Lum/nex ® xPONENT 3.
© Luminex Corporation, 2001-2009. All rights reserved. No part of this publication may be reproduced, transmitted, transcribed, or translated into any language or computer language, in any form or by any means without prior express, written consent of: LUMINEX CORPORATION 12212 Technology Boulevard Austin, Texas 78727-6115 U.S.A. Voice: (512) 219-8020 Fax: (512) 219-5195 Luminex® xPONENT Software Manual PN 89-00002-00-202 Rev. B January 2009 EC REP European Device Solutions, Ltd. 107 East St.
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ENTS" SPECIFICALLY EXCLUDES PATENT CLAIMS CONCEIVED AND REDUCED TO PRACTICE BY BUYER CONSISTING OF METHODS OF SAMPLE PREPARATION, METHODS OF CONJUGATING PRODUCT TO ANALYTES, THE COMPOSITION OF MATTER OF THE SPECIFIC CHEMISTRIES OF THE ASSAYS DEVELOPED BY BUYER AND METHODS OF PERFORMING THE ASSAYS (I.E., THE PROTOCOL FOR THE ASSAY).
End-User License Agreement (EULA) for Luminex® Software This Luminex End-User License Agreement (“EULA”) is a legal agreement between you (either an individual or a single entity, also referred herein as “you”) the end-user and Luminex Corporation (“Luminex”) regarding the use of the xPONENT software product provided to you above, which includes computer SOFTWARE and online or electronic documentation and may include associated media and printed materials (if any) (“SOFTWARE”).
purchaser, you may obtain a license under Luminex’s patents, if any, to use this unit of Luminex instrumentation with fluorescently labeled microsphere beads authorized by Luminex by purchasing such beads from Luminex or an authorized Luminex reseller. 4. RESTRICTIONS • SOFTWARE must only be installed and operated on a single computer running with a Luminex instrument, as set forth above.
8. NO WARRANTY. THE SOFTWARE IS LICENSED “AS IS.” ANY USE OF THE SOFTWARE IS AT YOUR OWN RISK. THE SOFTWARE IS PROVIDED FOR USE ONLY WITH LUMINEX PRODUCTS. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, LUMINEX AND ITS SUPPLIERS DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT. 9. LIMITATION OF LIABILITY.
Table of Contents Introduction .......................................................................................................................... 1 Software Packages ......................................................................................................... 1 About This Guide ............................................................................................................ 2 General Guidelines ...................................................................................
Luminex xPONENT 3.1 Software Manual Saved Batches Tab .................................................................................................. 38 Results Tab ......................................................................................................... 41 Settings Tab ........................................................................................................ 42 Log Tab .........................................................................................................
Contents Application Settings............................................................................................ 90 Arrange Main Navigation Buttons....................................................................... 90 LIS Settings ........................................................................................................ 90 Maintenance Options ......................................................................................... 90 External Analysis Program Settings ...........
Luminex xPONENT 3.1 Software Manual Protocols................................................................................................................. 107 Create Qualitative Assay Protocol .................................................................... 108 Edit Qualitative Analysis Settings...................................................................... 108 Create Quantitative Assay Protocol ..................................................................
CHAPTER 1 Introduction The Luminex system was developed to improve workflow and efficiency in the clinical laboratory and in research and development. End users in the laboratory must run microtiter plates using xMAP® based assay kits developed for use with xMAP technology. Software Packages xPONENT® software has different levels of functionality: 1. Allows you to perform analysis, create protocols and batches, review and print reports, and perform Luminex system maintenance. 2.
Luminex xPONENT 3.1 Software Manual About This Guide The conventions in this document assume a basic familiarity with computers and a knowledge of Microsoft® Windows® software. Commands are often available through more than one method, such as from the toolbar and from menus that appear when rightclicking an area of the screen. However, for ease of use the individual procedures in this manual describe only one method for accessing commands. This guide is formatted as a PDF, and can be printed.
Introduction Multiple pipetting from the original container may affect bead concentrations. Protect the xMAP beads from light at all times. Store xMAP beads at 2 to 8°C. NOTE: Refer to the product information sheet that accompanies your xMAP beads or assay for additional information. Limitations xMAP beads are susceptible to photobleaching; photobleaching effects are cumulative. Minimize exposure of xMAP beads to light during your development and manufacturing phases to maintain product integrity.
Luminex xPONENT 3.1 Software Manual each set of xMAP beads used for a particular assay will show a statistically even distribution of reporter molecules bound to the surface of each bead. During data acquisition, numerous beads of each set are analyzed and the median statistic is computed for that set by the software. The more beads of a set measured, the more confidence that can be given for that particular measurement.
Introduction Sample Dilution Dilute concentrated biological samples, such as plasma or serum, at least 1:5 with reagents as part of assay setup or as a final dilution step. If running an xMAP-based kit, follow the dilution instructions found on the kit’s product insert. Reagents Formulated reagents must be free of particulates other than xMAP beads. Do not dilute xMAP calibrators or verifiers. Gating Gate positions are dependent upon buffer composition.
Luminex xPONENT 3.
CHAPTER 2 Touring the Software This chapter explores each section of the software and its functionality. For information about using the software, see “Using the Software” on page 89. This chapter describes default views. Please note that views can be changed and functionality can be disabled by the xPONENT® system administrator. Log In To log in, type your user ID at the System Login tab. If you are using the secure version of the software, type your password.
Luminex xPONENT 3.1 Software Manual Help English-language help is available for each window in the software by clicking the blue “i” button in the upper right portion of the window in which you are working. You can also access the complete system-wide help by clicking Help at the very top of the screen, and then clicking Contents and Index. Help Icons FIGURE 1.
