PerkinElmer LabChip GX User Manual

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Page 2: Preface
PerkinElmer reserves the right to revise this publication and to make changes from time to time in the content hereof without obligation of PerkinElmer to notify any person of such revision or changes. Further, PerkinElmer may make modifications to the product described in this manual at any time without any obligation to notify any person of such modifications.
Page 3 Preface Contact Us If you have a question about the LabChip GX that is not answered in this manual or online Help, or if you need assistance with this product, contact the PerkinElmer Technical Support Center: Phone: (US Toll Free): 800-762-4000...
Page 4 NOTE: A cautionary statement; an operating tip or maintenance suggestion; may result in instrument damage if not followed. REMARQUE: Énoncé indiquant une précaution à prendre, un conseil de fonctionnement ou une suggestion d’entretien; son non-respect peut provoquer des dommages à l’instrument. V4.2 LabChip GX User Manual PerkinElmer...
Page 5 Lifting hazard. May result in injury. Levage dangereux. Peut entraîner 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). V4.2 LabChip GX User Manual PerkinElmer...
Page 6 Green Safe condition or information Les étiquettes de l’appareil Jaune Attention, danger potentiel sont codées Rouge Arrêter couleur: Intervention obligatoire Bleu Condition sûre ou informations de sécurité Vert Helpful hints, additional information Conseils utiles, informations supplémentaires V4.2 LabChip GX User Manual PerkinElmer...
Page 7: Instrument Safety
Instrument Safety Instrument Safety The following safety information about the LabChip GX is included in this documentation. Read and review all safety information before operating the LabChip GX. • Required Training • “Chemical Safety” on page 8 • “Laser Safety” on page 9 •...
Page 8: Chemical Safety
Instrument Safety Chemical Safety WARNING Some chemicals used with the LabChip GX are potentially hazardous and can cause illness. • 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.
Page 9: Laser Safety
WARNING BRIGHT LIGHT HAZARD. LabChip GX Instruments contain Class 3B laser diodes. The LabChip GX is classified as a Class 1 device because the lasers are appropriately enclosed (embedded) and indicated with Warning labels. Complies with 21 CFR 1040.10 except for deviations pursuant to Laser Notice 50, dated June 24, 2007.
Page 10: Electrical Safety
Power Cord Selection United States and Canada The LabChip GX instrument is shipped with a NEMA 5-15 / IEC 320 power cord. If the power cord needs to be replaced, substitute power cords must be UL Listed, Type SJT or equivalent, minimum No.
Page 11: Fuses
3) if blown fuses are suspected. Mechanical Safety The LabChip GX instruments have a three axis robot that moves quickly and can be a pinch hazard. Keep the front door of the instrument closed when the robot is moving. Keep hands away from the robot when not actually placing microplates in the instrument or changing the ladder and buffer vials.
Page 12: Table Of Contents
Introduction......................18 Principles of Operation ..................19 Software Modes Available ................. 21 Operation ......................22 Opening the LabChip GX Software..............23 Creating Desktop Shortcuts................23 Creating a New Assay ..................24 Running an Assay ..................... 25 Select the Auto Export Settings ................. 29 Monitoring the Run ....................
Page 13 Reanalyzing a Data File ..................95 Printing Workspace Information................. 96 Exporting Data ....................102 Exporting Data Manually ................105 Using the GX Software to Analyze GX Touch Data ........... 107 Understanding Peak Finding ................108 V4.2 LabChip GX User Manual PerkinElmer...
Page 14 Manually Backing Up and Restoring the CFR Files.......... 138 Backing Up CFR Files................138 Restoring CFR Files .................. 140 Software Reference .................... 142 LabChip GX Main Window................143 Menu Bar ....................144 Chip Status and Run Status ............... 151 Error Message Area ................... 153 Plate View or Plate List ................
Page 15 Well Table View ..................172 Peak Table View ..................174 Peak Table Properties ................179 Filter View ....................180 About LabChip GX Window ................183 Add New Expected Peak Window..............184 Add Plate Window ................... 185 Assay Analysis Window................... 186 Assay Information Tab ................
Page 16 Edit Users ....................263 Show User Info ..................264 De/Activate User..................266 Define Access.................... 267 Set Policies....................269 LabChip GX Instrument Description ..............270 Front View ....................... 270 Front Panel ..................... 271 Rear Connectors ..................... 272 Optics ......................273 Chip Pressure System ..................273 Barcode Reader ....................
Page 17 Computer Software Lock-Ups ..............299 Zipping the Log Files ..................300 Tips and Shortcuts ..................... 301 Glossary of Terms ....................302 PerkinElmer Product Warranty ................330 PerkinElmer Software License Agreement ............332 Index ........................336 V4.2 LabChip GX User Manual PerkinElmer...
Page 18: Introduction
Assay User Guides provide information about the assay. Instructions for preparing the chip, the plate, the ladder vial, and the buffer vial are included in the LabChip GX/GXII Assay User Guide for the specific assay that you are running. Detailed information...
Page 19: Principles Of Operation
The sample and sieving buffers also contain a fluorescent dye that gets brighter upon binding to double-stranded DNA, RNA, or protein/SDS complex. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) V4.2...
Page 20 The LabChip GX software plots fluorescence intensity versus time and produces electropherograms for each sample (see Figure Figure 2.
Page 21: Software Modes Available
If the LabChip GX software is installed in Instrument mode, shortcuts can be created on the desktop to run the LabChip GX software in Simulation or Reviewer mode (see “Creating Desktop Shortcuts”...
Page 22: Operation
Operation Operation This section includes general instructions for using the LabChip GX hardware and software to run an assay. This section contains the following information: • Opening the LabChip GX Software • Creating Desktop Shortcuts • Creating a New Assay •...
Page 23: Opening The Labchip Gx Software
If 21 CFR Part 11Security is installed, the Login Window opens. Type a valid LabChip GX user name and password into the text boxes and click the OK button. (For instructions on creating LabChip GX user names, see “Adding New Users” on page 118.)
Page 24: Creating A New Assay
Sciences\LabChip GX\LabChip.exe" /simulate Click OK in the Properties window. Creating a New Assay The LabChip GX software enables you to create a new assay by opening and editing an existing assay and then saving the assay with a new name.
Page 25: Running An Assay
Run button.) To start an assay to read a plate: Click the Run button on the LabChip GX Main Window (see page 143) to open the Start Run Window.
Page 26 CDR or if the 21 CFR Part 11 option is not installed and you want to save a second copy of the data files, see “Automatically Exporting Copies of Data Files” on page 126. V4.2 LabChip GX User Manual PerkinElmer...
Page 27 Excluded Peaks File, select the name of the .gep file that contains the excluded peaks, and click the Open button. The path and name of the file displays in the text box. V4.2 LabChip GX User Manual PerkinElmer...
Page 28 Operation 22 Click the Start button to start the assay. A new workspace opens to display the data. “Monitoring the Run” on page 30 for information about viewing data during the run. V4.2 LabChip GX User Manual PerkinElmer...
Page 29: Select The Auto Export Settings
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 are exported at the end of the run. V4.2 LabChip GX User Manual PerkinElmer...
Page 30: Monitoring The Run
Operation Monitoring the Run The following occurs after a run is started in the LabChip GX software: The priming and warming steps are performed. • The priming step fills the channels of the chip with reagent. (Only performed if the chip holder has been opened since the last run.)
Page 31: Stopping A Run
Click Yes to stop the run. The Status line displays Run stopped by user. Data for any completed wells displays in the LabChip GX Main Window. To continue to read wells from an aborted run, see Continuing a Stopped Run. V4.2 LabChip GX User Manual PerkinElmer...
Page 32: Continuing A Stopped Run
Select the same options for this run as were selected for the stopped run. Click the Start button to begin. The run starts with the well that was not completed in the previous run. A separate data file is created for the current run. V4.2 LabChip GX User Manual PerkinElmer...
Page 33: Saving Data Files
If the 21 CFR Part 11 option is installed, data files are saved in the Centralized Data Repository (CDR). The CDR is a secure folder that can only be accessed by the LabChip GX software. The location of the CDR is specified in the CDR Utility Window.
Page 34: Saving Workspace Files
Window. Saving Workspace Files When viewing plate data in the LabChip GX 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 plate in the run.
Page 35: Selecting Wells Using A Sample Names File
Editor window because the files created in the Sample Names Editor window always contain one row for each well in the plate. The Sample Names files for selecting wells are typically created by a LIMS or can be created in Microsoft Excel. V4.2 LabChip GX User Manual PerkinElmer...
Page 36: Using A Barcode To Specify The Sample Names File
“Sample Names%barcode%.csv” and save it in the location where the actual sample names files for the runs will be saved. In the Run File Editor Window, select the desired run parameters. V4.2 LabChip GX User Manual PerkinElmer...
Page 37 Sample Names file with the corresponding barcode is used to select the wells to sample. In the example above, if the plate barcode is 12345, then the file named “Sample Names12345.csv” will be used to select the wells in the run. V4.2 LabChip GX User Manual PerkinElmer...
Page 38: Adding A New Plate
Perform a Punch Test from the Plate Information window to verify the new plate settings are acceptable. • With a piece of the tape provided by PerkinElmer, cover the corner wells on the plate. • Use an old, dead chip with a good sipper.
Page 39 If the holes are too close to the edge (<0.5mm), adjust the X- Margin or Y-Margin values in the Add Plate window. Select the new plate name in the Start Run Window when starting the run. V4.2 LabChip GX User Manual PerkinElmer...
Page 40: Placing The Barcode On The Plate
(portrait) end of the microplate, closest to well A1. If the barcode is not positioned properly, the barcode reader will not be able to read the barcode. Figure 7. Barcode Label Position V4.2 LabChip GX User Manual PerkinElmer...
