40 e Saving workspace files See page 42 LabChip XT only V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Operation 24 Opening the LabChip XT or XTe Software To open the LabChip XT or XTe software 1 Double click on the LabChip XT or XTe icon on the Windows desktop If 21 CFR Part 11 Security is installed the Login Window opens a Type a valid LabChip XT user name and password into the text boxes and click the OK button For instructions on creating LabChip XT user names see Adding New Users on page 80 The LabChip XT XTe Main Window opens Do not use any other software applications while running the LabChip XT XTe software If the run file has not been created se
255. ton Restores the active collection to the default Layout options Cancel button Closes the Layout Properties window without changing the collection layout V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 156 Layout Options Window Continued NOTES e A view can only be displayed in one location Selecting a location automatically clears any other selected location e To hide a view click on the selected location to clear the selection e A location is hidden if it contains no views e The Gel View is always displayed and cannot be hidden Login Window Use the Login Window to log into the LabChip XT software when the 21 CFR Part 11 option is installed The LabChip XT software will not start until a valid user name and password are entered The Login Window opens when you start the LabChip XT software with the 21 CFR Part 11 option is installed LabChip XT Logan Enter usemame and password T L IE Bate or Password Figure 51 Login Window The Login Window contains the following options Username Type the username to log into the LabChip XT text box software Each user should have a unique user name Password Type the password assigned to the Username All text box passwords must be at least 5 characters long and must contain at least one uppercase letter and at least one number The User Account Policies specify additional password requirements V2 1 LabChi
256. ts Tab V2 1 Use the Expected Fragments tab on the Method Window to enter Expected Fragments for DNA assays See Using Expected Fragments on page 48 for more information After the data is analyzed any peaks matching the expected fragments are shown in the Peak Table View Channel Table View Gel View and Graph View if Type is selected as an Annotation in the Graph View Properties Figure 55 Method Window Expected Fragments Tab The Expected Fragments tab contains the following options and buttons Expected Fragments Table Lists the expected fragments for the method e Size Specifies the expected size of the fragment in BP e Window Specifies the tolerance window as a percent of the expected size for the fragment to allow for small variations in expected fragment size e Color Displays the color to use to mark the fragment in the Graph View or the Gel View LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 166 Expected Fragments Tab Continued e Name Specifies a name to display in the Type description for the fragment e Property Displayed in Channel Table Specifies the content of a column added to the channel table for each expected fragment e Apply to Channels Specifies the channels that the expected fragment is applied to lt All gt specifies that the expected fragment applies to all channels Clicking on the column opens the Select Channels window to choo
257. ts all of the listed columns to display box at the bottom of the Audit Trail window Clearing the check box clears all of the column check boxes Column list Only the selected columns display at the bottom of the Audit Trail window Cleared unselected columns are hidden Moves the selected column up or down in the list The columns Green Up and display in the Audit Trail window in order from the top column on Down Arrows the left to the bottom column on the right Save button Saves the selections and applies the current column view to the Audit Trails window Close button Closes the window without saving changes to the selections V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 143 CDR Manager Window Use the CDR Manager Window to select a data file to open to create rename or delete CDR data folders and to show or hide data files from view in the CDR Manager Window To open the CDR Manager Window select File gt Import Data File on the LabChip XT XTe Main Window The CDR Manager window only opens if the 21 CFR Part 11 Security option is installed with the LabChip XT software If the 21 CFR Part 11 Security option is not installed see Select a Data File Window on page 184 COR Manager A es da Emp rt TY A Figure 42 CDR Manager Window The CDR Manager Window contains the following options Left Side Buttons Import Imports a CDR data file into the open workspace