Touring the Software Screen Elements The following section details the screen elements and the common terms used in this manual to describe them. FIGURE 2. Screen Elements 1 2 3 1 Page 2 Tab 3 Right-Click Menu Page. The main elements at the top of the window are “Pages”. Click a page to go to that section of the software. All but the Home, and in some cases the Admin, page can be moved or deleted. For more information, see “System Setup Tab” on page 72. Tab.
Luminex xPONENT 3.1 Software Manual • • • • • Cut - Cuts the selected data. Copy All - Copies all data. Copy - Copies only the selected data. Paste - Pastes previously copied text or data into the box. Delete - Erases text or data from the selection. The histogram and dot plot within the Results page have specialty right-click menus. See those sections for more information. System Monitor The System Monitor remains at the bottom of all xPONENT® windows.
Touring the Software Pause. Pauses the system after the current command completes. Pause does not stop the system in the middle of running a command. You cannot run another command while the system is paused. Stop. Stops the system, regardless of command status. Eject. Ejects the plate. Once the plate is ejected, the Eject button changes to Retract. Retract retracts the plate, and the Retract button changes back to Eject. Temp.
Luminex xPONENT 3.1 Software Manual Home The Home page displays a welcome message, batch creation buttons, Daily Activities shortcuts, and the Installed Protocols list. FIGURE 4. Home Page Return to the Home page at any time by clicking Home in the Navigation toolbar. This page contains the following: Click to Create a new Batch from a new Protocol. Creates a new batch from a new protocol by opening the Settings tab of the Batches page.
Touring the Software View. Opens the Settings tab of the Protocols page to view the selected protocol. This tab enables viewing the settings, analytes, and plate layout for the selected protocol. Daily Activities. Contains shortcut buttons to common commands in the xPONENT® software: • System Initialization - Opens the System Initialization command in the Auto Maint tab on the Maintenance page. For more information about this tab, see “Auto Maint Tab” on page 61.
Luminex xPONENT 3.1 Software Manual Samples Tab FIGURE 5. Samples Tab This tab contains the following: Create New Samples. Opens the Create Sample tab. Sample Lists. Contains a list of protocols, including the version number and the number of samples associated with each protocol. Details. Opens the Edit Samples tab to view or edit sample details for the selected protocol. Create Batch. Opens the Protocol tab to create a batch.
Touring the Software Create Sample Tab Use this tab to type and view sample information. FIGURE 6. Create Sample Tab This tab contains the following: Protocol. Displays the protocol selected in the Samples tab. If xPONENT has an LIS license enabled, any sample details provided by the LIS also appear in the Sample list. Version. Displays the protocol version number. It is not editable.
Luminex xPONENT 3.1 Software Manual Undo. Reopens the Create Sample tab without saving any changes made using the Edit or New buttons. Save. Saves changes made to the Sample list. Close. Returns to the Samples tab. Batches Use the Batches page to create and run a new batch from an existing protocol, a new batch from a new protocol, or a new multi-batch. This page contains the following tabs: • Protocol - Displays when the Create a New Batch from an existing Protocol button is clicked.
Touring the Software Create a New Batch from an existing Protocol. Opens the Protocol tab, where you can create a new batch from an existing protocol. For more information, see “Create a New Batch from an existing Protocol” on page 18. Create a New Batch from a new Protocol. Opens the Settings tab, where you can create a new batch from a new protocol. For more information, see “Create a New Batch From a New Protocol” on page 24. Create a New Multi-Batch.
Luminex xPONENT 3.1 Software Manual Create a New Batch from an existing Protocol Creates a new batch from an existing protocol. The Protocol tab opens. Protocol Tab Use this tab to name a batch, type a description, select a protocol, and view active reagents. FIGURE 8. Protocol Tab This tab contains the following: Batch Name/Description. Used to name and describe a batch. Select a Protocol. Contains the protocol name, version, manufacturer, and creation date for each protocol. Active Reagents.
Touring the Software Stds & Ctrls Tab Use this tab to apply a kit or lot to the batch. FIGURE 9. Stds & Ctrls Tab This tab contains the following: Apply Std/Ctrl Kit. Opens the Select Std/Ctrl Kit dialog box. The dialog box displays the Std/Ctrl Kit Lot #, Std/Ctrl Kit Name, Expiration, and Manufacturer for the kit. Select a Std/Ctrl kit from the list and then click OK to close the dialog box. The kit information will display in the boxes to the right of the Apply Std/Ctrl Kit button.
Luminex xPONENT 3.1 Software Manual • 1:10 (Log) - Computes a value of one-tenth of the standard from each previous iteration. • 1/2 Log - Creates a 1:3.16 dilution, or half of each 1:10 (Log) from each previous iteration. • Alternatively, type a number for your own dilution factor. • Apply Dilution - Applies the dilution selected in the Dilution list. NOTE: Click a column header to resort the display.
Touring the Software Plate Layout Tab Use this tab to define commands that apply to one or more wells. You can define maintenance commands. FIGURE 10. Plate Layout Tab This tab contains the following: Plate Image. This is a representation of the plate. Each well appears as a circle on the grid. Well commands appear in the appropriate circles as you assign them to wells on the plate. Command Sequence. Contains the command sequence for the active plate.
Luminex xPONENT 3.1 Software Manual You can assign the following well commands. Each command is associated with a color. You can click and drag to highlight a series of wells, click a column or row header to highlight the entire column or row, or simply click and highlight different wells and then click a command below to assign that command to all the highlighted wells.