Page 41: Calibrating The Optics
The LabChip GX software provides an Optical Calibration function using Test Chip C to calculate a correction factor for each individual LabChip GX instrument. The correction factor is applied to all samples run on the instrument to provide a common absolute fluorescence across different instruments.
Page 42: Data Analysis
Data Analysis Data Analysis After a run is complete, use the LabChip GX software to view and analyze the plate data. The LabChip GX software can open multiple data files in the same workspace to compare the data from different plates.
Page 43: How The Software Analyzes Dna Data
The concentrations and sizes of the individual base pairs in the ladder can be changed on the Analysis Tab. Figure 8. Ladder Graph - DNA V4.2 LabChip GX User Manual PerkinElmer...
Page 44 The Lower Marker and Upper Marker are internal standards used to align the ladder data with data from the sample wells. Figure 10 shows an example of assigned marker peaks in a sample well. Figure 10. Markers - DNA V4.2 LabChip GX User Manual PerkinElmer...
Page 45: How The Software Analyzes Protein Data
Changing the markers causes quantitative changes in the calibration procedure, however, and therefore in the entire data evaluation. How the Software Analyzes Protein Data Protein assays are only supported on LabChip GX II instruments. The LabChip GX Protein Assay Analysis consists of the following...
Page 46 The standard curve derived from the data of the ladder well should resemble Figure V4.2 LabChip GX User Manual PerkinElmer...
Page 47 A Lower Marker is the internal standard used to align the ladder data with data from the sample wells. Figure 13 shows an example of the assigned Lower Marker peak (marked LM) in a sample well. Figure 13. Markers - Protein V4.2 LabChip GX User Manual PerkinElmer...
Page 48 • The software allows you to define the lower marker. Changing the selection of the marker will lead to quantitative changes in the calibration procedure, and therefore in the entire data evaluation. V4.2 LabChip GX User Manual PerkinElmer...
Page 49: How The Software Analyzes Rna Data
14), which is a mixture of RNA fragments of different known sizes, is run first from the ladder vial. The concentrations and sizes of the individual nucleotides in the ladder can be changed on the Analysis Tab. V4.2 LabChip GX User Manual PerkinElmer...
Page 50 RNA size is plotted from the RNA ladder by interpolation between individual RNA fragment size/migration points. The standard curve derived from the data of the ladder well should resemble Figure Figure 15. Standard Curve - RNA V4.2 LabChip GX User Manual PerkinElmer...
Page 51 16) is used to align the ladder data with data from the sample wells. Figure 16. Markers - RNA The standard curve and the markers are used to calculate RNA fragment sizes for each well from the migration times measured. V4.2 LabChip GX User Manual PerkinElmer...
Page 52 If a titer is being used, the ladder is not used for quantization. Instead, peak sample areas are normalized using the lower marker and then quantization is performed using the titer standard curve to convert normalized area to concentration; see “Titer” on page 328. V4.2 LabChip GX User Manual PerkinElmer...
Page 53 23S/16S) and Fast/Total RNA area ratio are computed. Figure 18. rRNA Graph Analysis 13 Messenger RNA Assay: The RNA contamination ratio is computed. This is the ratio of the area of all the fragments to total RNA area. V4.2 LabChip GX User Manual PerkinElmer...
Page 54: How The Software Analyzes Glycan Data
Data Analysis How the Software Analyzes Glycan Data Glycan assays are only supported on LabChip GX II instruments. The LabChip GX Glycan Assay Analysis consists of the following steps: Raw data is read and stored by the system for each individual well.
Page 55 A Lower Marker is the internal standard used to align the ladder data with data from the sample wells. Figure 21 shows an example of the assigned Lower Marker peak (marked LM) in a sample well. Figure 21. Markers - Glycan V4.2 LabChip GX User Manual PerkinElmer...
Page 56 7 to 13 CGU. • The software allows you to define the lower marker. Changing the selection of the lower marker will lead to quantitative changes in the calibration, and therefore in the entire data evaluation. V4.2 LabChip GX User Manual PerkinElmer...
Page 57: How The Software Analyzes Protein Charge Variant Data
Data Analysis How the Software Analyzes Protein Charge Variant Data Protein Charge Variant assays are only supported on LabChip GX II instruments. The LabChip GX Protein Charge Variant Assay Analysis consists of the following steps: Raw data is read and stored by the system for each individual well.
Page 58: How The Software Analyzes Genomic Dna Data
5 corresponding to intact gDNA and 0 corresponding to highly degraded gDNA. The GQS is calculated using the size distribution of the sample. Figure 22. Genomic DNA GQS Smear (in orange) V4.2 LabChip GX User Manual PerkinElmer...
Page 59: Organizing, Retrieving, And Backing Up Data Files
Data Analysis Organizing, Retrieving, and Backing Up Data Files As you work in the LabChip GX software, it's a good practice to organize the LabChip GX files. • Create a folder in which to save the data files. If desired, each person can save data files to their own subfolder to organize the data files.
Page 60: Opening A Data File
.gxd file extension. Data files generated by the LabChip HT software, which have a .cla file extension, can also be opened in the LabChip GX software if the 21 CFR Part 11 option is not installed. To open a data file:...
Page 61: Adding A Collection To A Workspace
Type for the collection: DNA, Protein, RNA, Glycan, CZE, or gDNA. (Protein, Glycan, and CZE are only supported on LabChip GX II instruments.) 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.
Page 62: Selecting The Wells In A Collection
Select all ladder wells: click the “L” icon at the bottom left corner of the microplate. • Clear individual wells: right-click on the well and select Remove Well. Save the workspace to save the wells selected in the collection. V4.2 LabChip GX User Manual PerkinElmer...
Page 63: Using Sample Names Files
If multiple values are entered, separated by semi-colons, each expected peak will use the corresponding Window value. If more expected peaks are entered than Window values, the last Window applies to all remaining expected peaks in the list. V4.2 LabChip GX User Manual PerkinElmer...
Page 64 Data Analysis Click the Export button, navigate to the desired location for the file, type the desired name for the file, and click the Save button. V4.2 LabChip GX User Manual PerkinElmer...
Page 65: Sample Name File Format (.Csv Format)
Column B: The desired sample name for each well. Column C: A user comment to be added to the well properties. Column D: A list of Expected Peak sizes for the well. This list is separated by semi-colons (;). V4.2 LabChip GX User Manual PerkinElmer...
Page 66: Applying Different Window Values To Expected Peaks Of The Same Size In Different Wells
If none of the rows can be interpreted, usually because the first column does not contain the well label, the following error message displays: “No rows found matching format: label, name, comment, EP, window.” V4.2 LabChip GX User Manual PerkinElmer...
Page 67: Using Expected Fragments/ Expected Proteins/Expected Glycans
Glycans (EGs), or peaks (EPs) for the samples in a DNA, gDNA, Protein, Glycan, or Protein Charge Variant assay, respectively. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) You enter the EFs, EPs, and EGs in the Assay Analysis Window.
Page 68: Exporting Efs, Eps, Or Egs
To apply the EFs, EPs, or EGs to the active plate, click the Apply button. To apply the EFs, EPs, or EGs to all plates in the workspace, click the Apply Global button. V4.2 LabChip GX User Manual PerkinElmer...
Page 69: Forcing Expected Peaks
Click the Properties tab on the right side of the Graph view to open the Graph View Properties. To view the size of all expected peaks, select Expected Fragments, Expected Proteins, or Expected Glycan in one of the Annotation list boxes. Figure 25. Expected Fragments V4.2 LabChip GX User Manual PerkinElmer...
Page 70: Viewing The Efs/Eps/Egs In The Gel View
To display the legend that identifies the colors and sizes of the expected peaks: Click the Properties tab on the right side of the Gel View open the Gel View Properties. Select the Show Expected Peaks Legend check box. Figure 27. Expected Peaks Legend V4.2 LabChip GX User Manual PerkinElmer...
Page 71: Viewing The Efs/Eps/Egs In The Well Table
Viewing the EFs/EPs/EGs in the Peak Table Expected Fragments, Expected Proteins, and Expected Glycans are identified in the Peak Table with the peak name displayed in the Type column. Figure 28. DNA Assay Peak Table V4.2 LabChip GX User Manual PerkinElmer...
Page 72: Modifying Analysis Parameters
“Changing the Time Window for Analysis” on page 80 • Aligning or Unaligning the Marker Peaks These settings can be changed after the run is complete or when reanalyzing a previously saved data file. V4.2 LabChip GX User Manual PerkinElmer...
Page 73: Changing The Peak Find Parameters
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 Assay Analysis window open. V4.2 LabChip GX User Manual PerkinElmer...
Page 74: Adding A Peak
X (excluded), and the value is not used in the analysis. Right-click on an Excluded Peak in the Graph view and select Include Peak to include the peak in the data analysis. V4.2 LabChip GX User Manual PerkinElmer...
Page 75: Splitting A Peak
“Excluding a Peak” on page Verify that Show Peak Baselines is selected in the Graph View Properties. Click and drag the baseline of the remaining peak to include the area under the excluded peak. V4.2 LabChip GX User Manual PerkinElmer...
Page 76: Adjusting The Peak Baseline
Manual Baseline mode is on. Clicking and dragging in the View still zooms in when Manual Baseline mode is on. To turn off Manual Baseline mode, right-click on the graph, away from a peak, and select Manual Baseline again. V4.2 LabChip GX User Manual PerkinElmer...
Page 77: Removing A Manual Baseline
Ladder button only displays when a ladder is selected.) Click the Apply button to save the default ladder settings. The Analysis Tab displays the ladder data in the Default Ladder table and the Markers table (see Figure 30 on page 78). V4.2 LabChip GX User Manual PerkinElmer...
Page 78 (This allows you to import the default ladder into a plate that does not include any good ladders on the plate.) “Using the Default Ladder for Alignment” on page 79 align wells in the plate using the default ladder. V4.2 LabChip GX User Manual PerkinElmer...
Page 79: Using The Default Ladder For Alignment
With the plate data file open, select Analysis  Analysis Settings to open the Assay Analysis Window, and then click the Analysis Tab. Click the Clear Default Ladder button at the bottom of the Default Ladder table. V4.2 LabChip GX User Manual PerkinElmer...
Page 80: Changing The Time Window For Analysis