258. type Each filter can be assigned a different color to determine which filter applies to each channel See Example Expected Peaks Filter for an example of a filter The Filter tab is only available in the LabChip XT software het DEE o WEE AAR lt lt Heladas lier idea F Oera Edi ike Phe Opio m OAF A Bis Figure 30 Filter View One or more filters can be defined independently by selecting the appropriate filter type range mode and range values and then clicking the Add button The Available Filters list box displays all of the filters that are part of the current collection The check box next to each filter in the list is used to include or exclude that filter from the analysis The Filter Options selection determines how multiple filters are logically combined The options available are OR AND Peak and AND Channel e OR Selects any channel that contains a peak that matches any of the filters selected in the Available Filters list e AND Peak Selects any channel that contains a single peak that matches all of the filters selected in the Available Filters list e AND Channel Selects any channel that contains peaks that match all of the filters selected in the Available Filters list Different peaks in the same channel can match different filters as long as all filter conditions are met in the same channel LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 125 Filter Vi
259. uired to save Update modified data files Signatures can be performed by any user who has the Perform Signature option selected in the Create New User or Edit Users tab Save button Saves the settings on the Set Policies tab Print Preview button Displays a preview for printing the policies Print button Prints a report of the policies V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 LabChip XT XTe Instrument Description 211 LabChip XT XTe Instrument Description This section identifies and describes the hardware components of the LabChip XT and XTe instruments This section includes the following topics Front View on page 212 Rear Connectors on page 213 Lid on page 214 Optics on page 215 Barcode Reader on page 215 XT Chips on page 216 USB Key for 21 CFR Part 11 Option on page 217 Specifications on page 218 LabChip XT XTe User Manual Caliper Life Sciences Inc LabChip XT XTe Instrument Description 212 Front View Figure 86 shows the front view of the LabChip XT XTe and identifies the parts on the front of the instrument Lid Status Light Lid Latch Figure 86 Front View Status Light Indicates the state of the instrument Dark not lit Power is off Solid green Power is on and instrument is idle Flashing green Running a chip Yellow Power is on cannot communicate with software Provides access to the chip and el
260. unning The method settings can be changed before resuming the run Clicking the Stop Run button immediately stops the run Runs that have been stopped cannot be continued or resumed Chip Info Chip ID The ID number of the chip read from the barcode on the Chip Expiration Date Displays the date when the chip will expire If the chip is expired the date displays in red Starting a run with an expired chip displays a warning but allows the run to continue if desired Available Channels Displays the number of unused channels on the chip Used channels are automatically disabled in the software Type Displays the type of assay that the chip will run Run Status Displays the current system activity and the time until the next collection time When all collections are complete displays the time until the end of the run LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 110 Error Message Area V2 1 Chip ID NF152101 21 19 Expiration Date Dec 28 2010 Available Channels 0 Type XT DNA 500 HR Run Status Run successfully completed Q Device 531Barcode Reader is disconnected Figure 23 Error Messages Displayed Chip errors can display on top of the instrument image or in the Chip Info section Errors in the Chip Info area are indicated by red text as shown in Figure 23 Connectivity and hardware error messages are displayed at the bottom of the Run Status and Chip Info area on the L
261. ure 218 Support plans 6 Supported Barcode Types 218 System Components Test 230 System Diagnostics Window 199 Systeml0Y9 247 System Status 109 T Text orientation 122 Time changing analysis time 56 Tooltip 257 Tools menu 106 Training required T Transient Overvoltages 218 Troubleshooting 38 224 232 Aborting arun 38 Cleaning the electrodes 221 Current Leakage Check Failed 227 Device Name is Disconnected 226 Excluding apeak 44 IV Check Failed 227 Troubleshooting 224 Troubleshooting Assay Problems 232 U Unlock Application Window 201 USB cable 213 USB KEY so 5 543 217 User Administration Window 203 User Info Tab Start Fractionation Window 195 User Standard 171 V Validation menu 107 Valley to Valley 171 Ventilation 218 Version assay 159 Caliper Life Sciences Inc View menu 107 Viewing Current Events in the Events Tab 225 Viewing Graphs in the Electropherograms Tab 64 Viewing Past Events in the Events Tab 225 VIEWS tee ede RD P RA 117 Channel Table View 133