Touring the Software Plate Navigation. Displays a smaller plate image for the current batch. Single Step. Instructs the system to acquire one well and then stop. Use this to ensure the system is working correctly before you run the whole batch. Off Plate Area. Designates an alternate location for maintenance commands in the Commands: list. Highlight a command, and then click the reservoir in the Off Plate Area to select a location for the command. Save Prtcl.
Luminex xPONENT 3.1 Software Manual Run Batch. Runs the batch and opens the Current Batch tab, where you can monitor the batch as it runs. Create a New Batch From a New Protocol Click Create a New Batch from a new Protocol to create a new batch without using a protocol. The Settings tab opens. Raw data results write to a .CSV file. You can define parameters for samples, gates, regions, events, and commands.
Touring the Software • Timeout - Select Enabled to enable a timeout. Acquisition stops once the timeout is reached. Type a value from 1 to 250 seconds. • XY heater - Select Enabled to enable the XY heater. In the box, type the desired value in degrees Celsius. The temperature range is 35 to 60°C in 0.5 increments. WARNING: Acquiring data before the heater has reached the proper temperature can compromise test results. • DD gating - Use this to set the minimum and maximum DD gating values.
Luminex xPONENT 3.1 Software Manual ^ f) and the widely used Logic 5P regression fomula is calculated as y = a + ((b-a)/(1 + ((x/c) ^ d )) ^ f). NOTE: Luminex recommends Fit of All Standards as the most accurate calculation of the curve fit. Based on a range of quantitative, numerical results, a threshold range can be applied to a quantitative analysis, for example, high, low, saturated, and expected. • Allele Call - Sets analysis for an allele call. Analytes must put in groups of 2, 3, or 4 analytes.
Touring the Software Analytes Tab Use this tab to select or edit analytes used in the batch or protocol. FIGURE 13. Analytes Tab This tab contains the following: Analyte grid. A grid representing each analyte from 1 to 100. Select All selects all analytes, and Deselect All deselects all analytes. Click a numbered analyte to select it; click the analyte again to deselect it. You can also click and drag to select groups of analytes. Selected analytes are red. Deselected analytes are gray.
Luminex xPONENT 3.1 Software Manual FIGURE 14. Analysis Settings Dialog Box If you selected Quantitative on the Settings tab, the default analysis formula is 5P weighted. To change the default, select one of the following from the Method list: • No Analysis • Cubic Spline • Linear Fit • Logistic 4P • Logistic 5P • Luminex Logistic 4P • Luminex Logistic 5P If you select Logistic 4P, Logistic 5P, Luminex Logistic 4P or Luminex Logistic 5P, select a weight type of either None or 1/Y2.
Touring the Software sets that are not in the sample. Therefore, choose only the bead sets present in your sample. Apply All. Applies the information in the Units and Count boxes to all analytes. Total Count. Select Stop after bead count reaches: to stop acquisition when the bead count reaches a certain number determined by the user. Type the desired value in the box. The default value is 100. You can also specify the minimum allowable bead count per well that the xPONENT® software analyzes.
Luminex xPONENT 3.1 Software Manual • Add a range to the analysis by clicking Add Range. • Select Use Threshold Ranges to enable ranges for the analysis. • Click Add Range to add a range. • Type a Range Name, a Low Value, a High Value, and select Inclusive if you wish to include the low and high values in the range. Click OK to exit the dialog box. • Units - The unit of measurement you specified in the Unit box. Click this box to type a value for the analyte.
Touring the Software Stds & Ctrls Tab If you have specified standards and controls, use this tab to apply a lot or a kit. For more information about the functionality of this tab, see “Stds & Ctrls Tab” on page 19. FIGURE 16.
Luminex xPONENT 3.1 Software Manual Plate Layout Tab Use this tab to select wells to add samples and maintenance commands to the plate. For more information about the functionality of this tab, see “Plate Layout Tab” on page 21. FIGURE 17.
Touring the Software Create a New MultiBatch Use this button to add or remove pending batches to the multi-batch set up and to run a multi-batch. A multi-batch is composed of one or more pending batches which, together, will fit on one plate. Use the multi-batch feature to conserve plates. NOTE: FIGURE 18. You must first create and save pending batches, ensuring that wells do not overlap. If an overlap exists, edit the pending batch and select a new “Start at” well.
Luminex xPONENT 3.1 Software Manual Results Once data is collected in a batch, observation and analysis take place in the Results page. This page contains the following tabs: • • • • • • • • Current Batch Saved Batches Results Settings Log Sample Details Reports LIS Results Current Batch Tab Use this tab to view results, statistics, and log information related to the current batch, and to perform statistical analysis on batch results.
Touring the Software Statistic. To view a particular statistic for analytes in a batch, select one of the following: • Median - The point in a data set where there are as many values occurring above it as there are below it. • Test Result - The calculated analysis value for quantitative or qualitative assays derived from standards with known values. • • • • Count - Gated events, if gates are set. Net MFI (Median Background) - Net MFI median background. Mean - Average of all values in a set of results.
Luminex xPONENT 3.1 Software Manual Plate. A list of the available plates (if more than one). WARNING: If using multiple plates, be careful to ensure that plates are used in the proper order. Failure to do so can result in inaccurate data and test results. Histogram/Dot Plot. Displays real-time monitoring of batch sampling during acquisition.
Touring the Software NOTE: Gate positions are dependent upon buffer composition. Any changes made to your assay buffer composition may result in a different optimal gate location. Right-click inside the histogram area to access the following options: X Axis - Use this to change the X axis to the following: Doublet Discriminator, Reporter 1, Classification 1, and Classification 2. Doublet Discriminator is the default. NOTE: You can change the X axis of the histogram for troubleshooting purposes.