Assay Analysis window open. Aligning or Unaligning the Marker Peaks To perform data analysis for DNA, Protein, RNA, and Glycan assays, the LabChip GX software aligns marker peaks included in the sample wells with markers from the ladder. •...
Page 81 If the marker peaks found using this calculated method fail to align with those of a sample, the LabChip GX software will use the minimum peak height threshold setting instead (if this value is lower than the value for the marker peak).
Page 82 Protein or RNA assay opens a shortcut menu with the following commands: • Include Peak (only for peak type “Xsys” or “?”) • Exclude Peak • Force Lower Marker • Force Expected Peak V4.2 LabChip GX User Manual PerkinElmer...
Page 83 Glycan assay opens a shortcut menu with the following commands: • Include Peak (only for peak type “Xsys” or “?”) • Exclude Peak • Force Lower Marker • Force Expected Peak V4.2 LabChip GX User Manual PerkinElmer...
Page 84: Saving And Exporting Assays
Saving and Exporting Assays Assays are created by PerkinElmer and are included with the LabChip GX software. The instrument and software settings used to run each plate and to analyze the plate are contained in an assay (.asy or .asyx) file, which is selected at the start of the run in the Start Run Window.
Page 85: Changing The View Of The Data
Data Analysis Changing the View of the Data The views in the LabChip GX Main Window can be customized to display data according to the preferences of the user. These options do not change the raw data but provide different means of displaying the data.
Page 86: Viewing Zero Baselines
Data Analysis Viewing Zero Baselines All electropherograms produced with the instrument show some amount of background fluorescence. By default, the LabChip GX software enables the zero baseline function. To remove the zeroing, select Analysis  Analysis Settings to open the...
Page 87: Adjust Pane Widths
To hide a view: Select Collection  Layout on the LabChip GX Main window. Layout Options Window opens. Click on the location that is selected for the view to clear the selection.
Page 88: Zoom In And Zoom Out
Unzoom All to zoom out to the default view. For more information, see Viewing Graphs in the Overlay Electropherograms Tab Viewing Graphs in the Electropherograms Tab. V4.2 LabChip GX User Manual PerkinElmer...
Page 89: Viewing Graphs In The Overlay Electropherograms Tab
+ clicking the corresponding wells (the bounding box disappears). Use the Overlay Offset text box on the Graph View Properties offset each of the graphs by the RFU value specified. Figure 36. Overlay Offset V4.2 LabChip GX User Manual PerkinElmer...
Page 90: Viewing Graphs In The Electropherograms Tab
Layout on the LabChip GX Main Window, select the location where you want to display the Electropherograms tab, and click the Apply button. The Electropherograms tab opens. Figure 37. Electropherograms Tab with Multiple Graphs V4.2 LabChip GX User Manual PerkinElmer...
Page 91 CTRL or Shift key and move the cursor over the graph. To view the point coordinates and slope of a point on the trace, hold down the ALT key and the CTRL key and move the cursor over the trace. V4.2 LabChip GX User Manual PerkinElmer...
Page 92: Viewing Analysis Errors And Warnings
Select Analysis Error in the Well Annotation drop-down list. If desired, click the Well Annotation Location button to change the location. Click off of the Graph View Properties tab to close the tab. V4.2 LabChip GX User Manual PerkinElmer...
Page 93: Viewing Multiple Properties In The Well Table View
Repeat until all desired properties have been added to the table. Click the Apply button to display the new columns in the Well Table. Duplicate properties in the table will be removed when the settings are applied to the plate. V4.2 LabChip GX User Manual PerkinElmer...
Page 94: Copying Information
Data Analysis Copying Information The Edit menu and some of the right-click pop-up menus offer the following choices for copying information from the LabChip GX software for use with other applications, depending on the selection: • Copy Gel • Copy Lane •...
Page 95: Reanalyzing A Data File
Window, the data is automatically re-analyzed and the updated information is displayed. To view previous analysis settings, click the Restore Plate button at the bottom of the Assay Analysis window and select the version to view. V4.2 LabChip GX User Manual PerkinElmer...
Page 96: Printing Workspace Information
The header of each printout contains the workspace name, the collection name, and the page number. The footer of each printout contains information about the LabChip GX software, data file, assay, and instrument. If the 21 CFR Part 11 option is installed, the footer also includes the data file version, signed state, and lock state.
Page 97 This option prints a gel image with the lanes marked by the sample name. Figure 38. Printed Gel Electropherogram Choosing this option prints an individual electropherogram of each of the selected wells. Figure 39. Printed Electropherogram V4.2 LabChip GX User Manual PerkinElmer...
Page 98 Data Analysis Overlay Electropherogram Choosing this option prints one graph with the electropherograms for all of the selected wells overlaid onto a single graph. Figure 40. Printed Overlay Electropherogram V4.2 LabChip GX User Manual PerkinElmer...
Page 99 Selecting both the Well Table and the Peak Table prints each well on a separate page with the Well Table row at the top of the page and the Peak Table for the well below it. Figure 41. Printed Well Table V4.2 LabChip GX User Manual PerkinElmer...
Page 100 Selecting both the Well Table and the Peak Table prints each well on a separate page with the Well Table row at the top of the page and the Peak Table for the well below it. Figure 42. Printed Peak Table V4.2 LabChip GX User Manual PerkinElmer...
Page 101 Data Analysis 101 Multiple Electropherogram Choosing this option prints the selected electropherograms or the entire collection of electropherograms, in the specified number of rows and columns per page. Figure 43. Printed Multiple Electropherograms V4.2 LabChip GX User Manual PerkinElmer...
Page 102: Exporting Data
Peaks that are excluded are not exported and are missing in the exported file. For example, if peaks 3, 5, and 7 are excluded, when the data is exported into Microsoft Excel, peaks 3, 5, and 7 are not included. V4.2 LabChip GX User Manual PerkinElmer...
Page 103 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 104 Gels can be exported into the same image file or into separate files for each gel. Figure 45 shows multiple selected gels exported to the same image file. Figure 45. Exported Gel V4.2 LabChip GX User Manual PerkinElmer...
Page 105: Exporting Data Manually
Gel view. • Select either Single File to include gels for all wells in the same image file, or select Separate Files to export each gel to a separate image file. V4.2 LabChip GX User Manual PerkinElmer...
Page 106 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 107: Using The Gx Software To Analyze Gx Touch Data
Using the GX Software to Analyze GX Touch Data After a GX Touch run is complete, you can use the LabChip GX software or the LabChip GX software in Reviewer mode to view and analyze the plate data. The LabChip GX software can open multiple data files in the same workspace to compare the data from different plates.
Page 108: Understanding Peak Finding
Removing the noise in the broad tail of the upper marker by setting the filter width to 1.0 sec causes the early sharp peaks to lose height and become distorted. Figure 46. Filtering Examples V4.2 LabChip GX User Manual PerkinElmer...
Page 109: Peak Detection - Slope Threshold
End Point of a peak. A baseline is drawn under each peak region using a signal average in the baseline regions on each side of the peak. V4.2 LabChip GX User Manual PerkinElmer...
Page 110 On the same data signal, near the lower marker there is sufficient noise to create variation in the slope values as shown in Figure 49 on page 111. V4.2 LabChip GX User Manual PerkinElmer...
Page 111 Minimum Height and/or Minimum Width thresholds, but the analysis runs much slower as it carefully explores each bump. Also, the analysis will have difficulty finding baseline regions of qualifying width. V4.2 LabChip GX User Manual PerkinElmer...
Page 112: Peak Splitting - Inflection Threshold
In this example, a value of 150/sec splits off both shoulders. A value of 110/sec only splits off the left shoulder. (See Figure 51 on page 113.) V4.2 LabChip GX User Manual PerkinElmer...
Page 113: Peak Identification
The Minimum Height threshold sets the minimum peak baseline-to-peak apex value needed for a peak to be identified by the analysis. The Minimum Width is the minimum left edge-to-right edge value needed for a peak to be identified. V4.2 LabChip GX User Manual PerkinElmer...
Page 114: Software Security
Data is stored in a secure folder on the local computer. To create and maintain the Audit Log and LabChip GX user accounts, Microsoft SQL Server 2005 Express is provided with the LabChip 21 CFR Part 11 option.
Page 115 “Viewing the Files in the Remote CDR Folder” on page 137 “Manually Backing Up and Restoring the CFR Files” on page 138 • “Backing Up CFR Files” on page 138 • “Restoring CFR Files” on page 140 V4.2 LabChip GX User Manual PerkinElmer...
Page 116: Locking And Unlocking The Software
OK button. The Administrator is logged into the LabChip GX software. To change the user to a non-administrator user, close and restart the LabChip GX software and then log in as the desired user. V4.2 LabChip GX User Manual...
Page 117: Managing User Accounts
Software Security 117 Managing User Accounts Access to the LabChip GX software is controlled by user names when the 21 CFR Part 11 Security option is installed. Each user must sign into the LabChip GX software. The user’s Access Level controls which options are available for each user name.
Page 118: Adding New Users
Software Security 118 Adding New Users Each person who uses the LabChip GX should have a unique LabChip GX user account. To add a new user: Window, select Security  User and On the LabChip GX Main System Administration. The User Administration Window opens.
Page 119: Changing User Information
• Last Name • Position • Access Level • User Can Perform Signature • Accept/Reject/Lock Data File • Unlock Data File • User Password Click the Save button to save the updated user information. V4.2 LabChip GX User Manual PerkinElmer...
Page 120: Printing User Information
If a user name is not going to be used, the user account can be deactivated. The user name is not removed from the system, but cannot be used to log into the LabChip GX software. User names cannot be deleted. A deactivated user name can be activated to continue to be used.
Page 121: Changing Access Rights
Changing Access Rights The rights assigned to each Access Level control the actions that a user is allowed to perform in the LabChip GX 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.
Page 122: Printing Access Rights
On the LabChip GX Main System Administration. The User Administration Window opens. Click the Define Access button. To preview the printout, click the Print Preview button. To print the selected information, click the Print button. V4.2 LabChip GX User Manual PerkinElmer...