262. utomatically Exporting Copies of Data Files on page 87 e Audit Trail on page 88 Viewing the Audit Trail on page 89 Exporting the Audit Trail on page 89 e Central Data Repository CDR on page 90 CDR Security Suggestions on page 90 Creating New Data Folders on page 91 Moving Data Files into Folders on page 91 Deleting Data Folders on page 91 Hiding Data Files in the CDR Manager Window on page 92 Showing Hidden Data Files in the CDR Manager Window on page 92 e Remote CDR Server Backup on page 93 setting Up the Remote CDR Server on page 93 Backing Up Data Files to the Remote CDR on page 95 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Security 79 Restoring Data Files from the Remote CDR on page 96 e Manually Backing Up and Restoring the CFR Files on page 97 Backing Up CFR Files on page 97 Restoring CFR Files on page 99 Locking and Unlocking the Software The LabChip XT software with the CFR option installed allows you to lock the LabChip XT software This prevents unauthorized users from accessing the software while you are away from the computer After the software is locked only the logged in user or a LabChip XT Administrator can unlock the software To lock the LabChip XT software 1 On the LabChip XT XTe Main Window click Security gt Lock Applicati
263. w select the location where you want to display the Electropherograms tab and click the Apply button The Electropherograms tab opens HHHH ERR 11 Electropherograms Tab with Multiple Graphs Data from multiple channels can be displayed in the same tab for visual comparison A separate graph for each channel in the collection is displayed in the Electropherograms tab The data file name and channel name display at the top of each graph To only display the channels selected in the Gel View or Channel Table View select the Graph Selected Gels Only check box in the Graph View Properties To move the graphs in the tab in the Gel View click and drag the channel to the desired position To change the number of graphs displayed in the tab select the desired Maximum Graphs per Page value in the Graph View Properties To view the point coordinates and size at the position of the cursor hold down lt CTRL gt or lt Shift gt and move the cursor over the graph To view the point coordinates and slope of a point on the trace hold down lt ALT gt lt CTRL gt and move the cursor over the trace LabChip XT XTe User Manual Caliper Life Sciences Inc Data Analysis 65 Viewing Multiple Properties in the Channel Table View V2 1 Properties for Expected Peaks and Smears display in the Channel Table View When entering the settings in the Expected Fragments Tab or the Smear Analysis Tab on the Method Window the property to disp
264. ware Reference 185 Software Installation Qualification Window Application Information Directory Structure Files Summary Progress Previous Result button Save As button Start IQ button Close button V2 1 Use the Software Installation Qualification Window to perform the IQ test The IQ test verifies proper installation of the LabChip XT XTe software and verifies no unauthorized changes have been made to the software To open the Installation Qualification Window select Validation gt Software IQ on the LabChip XT XTe Main Window Sofware Attlee rukke eon Sabre nato Gusha Demas re eg EE ne Prog Figure 69 Software Installation Qualification Window The Software Installation Qualification Window contains the following information Verifies that the LabChip XT XTe Registry Entries exist If all expected registry entries are found displays Passed If any problems are found displays Failed Verifies that all folders exist If all expected folders exist displays Passed If any folders are not found displays Failed Verifies that all files that were installed by the LabChip XT XTe software still exist If all files exist displays Passed If any files are not found displays Failed Displays Passed if all tests passed Displays Failed if any of the IQ tests failed Displays a progress bar while the IQ test is running Displays the results of the last IQ that was completed Only available
265. waste well Figure 1 LabChip XT Chip When the channels in the chip are filled with sieving gel and buffer the chip functions as an integrated electrical circuit The circuit is driven by the electrodes in the lid that contact the chip s electrodes when the lid is closed The polymer filling the channels in the chip is designed to sieve DNA fragments by size as they are driven through the chip channels by electrophoresis similar to using agarose or polyacrylamide gels LabChip XT XTe User Manual Caliper Life Sciences Inc Introduction 21 Principles of Operation Continued The sample is loaded into the sample well on the chip A fluorescent dye is added to or already contained in the waste well at the opposite end of the separation channel The sample then moves electrophoretically into the separation channel The dye migrates in the opposite direction toward the sample well As the DNA fragments move down the separation channel they separate by size and bind with the dye The dye increases in fluorescence when bound to the DNA in the separation channel The complex then moves past the laser which excites the fluorescent dye bound to the DNA The software plots fluorescence intensity versus time and produces electropherograms for each sample see Figure 2 Figure 2 oer ee or The data can also be viewed in a gel like format on the Gel Tab to achieve the appearance of a slab gel The colors of the gel can be changed