Luminex xPONENT 3.1 Software Manual • Yellow - Well acquired, but the system detects a possible problem (select the Log tab for more information). • Green - Well acquired successfully. • Red - Well acquisition unsuccessful, the system may have stopped, depending on the circumstances (select Log tab for more information). Default. Returns to the histogram and dot plot display. Saved Batches Tab Use this tab to open a batch that has been run, and view its details, export, approve, or replay a batch.
Touring the Software FIGURE 21. Filter Setup Dialog Box This dialog box lets you choose the saved batches you want to display in the Completed Batches list based on options you select or clear in the following check boxes: • • • • • • • • • • • Batch Name Protocol Batch Status Lot ID Kit ID Analyte Sample ID First Name Last Name User ID Date Reset - Clears all check boxes. OK - Closes the dialog box and applies any changes you made. Cancel - Closes the dialog box and cancels any changes you made.
Luminex xPONENT 3.1 Software Manual Exp Results. Opens the Save As dialog box to choose an export destination for the .CSV file containing your results. Import. Opens the Open dialog box to choose a batch file (.mdf) to import. Select Include Raw Files (LXB) to import the raw data file as well. Export. Opens the Export Batch dialog box to choose a destination for the batch file (.mdf). Select Include Raw Files (LXB) to include the raw file in the export. Select Overwrite to overwrite pre-existing files.
Touring the Software protocol. The functionality of the tabs you see while configuring the replay batch is the same as described in “Batches Tab” on page 16. Open. Opens the Results tab. Use this tab to view the saved batch results for the selected batch. Results Tab FIGURE 23. Results Tab The Results tab has the same Save Image, Progress, and Well Report buttons as the Current Batch tab. For more information about these buttons, see “Current Batch Tab” on page 34.
Luminex xPONENT 3.1 Software Manual • Analyze - Analyzes data that has been invalidated. This button only appears if you have clicked Invalidate on a portion of the data, or if you have clicked Validate on an invalidated portion of the data. This will analyze the data again with the invalidated standard removed. • Close - Closes the batch and reopens the Saved Batches tab. Settings Tab Use this tab to view the acquisition parameters of the selected saved batch and print the batch settings report.
Touring the Software Log Tab This tab displays a log of the activity which occurred during the acquisition of the selected batch. FIGURE 25. Log Tab This tab displays the following information about each activity: • Date • Message • Code Log entries display yellow if a well was acquired but there was a possible problem. They display red if the acquisition was stopped due to a problem. Print. Prints the log. Export. Opens the Save As dialog box to save the batch log file.
Luminex xPONENT 3.1 Software Manual Sample Details Tab Use this tab to view sample results. FIGURE 26. Sample Details Tab Arrows. Scrolls through the sample details. Transmit. For systems configured for LIS transmission, select a single analyte or the entire sample and click Transmit to send the results. Close. Reopens the Saved Batches tab.
Touring the Software Reports Tab Use this tab to view, generate, and print reports. FIGURE 27. Reports Tab Report and Type lists. Choose a report from one of the following categories: • Batch Reports - A list of batches appears below the Type list. The list includes Name, Protocol, Protocol Version, Date, Status, and User information.
Luminex xPONENT 3.1 Software Manual • New Report - Click to return to the main Reports window. NOTE: If running a data interpretation of an allele call batch report, be aware that when choosing analytes from the Select Analytes list, selecting one analyte will select all analytes in that group. • Protocol Reports - A list of protocols displays. Choose from the following reports: • Protocol Settings • Plate Layout • Protocol Audit Select a protocol and then click Generate to generate the report.
Touring the Software LIS Results Tab This tab displays saved batches containing LIS samples. FIGURE 28. LIS Results Tab Filter. Opens the Filter Setup dialog box. For more information, see Figure 21 on page 39. Clear. Click to turn off the filter. Completed Samples. Displays Name, Protocol, Sample Count, Date, Status, and User information for each batch displayed in this list. Transmit. Transmits a batch to an LIS if xPONENT is connected to one. Details.
Luminex xPONENT 3.1 Software Manual Protocols Tab Use this tab to create, import, export, edit, or delete a protocol. You can also add new assay standard and or control information using one of the installed protocols. FIGURE 29. Protocols Tab This tab contains the following: Create New Protocol. Opens the Settings tab to create a new protocol. For more information, see “Settings Tab” on page 49. Installed Protocols. Displays installed protocols.
Touring the Software tabs to return to the main Protocols tab, or Back to return to a preceding tab. The View option does not allow any changing of the protocol settings. Settings Tab Use this tab to name your new protocol and configure acquisition settings. FIGURE 30. Settings Tab This tab contains the following: Name and Description boxes. Type a name and a description in the appropriate boxes. Acquisition Settings.
Luminex xPONENT 3.1 Software Manual box, type the maximum value. The default minimum and maximum values are 7500 and 13500 respectively. • Reporter Gain - Select High PMT to increase the reporter gain level. Refer to assay application instructions for more detailed information. Analysis Settings. Use this section to set the analysis type, set the number of standards and controls, select an external analysis program, and choose whether to analyze results while acquiring samples.
Touring the Software • Number of Standards - Click to type the number of standards for the protocol. • Number of Controls - Click to type the number of controls for the protocol. • Fit of all Standards - The standard curve will be determined by using each individual standard replicate when calculating the standard curve. For example if one runs duplicates of a 7 point standard curve, the software will calculate the standard curve by using 14 points.