Page 123: Setting Policies For User Accounts
Maximum Login Attempts - The maximum number of times the user can attempt to log in before being locked out of the LabChip GX software. Range is from 3 to 20. This option can be disabled to allow unlimited retries without locking the user out.
Page 124: Printing User Policies
On the LabChip GX Main System Administration. The User Administration Window opens. Click the Set Policies button. To preview the printout, click the Print Preview button. To print the selected information, click the Print button. V4.2 LabChip GX User Manual PerkinElmer...
Page 125: Electronic Signatures
Signature. The Perform Signature Window opens on top of the LabChip GX Main Window. Select the username of the user that is signing the data file in the Username drop-down list. Type a comment describing the reason for the signature, approval state, or lock state in the Enter Comment text box.
Page 126: Automatically Exporting Copies Of Data Files
Reverting to a Specific Data File Revision Each time a data file is changed, a new version of the data file is created and saved. The LabChip GX software enables you to revert to a previous version of a data file.
Page 127: Audit Trail
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 GX software. In Windows 7, the “Computer User Role” records either User or Administrator, depending on how the LabChip GX software is started.
Page 128: Viewing The Audit Trail
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. V4.2 LabChip GX User Manual PerkinElmer...
Page 129: Exporting The Audit Trail
Choose the desired location for the file, type the desired file name, and click the Save button. By default, the file name is ATexport_<date>_<time>, where <date> and <time> are the current date and time. V4.2 LabChip GX User Manual PerkinElmer...
Page 130: Central Data Repository (Cdr)
“Showing Hidden Data Files in the CDR Manager Window” on page 132 CDR Security Suggestions To ensure proper security of data files, the LabChip GX Administrator should: Change the LabChip GX Administrator password. Make sure to keep a copy of the password in a safe place. This password cannot be reset if forgotten.
Page 131: Creating New Data Folders
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. V4.2 LabChip GX User Manual PerkinElmer...
Page 132: Hiding Data Files In The Cdr Manager Window
Manager Window, even if the files are not set to hidden. To show files, the folder cannot be set to hidden. Click the Hide Hidden Files button at the top right of the Manager Window. Close the CDR Manager Window. V4.2 LabChip GX User Manual PerkinElmer...
Page 133: Remote Cdr Server Backup
Window. Setting Up the Remote CDR Server To back up copies of LabChip GX 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. To set up the Remote...
Page 134 Type a Username for the folder in the Username text box. (This is a separate username from the user names created in the LabChip GX software. This username is only used to access the data folder on the Remote CDR Server.) •...
Page 135: Backing Up Data Files To The Remote Cdr
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 GX default Administrator. To set up Remote CDR Backup: Verify that the Remote CDR Server is set up on an accessible network server.
Page 136: Restoring Data Files From The Remote Cdr
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 GX data from. (Make sure to select the same folder to which the data was backed up.)
Page 137: Viewing The Files In The Remote Cdr Folder
Any files that are in the Remote CDR but are not in the local CDR are indicated by a red error icon as shown below. Figure 53. CDR Server Viewer V4.2 LabChip GX User Manual PerkinElmer...
Page 138: Manually Backing Up And Restoring The Cfr Files
Software Security 138 Manually Backing Up and Restoring the CFR Files The LabChip GX software with the 21 CFR Part 11 option installed supports backing up data files to a remote server (see “Remote CDR Server Backup” on page 133). The CDR data files and the Audit Trail database can also be backed up manually to another secure location.
Page 139 Software Security 139 Setting the CDR folder back to not accessible For Windows 7: Right-click on the LabChip GX icon on the Windows desktop and select Run as Administrator. For Windows XP: Double-click on the LabChip GX icon on the...
Page 140: 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 LabChip GX software and then restore the CFR files.
Page 141 Software Security 141 Setting the CDR folder back to not accessible For Windows 7: Right-click on the LabChip GX icon on the Windows desktop and select Run as Administrator. For Windows XP: Double-click on the LabChip GX icon on the...
Page 142: Software Reference
Software Reference 142 Software Reference This section describes the windows in the LabChip GX software. Each topic describes the options and buttons on the window, and how to open the window. This section includes: • “LabChip GX Main Window” on page 143 •...
Page 143: Labchip Gx Main Window
Software Reference 143 LabChip GX Main Window Figure 54. LabChip GX Main Window The main window of the LabChip GX software includes: • “Menu Bar” on page 144 • “Chip Status and Run Status” on page 151 • “Error Message Area” on page 153 •...
Page 144: Menu Bar
The menu bar is directly below the title bar on the LabChip GX Main Window. Clicking a menu name displays a list of commands to access software functions. The LabChip GX software contains the following menus: • “File Menu” on page 145 •...
Page 145 CDR Manager Window. A graphical representation of the microplate displays. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Data files can be .GXD (LabChip GX) or .CLA (LabChip HT software). Export - Opens the...
Page 146 These settings apply to all wells in the microplate. Use these settings to change the analysis and peak finding parameters to help resolve hard-to- decipher data. V4.2 LabChip GX User Manual PerkinElmer...
Page 147 Assay Editor - Opens the Select Assay To Edit window. Selecting an assay opens the Assay Analysis Window to make changes to the selected assay. V4.2 LabChip GX User Manual PerkinElmer...
Page 148 Lock Application - Opens the Unlock Application Window to lock the LabChip GX software and prevent other users from using the software until the software is unlocked by the current user or an Administrator. V4.2...
Page 149 Collection Pane. Tile Horizontal - Displays each Collection in separate top to bottom windows in the Collection Pane. Tabbed - Displays each Collection in a separate tab in the Collection Pane. V4.2 LabChip GX User Manual PerkinElmer...
Page 150 Software Reference 150 Help Menu The Help menu contains the following commands: LabChip GX Help Opens the Contents/Index page for the LabChip GX Help file. About LabChip GX Opens the About LabChip GX Window, showing the software version number and firmware version number.
Page 151: Chip Status And Run Status
NOTE The Chip status and Run status area does not display if the LabChip GX software is in Reviewer mode. System Status - Displays the status of the system. Displays Ready when the system is ready to run an assay. While an assay is running, each stage of the assay displays: Priming, Warming, Running, etc.
Page 152 (whichever comes first) until the chip reagents expire. Reagent expiration depends on the type of chip inserted in the instrument. The LabChip GX automatically detects the chip type from an embedded RF ID tag in each chip. The expiration time and number of samples reset whenever the chip holder is ejected.
Page 153: Error Message Area
View) or changing the start or end times for a run can cause errors with the peak find algorithm. “Error Messages” on page 285 for a list of errors and tips on preventing or resolving errors. V4.2 LabChip GX User Manual PerkinElmer...
Page 154: Plate View Or Plate List
• Save Plate - Saves the current data file. • Copy Plate - Saves a copy of the plate data file (.gxd) to the selected folder. V4.2 LabChip GX User Manual PerkinElmer...
Page 155 Red Exclamation Point in Well - An analysis error has occurred in the well, such as no lower marker detected (well C1 above). • Yellow Exclamation Point in Well - An analysis warning has occurred in the well (well C7 above). V4.2 LabChip GX User Manual PerkinElmer...
Page 156 Light Blue well names are selected in the Gel View Well Table View. • Well names outlined in Yellow have an analysis warning. • Well names outlines in Red have an analysis error. Figure 56. List View V4.2 LabChip GX User Manual PerkinElmer...
Page 157: Collection Pane
Software Reference 157 Collection Pane The Collection Pane in the LabChip GX 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 Plate View or Plate List.
Page 158: Graph View
Graph data can be exported to a graphic file by choosing Export on the File menu. (See “Exporting Data” on page 102 for details.) If the workspace contains multiple collections, the data exported is from the active/selected collection. V4.2 LabChip GX User Manual PerkinElmer...
Page 159 Copy - Copies the selected graph to the clipboard in a BMP format. Analysis Settings - Opens the Assay Analysis Window to change the analysis settings. V4.2 LabChip GX User Manual PerkinElmer...
Page 160 Right-click near the bottom of a peak in the graph for an RNA assay to display a shortcut menu containing the following commands: Reset to Defaults - Sets the Peak Baseline endpoints back to the default values. V4.2 LabChip GX User Manual PerkinElmer...
Page 161 Figure 58. Active Data Tab The Active Data tab does not show any peak labels or marker indicators. The labels and markers are identified during analysis, which occurs after all data from the well is collected. V4.2 LabChip GX User Manual PerkinElmer...
Page 162 For information on changing the view in the Overlay Electropherograms tab, see “Viewing Graphs in the Overlay Electropherograms Tab” on page “Graph View Properties” on page 164 for descriptions of the properties that can be set for the Overlay Electropherograms tab. V4.2 LabChip GX User Manual PerkinElmer...
Page 163 For information on changing the view properties in the Electropherograms tab, see “Viewing Graphs in the Electropherograms Tab” on page “Graph View Properties” on page 164 for descriptions of the properties that can be set for the Electropherograms tab. V4.2 LabChip GX User Manual PerkinElmer...
Page 164: Graph View Properties
Default is Type. The Annotations available depend on the columns selected in the Peak Table View. Text Orientation Specifies the orientation of the text for the annotation: horizontal, (A) button vertical up, or vertical down. V4.2 LabChip GX User Manual PerkinElmer...
Page 165 The legend shows the color used for each well. (Only for the Overlay Electropherograms Tab.) Overlay Offset Offsets each of the graphs by the RFU value specified. V4.2 LabChip GX User Manual PerkinElmer...
Page 166 The selected font is also used when exporting the graphs. Pin icon In the top right corner, this is used to lock in place or unlock the Properties tab. If locked in place, the Graph is resized to accommodate the tab. V4.2 LabChip GX User Manual PerkinElmer...