266. window LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 204 Create New User Use the Create New User tab on the User Administration Window to add a new user name to the LabChip XT software This window creates the LabChip XT user account it does not create a Windows user account to log into the computer Ed Lan in ET Leur Adrann A Fa Pra pre Figure 80 User Administration Window Create New User The Create New User tab contains Option Button Username Type the user name that the new user will use to log into the LabChip XT software Access Level Choose the access level for the user The access level controls the user s rights in the LabChip XT software see Define Access on page 208 to view the rights for each access level The following access levels are available e Restricted User e Operator e Supervisor e Administrator e Service Password Type the desired password for the user The password must meet the password policies selected on the Set Policies tab Confirm Password Repeat the desired password for the user V2 1 LabChip XT XTe User Manual Caliper Life Sciences Inc Software Reference 205 User Can Perform If selected the user can sign data files using the Perform Signature Signature Window Accept Reject Lock If selected the user can accept reject and lock data files Data File using the Perform Signature Window Unlock Data File If selected the
267. xport Settings on page 31 e To manually export data see Exporting Data Manually on page The LabChip XTe software does not support exporting analyzed data Peak Tables Channel Tables and Raw Data are exported to CSV files which can be imported into a spreadsheet program such as Microsoft Excel Gel and Graph data is exported to the selected image format This section shows export examples for the following e Peak Table e Raw Data e Gel Peak Table ASCII text file that contains the data in all columns in the Peak Table Figure 18 is an example of part of an exported Peak Table file data truncated for this example B C D E F G H 1 Chip Name Sample Name Size BP Conc ng ul Purity Expected Type Molarity nmol l 2 Caliper 04 31 25 Sizing Ladder i 30 LM 45454 5 3 Caliper_04 31 25 Sizing Ladder 25 20 L 1212 12 4 Caliper_04 31 25 Sizing Ladder 50 20 L 606 06 5 Caliper_04 31 25 Sizing Ladder 100 20 L 303 03 6 Caliper_04 31 25 Sizing Ladder 150 20 L 202 02 7 Caliper_04 31 25 Sizing Ladder 200 20 L 151 515 8 Caliper_04 31 25 Sizing Ladder 300 20 L 101 01 9 Caliper 04 31 25 Sizing Ladder 400 20 L 75 7575 10 Caliper_04 31 25 Sizing Ladder 500 20 L 60 606 11 Caliper_04 31 25 Sizing Ladder 700 20 L 43 29 12 Caliper_04 31 25 Sizing Ladder 850 20 L 35 65058824 13 Caliner 04 31 25 Sizing Ladder 1000 20 L 30 303 Figure 18 Exported Peak Table Peaks that are excluded are not exported and are missing in the e
268. xported file For example if peaks 3 5 and 7 are excluded when the data is exported peaks 3 5 and 7 are not included in the csv file LabChip XT XTe User Manual Caliper Life Sciences Inc V2 1 Data Analysis 75 Raw Data ASCII text file that contains the signal data from the run as one file per channel or multiple channels in the same file Note that data that is exported has been smoothed using the polynomial filter In addition to exporting time and value information you can choose to export Size information This information is determined based on aligned data and is used to correlate the peaks across different runs or from one row to another When Include Size Data is not checked and only time and values are exported the state of the analysis function peaks aligned or not aligned with the ladder data determines whether or not data that is exported is or is not aligned The same is true for the Zero Baseline function if enabled data that is exported is also zeroed to the baseline Below is an example of part of a raw data file exported from a DNA assay header not included and data truncated in this example B C D E F G 1 Time Size BP Sizing Ladder Sample3 Sample4 Sample 2 2 0 45 75 213 87 315 7 391 02 206 53 3 1 40 00 220 54 341 78 407 71 293 85 4 2 46 58 194 32 347 49 424 85 275 85 5 3 46 5 112 26 273 78 363 182 68 6 4 46 41 27 27 142 69 223 599 603 08 7 5 46 33 10 92 28 77

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