Luminex xPONENT 3.1 Software Manual click the analyte again to deselect it. You can also click and drag to select groups of analytes. Selected analytes are red. Deselected analytes are gray. An analyte marked as an intra-well normalization bead is blue. Default Analysis. The default analysis changes based on the Analysis Type you selected in the Settings tab. You can change the analysis settings for all analytes by clicking Change if the button is enabled in this tab.
Touring the Software Click Apply to All Analytes to apply your selection to all selected analytes. Click OK to change the default analysis to the analysis you selected. Click Cancel to close the dialog box without saving. For more information, see “Analysis Settings” on page 25. Units. Type the desired units for the analytes in this box. Count. Type the desired bead count for the analytes by clicking in the Count box.
Luminex xPONENT 3.1 Software Manual FIGURE 33. Analysis Settings Dialog Box • Select a method from the Method list. • If necessary, select a weight type from the Weight Type list. • Apply the analysis to all analytes in the list by clicking Apply to All Analytes. • Select Mark as Intra-Well Normalization Bead to make the analyte an intra-well normalization bead. • Add a range to the analysis by clicking Add Range. • Select Use Threshold Ranges to enable ranges for the analysis.
Touring the Software Cancel. Click to return to the Protocols tab. Back. Click to return to the Settings tab. Next. Click to go to the next tab. Plate Layout Tab Use this tab to define commands that apply to one or more wells. You can define commands. FIGURE 34. Plate Layout Tab This tab contains the following: Plate Image. This is a representation of the plate. Each well appears as a circle on the grid. Well commands appear in the appropriate circles as you assign them to wells on the plate.
Luminex xPONENT 3.1 Software Manual Grouping. Selects the sequence in which the replicates are laid out in plate wells. The options are: • 123123123. . . Lays out one of each replicate set at a time in numerical order. • 111222333. . . Lays out all the replicates in a set before moving on to the next set in numerical order. You can assign the following well commands. Each command is associated with a color.
Touring the Software • Clear Command - Select a well and click Clear Commands to remove all maintenance commands from the well. Plate. Specifies the plate you want to display in the plate image in the list. Add Plate adds a new plate to the batch, and Delete Plate deletes the plate highlighted in the list. Direction. Specifies the direction to run the plate commands. Select either horizontally or vertically.
Luminex xPONENT 3.1 Software Manual This tab contains the following: Create New Std/Ctrl Lots. Opens the Std/Ctrl Details tab to create a new lot or kit. For more information, see “Std/Ctrl Details Tab” on page 59. Installed Kits And Lots. Displays information about the kits and lots currently installed on the system. • Show - Click either Std/Ctrl Kits Only or All Lots to choose what to display. • Group lots from the same Std/Ctrl Kit together - Select to group lots from the same kit together.
Touring the Software Std/Ctrl Details Tab The Std/Ctrl Details tab lets you create or edit a standard and control lot. You can also group a lot as a kit. FIGURE 36. Std/Ctrl Details Tab This tab contains the following: Apply Std/Ctrl Kit. Opens the Select Std/Ctrl Kit dialog box. The dialog box displays the Std/Ctrl Kit Lot #, Std/Ctrl Kit Name, Expiration, and Manufacturer for the kit. Select a Std/Ctrl kit from the list and then click OK to close the dialog box.
Luminex xPONENT 3.1 Software Manual • 1:10 (Log) - Computes a value of one-tenth of the standard from each previous iteration. • 1/2 Log - Creates a 1:3.16 dilution, or half of each 1:10 (Log) from each previous iteration. • Alternatively, type a number for your own dilution factor. • Apply Dilution - Applies the dilution selected in the Dilution list. NOTE: Click a column header to resort the display.
Touring the Software Auto Maint Tab This tab contains routines to initialize, verify, and maintain the analyzer. FIGURE 37. Auto Maintenance Tab Automated Maintenance Options. Provides buttons for commonly used maintenance routines for the machine. Select from the following: • System Initialization - Select this routine to use with the System Initialization kit. • Performance Verification - Select this routine to use with the Performance Verification kit.
Luminex xPONENT 3.1 Software Manual Import Kit. Opens the Import Calibration or Performance Kit dialog box. Select a kit and click Open to import a kit. Run. Initiates the selected routine. Lot Management Tab Use this tab to manage calibration and verification kits. FIGURE 38. Lot Management Tab Active Reagents. Use this section to change calibration or performance verification kits, lot numbers, and expiration dates, or to delete a kit. • Calibration Kit - Select a calibration kit from this list.
Touring the Software • Calibrator - If a calibration reagent is selected, the Lot Details table displays Channel and Target information. • Verifier - If a verification reagent is selected, the Lot Details table displays target information. Import Kit. Opens the Import Calibration or Performance Kit dialog box to import a kit. Import. Opens the Import Calibrator or Verification Lot dialog box to import a lot. Export. Opens the Export Calibrator or Verification Lot dialog box.
Luminex xPONENT 3.1 Software Manual • • • • • • • • • • Daily Instrument Shutdown (Luminex) Daily Instrument Startup (Luminex) Fluidics Maintenance (Luminex) None Prepare for Storage (Luminex) Remove Air Bubbles (Luminex) Remove Clog (Luminex) Revive After Storage (Luminex) Sanitize (Luminex) Weekly Maintenance (Luminex) Commands. This section contains the following commands: • Wash - Sends distilled water through the fluidic lines in the system.
Touring the Software • • • • Flash memory • • • • • • • • DSP run Microcontroller RAM Nonvolatile memory DSP CRC High voltage Background Pressurization Actuator Syringe Debubbler Backflush valve NOTE: You should perform a Self Test as part of your scheduled weekly maintenance. Click a command to add it to a new routine, or to run the single command. It will appear in the plate image to the right of the Commands.