Page 167: Gel View
DNA, Protein, or RNA data. The data is shown in Time vs. Fluorescence (or digital form). (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Click on a gel lane (well) to select the well. Ctrl + click to select multiple wells.
Page 168 Scale Gel Contrast to Collection - Restores the minimum and maximum RFU values for all lanes in the collection to the default values. (Only available when Scale Gel Contrast to This Lane has been selected for a lane.) V4.2 LabChip GX User Manual PerkinElmer...
Page 169 The comment displays in the Well Table View and in printed reports. Rename Plate - Opens the Rename Plate window to specify a new name for the plate. V4.2 LabChip GX User Manual PerkinElmer...
Page 170: Gel View Properties
Show EP/ Displays a legend of the band colors and expected peak sizes or Smear Legend smear sizes in the Gel view. Click and drag to move the legend. V4.2 LabChip GX User Manual PerkinElmer...
Page 171 Filter tab. 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 172: Well Table View
Well Table at export time. A Well Table is exported to a CSV format, which can be opened in a program such as Microsoft Excel. If the workspace contains multiple collections, the data is exported from the active/selected collection. V4.2 LabChip GX User Manual PerkinElmer...
Page 173 To change the order of the columns displayed in the Well Table, drag and drop the column names in the Selected Columns list. The columns display on the order listed in the Selected Columns list. V4.2 LabChip GX User Manual PerkinElmer...
Page 174: Peak Table View
Available Columns list and the Selected Columns list in the Select Peak Table Columns window. Drag and drop the column names in the Selected Columns list to change the order of the columns displayed in the Peak Table. V4.2 LabChip GX User Manual PerkinElmer...
Page 175 Peak Table Properties. Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments. DNA, RNA, and gDNA assays are supported on LabChip GX, and GX II instruments. Peak Table Columns The Peak Table can display the following columns: %Area - (Glycan assay only) The peak's area as a percentage of the total area of peaks within the sample range (>...
Page 176 Fragment Area - (RNA assays only) The sum of the trapezoids between the fragment start and end times. The trapezoid base is a line drawn across the fragment base from the start point to the end point. V4.2 LabChip GX User Manual PerkinElmer...
Page 177 Window. The Sample name can also be changed in the Well Table View or the View. Signal Noise - The statistical standard deviation of 1 second of data just before the Peak Find Start Time. V4.2 LabChip GX User Manual PerkinElmer...
Page 178 Force Lower Marker • Force Upper Marker (DNA assays only) • Force Expected Peak NOTE: Excluding a peak or manually setting a peak to be an upper or lower marker can cause analysis errors. V4.2 LabChip GX User Manual PerkinElmer...
Page 179: Peak Table Properties
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. V4.2 LabChip GX User Manual PerkinElmer...
Page 180: Filter View
AND(Well) - Selects any well that contains peaks that match all of the filters selected in the Available Filters list. Different peaks in the same well can match different filters, as long as all filter conditions are met in the same well. V4.2 LabChip GX User Manual PerkinElmer...
Page 181 (checked) under Available Filters, indicating that the filter is being applied to the data. To select wells that contain any of the three peaks, create a separate filter for each peak and select OR as shown below. V4.2 LabChip GX User Manual PerkinElmer...
Page 182 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 wells that contain all the peaks listed. V4.2 LabChip GX User Manual PerkinElmer...
Page 183: About Labchip Gx Window
About LabChip GX Window The About LabChip GX window displays the software and firmware versions. Selecting About LabChip GX on the Help Menu opens this window.
Page 184: Add New Expected Peak Window
Specifies the wells that the expected peak is applied to. <All> Wells specifies that the expected peak applies to all wells. Clicking on the column opens the Select Wells window to choose the specific wells to apply the expected peak to. V4.2 LabChip GX User Manual PerkinElmer...
Page 185: Add Plate Window
The distance from the top of the plate to the bottom of the well. Sip Height The distance from the bottom of the well to the bottom of the sipper when the sipper is positioned to sip sample from the well. V4.2 LabChip GX User Manual PerkinElmer...
Page 186: Assay Analysis Window
Opens the Print window to print the analysis settings. 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 187: Assay Information Tab
Version - The version of the assay that was run. Format - The format of the data file. Compatibility - The version of LabChip GX software that supports the assay. Plate - The name of the plate in the workspace. Usually the same as the name of the data file that was created when the plate was run, unless the name is changed after it is added to the workspace.
Page 188: Alignment Tab
If selected, each row is aligned with the ladder at the beginning of the row and a ladder at the end of the row. (Protein and Glycan assays are only supported on LabChip GX II instruments.) V4.2 LabChip GX User Manual PerkinElmer...
Page 189: Analysis Tab
Range, Marker Concentration (DNA) Dilution Ratio (Protein), and System Peak Exclusion (Protein). Protein Charge Variant assays only show the Data Range. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Figure 75. Assay Analysis Window - Analysis Tab Ladder Sizes...
Page 190 • Ladder - Reflects a dilution of ladder in a total volume of ladder and sample buffer according to the LabChip GX/GXII Assay User Guide. • Sample - Reflects a dilution of sample in a total volume of sample, water, and sample buffer according to the LabChip GX/GXII Assay User Guide.
Page 191 • Glycan assays: The size of the lower marker. • If a default Ladder is defined for the plate, the Marker Migration Time, Height, and Area are available for editing. V4.2 LabChip GX User Manual PerkinElmer...
Page 192: Peak Find Tab
The Plate and Well Name fields are read only, and cannot be changed from the Peak Find Tab. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) V4.2 LabChip GX User Manual...
Page 193 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 194 Time on the Analysis tab and less than the Well End time. Table 2. Well Peak Find Settings Well Settings Function Well Displays the well being edited. Select any well or ladder on the plate belonging to the current collection. V4.2 LabChip GX User Manual PerkinElmer...
Page 195 (Displays only if a ladder is selected in the Well field.) Applies peak Ladders find settings to all ladders in the plate. Apply Plate Apply well-specific peak find settings to all wells on the same plate. V4.2 LabChip GX User Manual PerkinElmer...
Page 196: Expected Fragments/Proteins/Glycans Tab
Time - Specifies the expected time of the peak (Protein Charge Variant only). • Window (%) - Specifies the tolerance window as a percent of the expected size for the peak to allow for small variations in expected peak size. V4.2 LabChip GX User Manual PerkinElmer...
Page 197 Export button - Opens the Export Expected Fragments/ Proteins/ Glycans window to create an Expected Peak File (.gep) from the current settings in the tab. Import the .gep file into another assay to use the same expected peaks in another assay. V4.2 LabChip GX User Manual PerkinElmer...
Page 198: Excluded Peaks Tab
(Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Figure 78. Assay Analysis Window - Excluded Peaks Tab The Excluded Peaks tab contains the following options and buttons: Excluded Peak Table - Lists the excluded peaks for the assay analysis.
Page 199 Import button - Opens the Import Excluded Peaks window to select an Excluded Peak File (.gep) to import. The .gep file is created by exporting excluded peaks from another assay. Clear button - Deletes all Excluded Peaks from the table. V4.2 LabChip GX User Manual PerkinElmer...
Page 200: Smear Analysis Tab
Apply to Wells - Specifies the wells that the smear is applied to. <All> specifies that the smear applies to all wells. Clicking on the column opens the Select Wells window to choose the specific wells to apply the smear to. V4.2 LabChip GX User Manual PerkinElmer...
Page 201 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 202: Titer Tab
Normalized Area - Specifies the titer peak normalized area for imported titers. The table for imported titers is Read Only and cannot be edited. (Not displayed for manually entered titers.) Concentration - Specifies the concentration of the standard in • the specified well. V4.2 LabChip GX User Manual PerkinElmer...
Page 203 User Titer Window. Printing the Titer from the User Titer Window prints a report that contains the Titer graph, the fit parameters (fit model, concentration weight, origin option), fit coefficients, fit quality (R^2), and the data table (normalized area vs concentration). V4.2 LabChip GX User Manual PerkinElmer...
Page 204 Titer Import File (.ttr) to import. The .ttr file is created by exporting a titer from another assay. Clear button - Deletes all entries from the table. Clear the entries to use the default Standard Curve instead of the Titer Standard Curve. V4.2 LabChip GX User Manual PerkinElmer...
Page 205: Advanced Tab
User Standard instead of the default ladder settings. Not available for Glycan or Protein Charge Variant assays. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Peak Size Calibration Point Specifies which part of the peak is used as the size calibration point.
Page 206 Linear - The ladder migration time correction is proportional to the sample to ladder concentration ratio. • Nonlinear - The ladder migration time correction is a function of the ratio of sample and ladder concentrations and saturates at very high sample concentrations. (Default) V4.2 LabChip GX User Manual PerkinElmer...
Page 207 Assay Editor window when creating an assay. After the sample is run, edit the start time in the Smear Analysis Tab on the Assay Analysis window or by drag the start of the smear in the Graph View. V4.2 LabChip GX User Manual PerkinElmer...
Page 208: Audit Trail Window
Clicking the Browse (...) button opens the Audit Trail CDR Browser window to open the audit trail for a different data file. Event Category Specifies the Event Category of events to search for. Default selects all event categories. V4.2 LabChip GX User Manual PerkinElmer...
Page 209: Audit Trail Export Window
XML File - If selected, the file is saved as a .xml file. • MS Excel - If selected, the file is saved as a .xls file. Number of Events Included - Displays the number of events that will be exported. V4.2 LabChip GX User Manual PerkinElmer...
Page 210: Audit Trail Manage Columns Window
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. V4.2 LabChip GX User Manual PerkinElmer...
Page 211: Cdr Manager Window
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. V4.2 LabChip GX User Manual PerkinElmer...
Page 212 The icon next to the data file name indicates whether the data file is Accepted/Rejected and Locked as shown in the table below: File Status Icon Locked Accepted Accepted and Locked Rejected Rejected and Locked V4.2 LabChip GX User Manual PerkinElmer...
Page 213: Cdr Server Utility Window
Username, and Password for the new data folder. Apply button Creates the specified data folder. View Contents Opens the CDR Server Viewer to view contents of the Remote button CDR folders on the computer. V4.2 LabChip GX User Manual PerkinElmer...
Page 214: Cdr Utility Window
Figure 87. CDR Utility Window The CDR Window contains the following options: CDR Folder Displays the location of the CDR folder where the LabChip GX data files will be saved. This location cannot be changed. Accessible by Windows XP: If selected, Windows Administrators...
Page 215 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 V4.2 LabChip GX User Manual PerkinElmer...
Page 216: Change Password Window
(To change passwords for other users, see User Administration Window.) This window is only available if the CFR Support option is installed with the LabChip GX software. To open the Change Password Window, select Security  Change Password on the LabChip GX Main Window.
Page 217: Data File Version Window
Print Opens the Print Preview window to preview the Preview printed version information. Print Opens the Print window to print the data file version information. Close Closes the Data File Version window. V4.2 LabChip GX User Manual PerkinElmer...
Page 218: Event Viewer Window
The data and time the event or error occurred. Source The system component that generated the event or error. Event Code The event/error ID number used by PerkinElmer to troubleshoot errors. Description Text describing the event or error. Click the OK button to close the Event Viewer window.
Page 219: 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 220 Entire Collection: If selected, a separate graph is exported for each well in the collection. • Selected Wells: If selected, a separate graph is exported for each of the wells selected in the Gel View Plate View or Plate List. V4.2 LabChip GX User Manual PerkinElmer...
Page 221 (Not available on the Auto Export window.) • 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 222: Installation Qualification Window
Installation Qualification Window Use the Installation Qualification Window to perform the IQ test. The IQ test verifies proper installation of the LabChip GX software and verifies no unauthorized changes have been made to the software. To open the Installation Qualification Window, select Validation ...
Page 223: Layout Options Window
Restore to Factory Defaults button - Restores the active collection to the default Layout options, table views, table columns, and viewer properties. Cancel button - Closes the Layout Properties window without changing the collection layout. V4.2 LabChip GX User Manual PerkinElmer...
Page 224: Login Window
Login Window Use the Login Window to log into the LabChip GX software when the 21 CFR Part 11 option is installed. The LabChip GX software will not start until a valid user name and password are entered.
Page 225: New Collection Window
If a workspace already contains a collection, all new collections are the same type as the existing collections. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Name - Specifies the name of the new collection. V4.2...
Page 226: Optics Calibration Window
The chip is always warmed to the target temperature to more accurately calibrate the optics. Background - The background measured on the current instrument after focusing. Contrast - The contrast measured on the current instrument. V4.2 LabChip GX User Manual PerkinElmer...
Page 227 • Abort: stops the scan or warm currently in progress. Apply button - Saves the New Correction Factor to the instrument’s non-volatile flash memory. Done button - Closes the Optics Calibration window. V4.2 LabChip GX User Manual PerkinElmer...
Page 228: Perform Signature Window
Username Select the username of the user that is signing the data file. Role Displays the Access Level of the selected LabChip GX user. Comment Details on why the signature is being performed and what actions have taken place. It is the signer’s responsibility to ensure all details required by the company’s procedures are included.
Page 229: Plate Information Window
Opens the Verify Plate window to perform a puncture test using the selected plate information. Follow the instructions in the Verify Plate window to test the settings for the selected plate. Close button Closes the Plate Information window. V4.2 LabChip GX User Manual PerkinElmer...
Page 230: Print Window
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. • Exclude Marker - If selected, markers are not printed. V4.2 LabChip GX User Manual PerkinElmer...
Page 231 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 collection to the default Windows printer. Cancel button - Closes the Print window without printing. V4.2 LabChip GX User Manual PerkinElmer...
Page 232: Print Validation Reports Window
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. V4.2 LabChip GX User Manual PerkinElmer...
Page 233: Rename Collection Window
LabChip GX Main Window. To open the Rename Collection window, select Collection  Rename Collection on the LabChip GX Main Window. Figure 101. Rename Collection Window Name - Type the desired name for the selected collection. V4.2 LabChip GX User Manual PerkinElmer...
Page 234: Robot Teaching Wizard
“Verify a Plate Window” on page 238 • “Verify Positions Window” on page 239 • “Finished Window” on page 240 • “Verify All Target Positions Window” on page 241 • “Verify All Target Positions Correct Window” on page 242 V4.2 LabChip GX User Manual PerkinElmer...
Page 235: Welcome Window
If Verify Target Positions Only is not selected, displays the Teach Robot Window. If Verify Target Positions Only is selected, displays the Verify All Target Positions Window. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 236: Teach Robot Window
Displays the Teach the X, Y and Z Reference Positions Window. Follow the instructions in the window before clicking the Next button. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 237: Teach The X, Y And Z Reference Positions Window
Test button Moves the plate holder to verify that the reference position is set properly. If set properly, the sipper moves into the hole on the plate holder without hitting the sides of the hole. V4.2 LabChip GX User Manual PerkinElmer...
Page 238: Verify A Plate Window
Back button Displays the Teach the X, Y and Z Reference Positions Window. Next button Displays the Verify Positions Window. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 239: Verify Positions Window
Moves the plate holder to test the selected positions. Back button Displays the Verify a Plate Window. Next button Displays the Finished Window. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 240: Finished Window
Back button Displays the Verify Positions Window. Finish button Saves the changes to the reference position and closes the Robot Teach Wizard. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 241: Verify All Target Positions Window
Back button Displays the Welcome Window. Next button Displays the Verify All Target Positions Correct Window. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 242: Verify All Target Positions Correct Window
Verification Failed Window. Click the Next button to display Teach Robot Window to adjust the taught positions. Finish button Closes the Robot Teach Wizard. Cancel button Closes the Robot Teach Wizard without saving changes to any positions. V4.2 LabChip GX User Manual PerkinElmer...
Page 243: Run File Editor Window
Run File Editor Window Use the Run File Editor window to create run files (*.xml) for use with Caliper's automation control software. When the LabChip GX is running in automation mode and is being controlled by software such as iLink Pro, you must create a run file to specify the settings for the assay that will be run.
Page 244: Run Info Window
The Run Info window contains the following buttons: Print Opens the Print Preview window to view the run information before Preview printing. Print Opens the Print window to print the run information. Cancel Closes the Run Info window. V4.2 LabChip GX User Manual PerkinElmer...
Page 245: Sample Name Editor Window
To open the Sample Name Editor window, choose Tools  Sample Name Editor on the LabChip GX Main Window or click the Edit button next to the Sample Name File text box on the...
Page 246 Closes the Edit Sample Names window. If changes have not been applied to the plate, prompts you to discard the changes. To save the changes, click the Apply button before clicking the Close button. V4.2 LabChip GX User Manual PerkinElmer...
Page 247: Save Workspace As Window
Figure 113. Save Workspace As Window Tip: You may want to save the workspace file in the same location as the plate data files to prevent missing plate data files when moving workspace files. V4.2 LabChip GX User Manual PerkinElmer...
Page 248: Select A Data File Window
Part 11 option is installed, the CDR Manager Window opens.) Data files generated by the LabChip GX software have a .gxd file extension. Data files generated by the LabChip HT software have a .cla file extension; change the File Type to display .cla files.
Page 249: Start Run Window
Imports the settings from a run file (*.xml) into the Start Run window. (Use the Run File Editor Window to create a run file.) Cancel Closes the Start Run window without saving any changes and without starting the run. V4.2 LabChip GX User Manual PerkinElmer...
Page 250: Run Tab
(Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) Figure 116. Start Run Window - Run Tab Assay Type Select the type of assay to run.
Page 251 Only available if a Sample Names File is selected and the Use This File for Sample Selection check box is selected on the Advanced Tab, V4.2 LabChip GX User Manual PerkinElmer...
Page 252: Output Tab
NOTE If you choose not to use the time of the run as part of the data file name, the LabChip GX software automatically appends _1, _2, etc., for each subsequent run on the same day. Figure 117. Start Run Window - Output Tab Data Path Specifies the location where the data files will be saved.
Page 253 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 format for the data file name. V4.2 LabChip GX User Manual PerkinElmer...
Page 254: Advanced Tab
For example, if 10 wells are selected, and the Random Selection percent is set to 50%, five wells, selected at random, will be sampled during the run. V4.2 LabChip GX User Manual PerkinElmer...
Page 255 Click the Browse button next to Excluded Peaks File, select the name of the .GEP file that contains the excluded peaks, and click the Open button. The path and name of the file displays in the text box. V4.2 LabChip GX User Manual PerkinElmer...
Page 256: System Diagnostics Window
System Diagnostics Window Use the System Diagnostics window to run the diagnostics tests on the LabChip GX or GX II 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.