Luminex xPONENT 3.1 Software Manual Probe and Heater Tab Use this tab to adjust the probe height and plate heater settings. FIGURE 40. Probe and Heater Tab Move Probe Down. Moves the probe down in the specified well(s). Plate Type. Defines the selection of either a 96-well plate or an Automated Maintenance plate. Plate Image. Identifies the location used to adjust the probe height. Clicking a well selects it and marks it with a blue pin. Plate Heater.
Touring the Software System Info Tab Use this tab to view information and diagnostics about the Luminex instrument. FIGURE 41.
Luminex xPONENT 3.1 Software Manual • • • • • • • • • Delta Calibration Temp System Temperature DD Temperature CL1 Temperature CL2 Temperature CL1 Voltage CL2 Voltage DD Voltage RP1 Voltage Items in this list relating to CAL/CON calibration and controls have one of the following states: • Passed - Indicates that the process completed successfully. • Failed - Indicates that the process was not completed successfully. Failed items appear in red. • Not Current - Indicates that verifiers are not current.
Touring the Software System Status Tab Use this tab to view, print, and save system status log information. You can also access this information by clicking the System Status button on the System Monitor. For more information, see “System Status” on page 10. FIGURE 42. System Status Tab This tab contains the following: Search By Log Type. Filters the type of log information. Select All, Maintenance, Security, or Warnings and Errors. Search By Log Date.
Luminex xPONENT 3.1 Software Manual Schedule Tab Use this tab to view reminders for scheduled maintenance due to be performed on the analyzer. FIGURE 43. Schedule Tab The Reminders section displays Subject, Reminder, Next Alert Date, Alert Time, and Notes. This schedule can be changed using the Schedule tab of the Admin page. For more information, see “Schedule Tab” on page 86.
Touring the Software FIGURE 44. Support Utility Tab This tab contains the following: Name, Phone, Company, and Email. Type your information in these boxes so that Luminex Technical Support can contact you. Clear. Clears all information in the Name, Phone, Company, Email, and Comment boxes. Comment. Type any comments in this box. Include Batch info. Includes batch information from a selected batch in the Support Utility.zip export folder. Select Batch. Displays a list of all batches.
Luminex xPONENT 3.1 Software Manual • • • • • • • Batch Options Alert Options CSV Options Archive Licensing Schedule Report Options System Setup Tab Use this tab to configure system settings. FIGURE 45. System Setup Tab Application Settings These settings change some of the basic ways that xPONENT® works, allowing customization of many of the basic functions. Enable Virtual Keyboard. Enables the touchscreen virtual keyboard. Allow the application to be minimized.
Touring the Software Add header when exporting data from grids. Adds a header row when exporting the data. LIS Settings This setting is only for those using xPONENT® with a Lab Information System (LIS). Connect to LIS. Enables connection to the LIS. Browse. Opens the Browse For Folder dialog box. Select a location for the system to watch for incoming orders. External Analysis Program Settings This option is for those using a program other than xPONENT to analyze collected data.
Luminex xPONENT 3.1 Software Manual Set Default. Sets the chosen analysis program as the default analysis program for xPONENT. OK. Saves the chosen settings and exists the dialog box. Cancel. Cancels changes and exits the dialog box. Remove. Removes the selected program from the Installed Analysis Programs list. Edit. Opens the New External Analysis Program dialog box where you can edit the settings for the selected program.
Touring the Software Group Setup Tab This tab is accessible only in the Security or 21 CFR Part 11 packages. Use this tab to assign permissions to different groups of users. Additionally, if you have the 21 CFR Part 11 package, you can require an electronic signature in order to perform selected tasks. NOTE: FIGURE 47. The 21 CFR Part 11 package also provides full access to the Secure Package functionality. Group Setup Tab Users are assigned to groups.
Luminex xPONENT 3.1 Software Manual • • • • • • System Administration Batch Management Protocol Management Lot and Std/Ctrl Kit management Import and export data Archiving The Allowed check box next to the desired permission in the Features section enables the selected group to perform that task. The Signature Required check box next to the desired permission requires a digital signature whenever a user in the selected group performs that task.
Touring the Software Lot and Std/Ctrl Kit Management • Create Std/Ctrl Kit and Lots • Edit Std/Ctrl Kit and Lots • Delete Std/Ctrl Kit and Lots Import and Export Data • Export Batch, Protocol, Std/Ctrl Kit/Lot Files • Import Batch, Protocol, Std/Ctrl Kit/Lot Files Archiving • Archive backup • Archive delete When you perform an action that requires an electronic signature, the Electronic Signature dialog box opens. The user ID autopopulates. Type your password and any comments.
Luminex xPONENT 3.1 Software Manual This tab contains the following: Create New User. Opens the Create User Account screen. Create User Account Screen Use this tab to set the options for a new user. Any user with access to this tab can assign rights to any and all groups. FIGURE 49. Create User Account Screen This tab contains the following: User ID. Type a user ID in this box. The user ID is not case-sensitive. You can change the required number of characters on the User Setup tab.
Touring the Software Save. Saves and returns to User Setup. Cancel. Returns to User Setup without saving. Global User Settings. This section contains the following: • Password Expiration - Type a length of time in days. The default is 180 days. • Unsuccessful Login Attempts - The default number of allowed unsuccessful logins is three attempts. • Automatic Logoff (seconds) - How many seconds pass until an automatic logoff. • Minimum User ID Length - The default minimum User ID length is six characters.
Luminex xPONENT 3.1 Software Manual This tab contains the following: Batch Options. This section displays the following options: • Allow canceling the warmup time to run batch - Allows batches to be run without system warmup. • Allow canceling the warmup time to run calibration - Allows calibration without system warmup. • Allow running a batch with expired reagents - Allows batches to run with expired reagents.
Touring the Software Alert Options Tab Use this tab to set options for alerts about various system events. FIGURE 51. Alert Options Tab Alert Options. Offers three check boxes for each alert - Dialog, Email, and Sound. This section displays the following events: • • • • • • • • • Locked User - The user is locked out of the login. Batch Complete - The batch is finished. Warmup Complete - The laser is warmed up. Heater In Range - The plate heater is warmed to the designated range.
Luminex xPONENT 3.1 Software Manual FIGURE 52. Setup Email Dialog Box Enable or disable email notification by selecting or clearing the Email Active check box. Contact your network administrator to determine the information needed in the Mail Server Host, From Email Address, From Email Password, and Mail Server Port boxes, and if you need to select the Enable SSL (Secure Sockets Layer) check box. The Test button tests the email settings.
Touring the Software CSV Options Tab Use this tab to set options for exporting batches to .CSV (comma separated values) files. FIGURE 53. CSV Options Tab This tab contains the following: CSV Export Options Automatically export results CSV file when batch is complete - Automatically exports the .CSV file when the system finishes analyzing the batch. This allows running programs on exported data without having to manually start the export.
Luminex xPONENT 3.1 Software Manual Archive Tab Use this tab to set options for backing up and restoring files. FIGURE 54. Archive Tab This tab contains the following: Archive. Use this section to choose file types to archive destinations for the archive file. This section contains the following: • File Type - Choose from Protocols, Batches, Std/Ctrl Kits, Lots, Patient Samples, or Log. The selected information appears in the list below the Archive Folder path.
Touring the Software Import. Select a file type to import in the File Type list and click Import to import all files of that type from the archive. The imported files will then display in the list below the Archive Folder path. Archive. Select a file type in the File Type list, and then select a file in the list below the Archive Folder path and click Archive to archive the file. If you have selected Keep data after archive, the file will still display in the list, otherwise it will no longer be displayed.
Luminex xPONENT 3.1 Software Manual Export. Opens the Save As dialog box to select an export name and location. License. Opens the Change License dialog box. • Type the file path for the license file in the License File box, or use the Browse button to display the Open License dialog box and navigate to the file. You can also update the xPONENT® license status by manually typing the license code in the License Code box. It is not necessary to update both the license file and the license code.
Touring the Software Report Options Tab Use this tab to change the look of reports generated by the system. FIGURE 57. Report Options Tab • Company - Type the company name you wish to display on reports. • Info - Type any information you wish to display below the company name. • Import Logo - Displays the Open dialog box and selects the file you wish to use for the logo at the top of reports. • Clear Logo - Returns to the default logo. Cancel. Cancels changes. Save. Saves changes.
Luminex xPONENT 3.
CHAPTER 3 Using the Software This chapter describes the steps needed to successfully use the xPONENT® software. Starting the Software When you turn on the computer for your Luminex system, xPONENT should launch automatically. If it does not, click the Luminex xPONENT icon on the PC desktop, or click Start>Programs>Luminex>xPONENT>Luminex xPONENT. If you have a trial license, a dialog box opens. Click OK to close the dialog box.
Luminex xPONENT 3.1 Software Manual To display software information, click the blue question mark at the top of the xPONENT window, then click About Luminex xPONENT. The xPONENT information dialog box opens, displaying the software version information. Setting Administrative Options Click Admin on the toolbar to display the tabs used to set administrative options. System Setup You must have xPONENT administrative privileges to perform System Setup tasks.
Using the Software 4. Click Browse to navigate to the .exe file for that program. Double-click on the file name. 5. Type the command line parameter for what parameters you want xPONENT® to use with the external analysis program. If the information is supplied with the external analysis program documentation, use that information. Otherwise, you can type the following parameters built into xPONENT, in any order: • • • • #c - Output.csv, full file path. #p - Protocol name. #b - Batch name.
Luminex xPONENT 3.1 Software Manual original file. In addition, when batch, template, or protocol files are converted, the microsphere count may be converted automatically to 100. To convert an earlier version of data: 1. Click Open to open the xCONVERT Utility dialog box. 2. Click ... in the Source File box to navigate to the source file you wish to convert. 3. Click ... in the Destination Folder box to navigate to the output location for the file conversion. 4. Click Convert to convert the source file. 5.
Using the Software 3. Type the user’s name in the Name box. 4. Type a password for the user in the Password box, then re-type it in the Reenter Password box. If you want the user to change the password on first login, select Change password after first login. 5. In the Group Profile list, select the role for the user you are creating. 6. Click Save. Editing User Permissions In the Users list, click the user ID, then click Edit User.
Luminex xPONENT 3.1 Software Manual ".CSV" file will contain, and where it will be stored. For more information on this tab, see “CSV Options Tab” on page 83. To set CSV Options: 1. In the CSV Export Options section, select the CSV Options you want to apply to the CSV file. If you select Maximum number of data columns in CSV file, type the maximum number of columns. 2. In the CSV File Export Folder box, type the location to which you want the file sent, or click Browse to navigate to the folder. 3.
Using the Software To restore the system using a backup file: 1. Click Restore. A Warning dialog box displays. CAUTION: All data and settings will be overwritten, and xPONENT® will restart once the restore task completes. 2. Click OK to continue restoring the system. The File Dialog box opens. The most recent backup file displays in the File Name box. To use a different backup file, click Browse to navigate to a different file. 3. Click OK to start the restore.