Page 257 Close button - Closes the System Diagnostics window. The bottom of the window displays a progress bar for the entire set of selected tests and a separate progress bar for the test that is currently running. V4.2 LabChip GX User Manual PerkinElmer...
Page 258: Unlock Application Window
Figure 120. Unlock Application Window The Unlock Application Window contains: Option/Button Function Username Type the user name of the current user or a LabChip GX administrator’s user name. Password Type the password for the specified user name. OK button Verifies the username and password and opens the LabChip GX software if the username and password are correct.
Page 259: Unlock Data File Window
Figure 121. Unlock Data File Window The Unlock Data File window contains: Username - Select the user name of the LabChip GX user that is unlocking the data file. Reason - Type the reason why the data file is being unlocked.
Page 260: User Administration Window
Software Reference 260 User Administration Window Use the User Administration window to create new LabChip GX 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 GX software policies.
Page 261: Create New User
Create New User Use the Create New User tab to add a new user name to the LabChip GX software. This window creates the LabChip GX user account, it does not create a Windows user account. Figure 123. User Administration Window - Create New User...
Page 262 If selected, the user can Accept, Reject, and/or Lock data files Data File in the Perform Signature Window. Unlock Data File If selected, the user can unlock data files using the Unlock Data File Window. V4.2 LabChip GX User Manual PerkinElmer...
Page 263: Edit Users
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 user. V4.2 LabChip GX User Manual PerkinElmer...
Page 264: Show User Info
Displays No if the user does not have rights. Account Created Displays the date and time when the account was created. Account Last Displays the date and time when the account was last Changed On changed. V4.2 LabChip GX User Manual PerkinElmer...
Page 265 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 266: De/Activate User
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 GX software. Figure 126. User Administration Window - De/Activate User The De/Activate User Info tab contains:...
Page 267: Define Access
Use the Define Access Tab to assign the desired rights to each access level. These rights control the actions each user is permitted to perform in the LabChip GX software. The Define Access tab is not available while an assay is running.
Page 268 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. Assay Editor If enabled, allows users to edit and save assays. V4.2 LabChip GX User Manual PerkinElmer...
Page 269: Set Policies
Software Reference 269 Set Policies Use the Set Policies tab to specify password, login, automatic lock, and signature policies for the LabChip GX software. Figure 128. User Administration Window - Set Policies The Set Policies tab contains: Access Right Function...
Page 270: Labchip Gx Instrument Description
Description This section identifies and describes the hardware components of the LabChip GX and GX II instruments. All of the components described in this section are the same for the GX and GX II instruments. The LabChip GX runs DNA and RNA assays. The LabChip GX II runs DNA, RNA, Protein, Glycan, and Protein Charge Variant assays.
Page 271: Front Panel
This button is illuminated when this function is available and flashes when movement is in progress. Power Turns the LabChip GX instrument On (Run) or Off (Standby). Note that Button power is still supplied to the power supply fans when the power switch is in the Standby position.
Page 272: Rear Connectors
LabChip GX Instrument Description 272 Rear Connectors The rear connectors are used to connect the LabChip GX instrument to the computer and power supply. Figure 131. Rear Connectors The following connectors are located on the back of the instrument: AC Power Plug the power cord into this connector and a power outlet.
Page 273: Optics
The LabChip GX instruments use back-reflected red diode laser light for automatic chip focusing. Photodiode Detectors The LabChip GX and LabChip GX II use two silicon photodiode detectors for fluorescence detection and autofocus. Fluorescence data can be acquired and stored at rates from 20 to 120 Hz.
Page 274: Dna, Rna, And Protein Chips
DNA, RNA, and Protein Chips The figures below show the format and parts of the microfluidic chips used in the LabChip GX instruments to perform DNA, Protein, RNA, and Glycan sizing and quantitation. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.)
Page 275: Chip Cartridge
LabChip GX Instrument Description 275 Chip Cartridge The Chip Cartridge holds the chip, provides the voltage to the chip channels to load, inject, and separate the sample, provides pressure to prime the chip with separation gel, and provides vacuum to the chip wells to pull samples from the microplate into the chip.
Page 276: High Voltage Interface
Supplies DC voltage to the separation channels in the chip via inert electrodes that are immersed in specific wells on the chip. There are 6 voltage channels for the LabChip GX chips. HV channels can be run in either constant voltage or constant current mode.
Page 277: Microplate Carrier
USB Key for 21 CFR Part 11 Option If the 21 CFR Part 11 option is installed, the USB Key must be plugged into a USB port on the LabChip GX computer. If the USB key is not plugged in, the LabChip GX software displays an error message when starting and then shuts down.
Page 278: Specifications
LabChip GX Instrument Description 278 Specifications This section lists the technical specifications for the LabChip GX instruments. Technical specifications are subject to change without notice. General Size (H x W x D) 18.75 in. (48cm) x 19.25 in. (49cm) x 25.375in.(64cm) Weight 88 lbs.
Page 279: Assay Voltage
LabChip GX Instrument Description 279 Assay Voltage Minimum Voltage/Current -100V (limited by current) Maximum Voltage/Current -3000V (limited by current) Chip Pressure Pressure Range +50 to -5 psig Chip Temperature Control Temperature Range Ambient + 5°C to 40°C (no active cooling) Accuracy ±...
Page 280: Maintenance And Service
SOP specifies more frequent calibration or diagnostics. See “Calibrating the Optics” on page The LabChip GX/GXII Assay User Guides and Quick Guides contain LabChip Kit Essential Practices and instructions for preparing reagents and plates. Make sure to follow the instructions to ensure the optimum performance of your instrument.
Page 281: Cleaning The Chip Cartridge
To reduce pressure leaks at the chip interface, clean the O-rings frequently. Remove the O-rings from the top plate of the chip interface on the LabChip GX instrument. Soak O-rings in DI water for a few minutes. Clean the O-ring faces by rubbing between two fingers.
Page 282: Cleaning Test Chip C
Dry the chip completely with a gentle air stream from oil free compressed and filtered house air or compressed air cans. Do not shake can before use. Hold can at a distance from the chip to prevent condensation. V4.2 LabChip GX User Manual PerkinElmer...
Page 283: Troubleshooting And Diagnostics
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 PerkinElmer to troubleshoot problems. Description - A detailed description of the event or error that occurred.
Page 284: Viewing Current Events In The Events Tab
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 PerkinElmer to troubleshoot problems. Description - A detailed description of the event or error that occurred.
Page 285: Error Messages
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 PerkinElmer Technical Support (see page For specific information about an error or warning message, click one of the links below.
Page 286: Device Is Disconnected
1. Cable between computer Verify that the USB communication cable is secure. and instrument unplugged. Verify the power cord is plugged in. 2. Instrument power loss. Press the Power button on the LabChip GX instrument. 3. Computer went into page 271. hibernation.
Page 287: Move Timeout
1. Robot failure Check for an object blocking the robot motion and remove the blockage. Restart the instrument. If the problem is not resolved, contact PerkinElmer Technical Support (see page Pressure Leak Detected Error Message: “Pressure leak detected. Check and clean the O- rings at the chip interface.”...
Page 288: Maximum Samples Exceeded
281). 2. Re-priming can sometimes clear chip clogs. Eject the chip drawer, push the drawer back in, and restart the run. See the LabChip GX/GXII Assay User Guide for troubleshooting. 3. If the problem is not resolved, contact PerkinElmer Technical Support (see page V4.2...
Page 289: Current Leakage Check Failed
Clean the O-rings (see page 281). Run the Current Leak Diagnostic Test (see page 291). If the problem is not resolved, contact PerkinElmer Technical Support (see page Chip Temperature Warning Warning Message: “Average chip temperature is out of range.” Possible Causes Recommended Actions Chip heater failed.
Page 290: Running Installation Qualification (Iq)
Troubleshooting and Diagnostics 290 Running Installation Qualification (IQ) The Installation Qualification (IQ) verifies proper installation of the LabChip GX software and verifies no unauthorized changes have been made to the software. The IQ can be run whenever required by your laboratory procedures.
Page 291: Diagnostics
Troubleshooting and Diagnostics 291 Diagnostics The LabChip GX software contains a set of diagnostic tests to verify proper operation of the LabChip GX or GX II instrument. These tests are not dependent on assay chemistry. All tests must pass to ensure the instrument is functioning properly.
Page 292: Description Of Diagnostic Tests
Remote server is down. Network is down. Connection (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 plates. V4.2 LabChip GX User Manual PerkinElmer...
Page 293 PerkinElmer Technical Support (see page Sipping Pressure Pressure sensor out of calibration. Sensor Test Contact PerkinElmer Technical Support (see page Sipping Pressure Chip Clog in pressure line. Contact Interface Clog Test PerkinElmer Technical Support (see page V4.2 LabChip GX User Manual PerkinElmer...
Page 294 Description Potential Cause of Failure Chip Heater Ramp Initial chip temperature not achieved in time. Temperature ramp time not within spec may indicate heater disconnected or burned out. Contact PerkinElmer Technical Support (see page V4.2 LabChip GX User Manual PerkinElmer...
Page 295 Channel (0, 1, 2, 5, 6, currents too high. Clean or replace the O- and 7) rings (see page 281) and clean the chip cartridge. If error persists, contact PerkinElmer Technical Support (see page Optics Test Test Chip A required Description Potential Cause of Failure Home Optics Optics Motor failure.
Page 296 Verify dimensions of plate are correct in Plate Information Window. If all punches are misaligned, teach plate position (see “Robot Teaching Wizard” on page 234). If the problem persists, contact PerkinElmer Technical Support (see page V4.2 LabChip GX User Manual PerkinElmer...
Page 297 Read barcode on test Plate missing barcode. Place barcode on plate. plate in correct position (see page 40). Barcode is not read correctly. Barcode reader disconnected or misaligned. Contact PerkinElmer Technical Support (see page V4.2 LabChip GX User Manual PerkinElmer...
Page 298: Troubleshooting Assay Problems
After a few seconds, restart the computer, open another file, and try resaving it to verify the Save function is working properly. LabChip GX software is corrupted. Reinstall the software. If the problem persists, contact PerkinElmer Technical Support (see page V4.2...
Page 299: Computer Software Lock-Ups
Troubleshooting and Diagnostics 299 Computer Software Lock-Ups If a computer or software lock-up occurs: Try to exit and then re-launch the LabChip GX software. If this is not successful, exit the application using the Task Manager: Right-click in the desktop menu bar and select Task Manager.
Page 300: Zipping The Log Files
Zipping the Log Files The Caliper Log Zipper is a small software utility that zips the LabChip GX 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 PerkinElmer Technical Support.
Page 301: Tips And Shortcuts
Tips and Shortcuts 301 Tips and Shortcuts This section describes the shortcuts and actions that can be performed in the LabChip GX software by clicking, right-clicking, etc. Single Click • In Plate View - Selects or de-selects a well. •...
Page 302: Glossary Of Terms
Hardware Diagnostics • Inflection Threshold • Lab-on-a-Chip • Ladder • Ladder Analysis • Lower Marker • Log Files • Marker Drift Tolerance • Microfluidics • Minimum Peak Height • Minimum Peak Width • Molarity V4.2 LabChip GX User Manual PerkinElmer...
Page 303 Assay File File created by the LabChip GX software to specify assay and analysis settings, such as Ladder and marker sizes and concentrations, peak find settings, expected peaks, and excluded peaks.
Page 304 Figure 141 on page 305 shows baselines established for DNA assay peaks (based on the settings in the Peak Find Tab). DNA peaks are determined on a peak-by-peak basis (the overall baseline is shown). V4.2 LabChip GX User Manual PerkinElmer...
Page 305 The file extension for data files created by the LabChip HT software. CLA files can be opened in the LabChip GX software. Opening a .CLA file (see page 60) creates a .GXD file with the...
Page 306 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  Apply Template on the main Menu Bar. V4.2 LabChip GX User Manual PerkinElmer...
Page 307: Data Files
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. For details on the data filtering process, see “Data Smoothing” on page 108. V4.2 LabChip GX User Manual PerkinElmer...
Page 308 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 309 Well Table View. GXD Files The file extension for data files created in the LabChip GX software. The data file contains the data from the read, assay information, analysis settings, and Run Information for the run. Data is saved to the file as each well is read. If a run is stopped before the run is complete, the data for any completed wells is saved in the data file.
Page 310 Peaks appearing above the upper marker do not have to be detected. The Peak Table View for the ladder well shows the peak size and concentration set in the Assay Analysis Window. Figure 142. Ladder Graph V4.2 LabChip GX User Manual PerkinElmer...
Page 311 Upper Marker. For Protein and RNA assays, the marker is the same as the first peak in the ladder. Protein Charge Variant assays do not use ladders or markers. V4.2 LabChip GX User Manual PerkinElmer...
Page 312 Glossary of Terms 312 Log Files The LabChip GX 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.
Page 313 The blue and yellow triangles shown in the figure below represent the weight assigned to a peaks migration time for a tolerance of 100% and 10% respectively. Figure 143. Marker Drift Tolerance V4.2 LabChip GX User Manual PerkinElmer...
Page 314 (nmol/l), Concentration is measured in nanograms per microliter (ng/µL), Size is measured in base pairs (bp), and 660 * [g/(mol * bp)] is the molecular weight of a single base pair V4.2 LabChip GX User Manual PerkinElmer...
Page 315 Optical Calibration The LabChip GX instrument reads fluorescence of a laser illuminated dye attached to compounds present in a sample. The absolute value of this fluorescence has little meaning as all...
Page 316 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 317 The default setting is 6 (for 6th order). A setting of 4 produces a straighter baseline, preventing quick changes in the signal. V4.2 LabChip GX User Manual PerkinElmer...
Page 318 The peak concentration is then calculated using the ladder peak areas and concentration for the ladder supplied in the Assay Analysis Window. The concentration is adjusted for the differing dilution ratios of sample and ladder. V4.2 LabChip GX User Manual PerkinElmer...
Page 319 The size of a peak is not calculated, only the % Rel amount of each peak. Protein Charge Variant assays and data files do not include any ladder or marker parameters or options. V4.2 LabChip GX User Manual PerkinElmer...
Page 320 These areas and rRNA peak heights and some relevant ratios are available for display in the Well Table View. A combination of the quantities is used to assess the quality of the RNA sample. V4.2 LabChip GX User Manual PerkinElmer...
Page 321 A value below 10 is obtained with high quality RNA but the user should determine their own threshold for discriminating between good and bad RNA. This quantity can be viewed and reported in the Well Table View. V4.2 LabChip GX User Manual PerkinElmer...
Page 322 Either ball dimension can be used to increase the smoothness of the curve, but increasing the Time Diameter increases the computation time required to compute the curve, while increasing the RFU Diameter does not. V4.2 LabChip GX User Manual PerkinElmer...
Page 323 After the run has begun, this button changes to Stop. See “Stopping a Run” on page NOTE The Run button does not display if the software was installed in Reviewer mode. V4.2 LabChip GX User Manual PerkinElmer...
Page 324 In the 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 that the fluorescence intensity shows through. V4.2 LabChip GX User Manual PerkinElmer...
Page 325 Log fit. For each sample peak, the apex is interpolated from the Standard Curve to determine the peak size in kDa (kiloDaltons). V4.2 LabChip GX User Manual PerkinElmer...
Page 326 Curve to determine the peak size in nt. Figure 149. RNA Assay Standard Curve For more information about the use of the standard curve during analysis, see “How the Software Analyzes RNA Data” on page V4.2 LabChip GX User Manual PerkinElmer...
Page 327 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. V4.2 LabChip GX User Manual PerkinElmer...
Page 328 Each workspace can contain multiple Collections for viewing the same data in different layouts. V4.2 LabChip GX User Manual PerkinElmer...
Page 329 All electropherograms produced with the instrument show some amount of background fluorescence. By default, the LabChip GX software enables the Zero Baseline function. To change the Baseline Algorithm, select None, Zero Baseline, or Baseline...
Page 330: Perkinelmer Product Warranty 330
LIMITED WARRANTY. LabChip GX/GX II Instrument Warranty: PerkinElmer warrants to the original purchaser (“Customer”) that at the time of shipment to the Customer, the LabChip GX/LabChip GX II instrument (“Instrument”) is free from defects in materials and workmanship, and shall substantially conform to its published specifications.
Page 331 • Customer must perform the appropriate level of revalidation required as a result of any maintenance or service provided. • For on-site services, Customer must ensure that the site where the product is located is safe for PerkinElmer personnel to enter, prior to PerkinElmer performing any services under this Warranty.
Page 332: Perkinelmer Software License Agreement
PerkinElmer, Inc. has a local sales subsidiary; and/or (iii) PerkinElmer Cellular Technologies Germany GmbH, if the Licensee is located outside the United States and in a country in which PerkinElmer, Inc. does not have a local sales subsidiary), with offices at 940 Winter Street, Waltham, Massachusetts 02451.
Page 333 Software. Data collected will not include any Licensee data created with the Software. Licensee consents to such detection and collection of data, as well as its transmission and use. PerkinElmer also reserves the right to use a hardware lock device, license administration software, and/or a license authorization key to control access to the Software.
Page 334 Software. Termination is not an exclusive remedy. Limited Warranty. PerkinElmer's sole warranty with respect to the Software is that for a period of ninety (90) days from the date of receipt, the Software will substantially contain the functionality described in the published specifications, and when properly installed on a computer meeting the specifications set forth in, and operated in accordance with, the Documentation, will substantially perform in accordance therewith.
Page 335 Agreement. PerkinElmer shall not be in default hereunder by reason of any failure or delay in the performance of its obligations hereunder where such failure or delay is due to strikes, labor disputes, civil disturbances, riot, rebellion, invasion, epidemic, hostilities, war, terrorist...
Page 336: Index
... . . 278 Charge Variant Data ..57 Barcode reader....273 V4.2 LabChip GX User Manual PerkinElmer...
Page 337 ....108 Chip Status ....151 Data Analysis ..42 V4.2 LabChip GX User Manual PerkinElmer...
Page 338 ..... . . 284 ladder ..... 43 V4.2 LabChip GX User Manual PerkinElmer...
Page 339 ....145 File Order ....250 V4.2 LabChip GX User Manual PerkinElmer...
Page 340 ....207 LM for Glycan ....83 LabChip GX main window ..143 LM for Protein and RNA .
Page 341 ... . . 278 Perform Signature Window..228 Operating Temperature ..278 V4.2 LabChip GX User Manual PerkinElmer...
Page 342 Index 342 PerkinElmer Center for Training and Gel View ....170 Development....3 Graph view .
Page 343 Test..293 Show all peaks ....179 System Diagnostics Window ..256 V4.2 LabChip GX User Manual PerkinElmer...
Page 344 ....118 Well Table View ....172 V4.2 LabChip GX User Manual PerkinElmer...
Page 345 ..... . 88 Zoom Out ..... 88 V4.2 LabChip GX User Manual PerkinElmer...
Page 346 PerkinElmer, Inc. 68 Elm Street Hopkinton, Massachusetts 01748 TEL 203-925-4602 FAX 203-944-4904 http://www.perkinelmer.com...

This manual is also suitable for:

Labchip gx ii

PerkinElmer LabChip GX User Manual

Preface

Instrument Safety

Introduction

Operation

Data Analysis

Using the GX Software to Analyze GX Touch Data

Understanding Peak Finding

Software Security

Software Reference

Labchip GX Instrument Description

Maintenance and Service

Troubleshooting and Diagnostics

Tips and Shortcuts

Glossary of Terms

Perkinelmer Product Warranty

Perkinelmer Software License Agreement

Index

Quick Links

Troubleshooting

Need help?

Questions and answers

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Summary of Contents for PerkinElmer LabChip GX