Luminex xPONENT 3.1 Software Manual 2. Click Import Logo and then Open after navigating to the desired file to import a graphic for the report header. 3. Click Clear Logo to remove the logo. 4. Click Save. Adjusting the Sample Probe Adjust the sample probe to ensure that it drops far enough into the well to acquire sample. NOTE: Ensure that there is no liquid in the wells or reservoirs. NOTE: You should adjust the probe height using row A unless you are using the Automated Maintenance Plate.
Using the Software System Initialization xPONENT® Software contains a pre-defined startup routine to prepare the analyzer for data acquisition.This section describes warmup, calibration, and performance verification of the system. Warm up the lasers to prepare the optics prior to sample acquisition. The system automatically begins warming up when you turn power on; however, you will need to use the Warmup command if the system is idle for four hours or longer.
Luminex xPONENT 3.1 Software Manual 4. Vortex the xMAP calibrator, verification, and fluidics containers to ensure homogeneity. Do not dilute xMAP calibrator or verification agents. 5. Click Eject on the status bar, then place the microtiter plate on the plate holder. 6. Load a microtiter plate with at least five drops of the beads in the Calibration and Performance Verification kit as indicated on the plate image and in the kit insert instructions. 7. Click Retract. 8. Click Run.
Using the Software Create Calibration Reports 1. Open the Results page, then open the Reports tab. 2. In the Report list, click Calibration Summary. 3. In the Type list, click the calibrator or verifier for which you want to create a report. 4. In the Dates list, select a start date for the date range you want to view. 5. 6. 7. 8. 9. In the Through list, select the end date for the date range you want to view. Click Generate to display the desired report.
Luminex xPONENT 3.1 Software Manual Setting Up Batches A batch consists of a group of samples processed under control of a protocol. Batches consist of protocols and samples for acquisition and can span more than one plate. Protocols contain predefined commands that must be included in every batch acquisition. You can also set up a custom batch that does not use a protocol. You can group batches together as a multi-batch.
Using the Software NOTE: If the batch spans more than one plate, the tray ejects automatically when all defined wells have been acquired. A dialog box displays prompting you to insert the next plate. Create a New Batch from a New Protocol This option creates a new batch to acquire data without using an existing protocol. It writes raw data results to a simple ".CSV" file format. You can define parameters for samples, gates, regions, events, and commands.
Luminex xPONENT 3.1 Software Manual • To add well commands, click the appropriate wells and mark them as unknown, standard, control, background, or wash. You can also delete commands that you’ve added and change the starting location on the plate. If you wish to run in replicate, change the Replicate Count to the appropriate number and the Grouping to your preferred grouping method. • To add maintenance commands, choose the desired command from the list.
Using the Software 4. Navigate to the location in which you want to save the file, then click Save. Click OK in the Export Batch dialog box. NOTE: When exporting a large batch and including the LXP files, such as a batch with hundreds of wells, the export process may take ten minutes or more. Delete Batch You can only delete unprocessed batches. Batches are deleted from the Open Batch list and moved to the Open Incomplete Batch list. 1. Open the Batches page. 2.
Luminex xPONENT 3.1 Software Manual Qualitative Analysis. Determines results as either positive or negative, reactive or nonreactive, and so on. The system is flexible in defining custom result ranges, such as negative, low positive, and high positive. Quantitative Analysis. Determines the sample concentrations from standard curves using regression methods, such as 4P or 5P logistic curve fitting. There are two main assay types: non-competitive and competitive.
Using the Software from the Show list, and enter the low value for each analyte. Click High Value from the Show list, and enter the high value for each analyte. Reagent information is not required to replay a custom batch, unless you want to use the analysis feature. 10.Click Next. 11.In the Plate Layout tab, you can do the following: • To add well commands, choose the appropriate wells and mark them as unknown, standard, control, background, or wash.
Luminex xPONENT 3.1 Software Manual Invalidate Standards and Controls Your xPONENT system administrator must give you privileges to invalidate standards if you are using the Secure xPONENT package. You can invalidate or remove a standard if doing so improves the curve fit. CAUTION: Observe caution when invalidating standards. Doing so greatly affects the curve fit and subsequent sample results.
Using the Software View and Print Reports The Luminex xPONENT software can format your batch or multi-batch results in a variety of export formats and provide different types of information in different types of reports. Three types of reports are available. See “Reports Tab” on page 45 for a description of available reports. NOTE: Install the printer before initiating the Print command. 1. 2. 3. 4. Open the Results page, then open the Reports tab. In the Report list, click the report you want to view.
Luminex xPONENT 3.1 Software Manual Create Qualitative Assay Protocol You define each Qualitative protocol using a single kit. The kit must contain one standard. The standard is assigned a “Quali” value for each test. Controls are optional, but are recommended for judging the acceptability of batch results. 1. Open the Protocols page, then open the Protocols tab. Click Create New Protocol. The Settings tab opens. 2. In the Name box, type the name of the protocol. 3.
Using the Software 5. Type a new name for the edited formula in the Formula Name box. 6. Edit the values for each range in the Negative, Low Positive, or High Positive if you selected Lum Qual in the Formulas list, or Negative, Low Positive, Moderate Positive, or Strong Positive if you selected Adv Qual in the Formulas list. Select the check box in the Inclusive column to include the value in the range.
Luminex xPONENT 3.1 Software Manual WeightType list. Click Apply to All Analytes to apply the selection to all analytes. To edit an analysis setting, see “Edit Quantitative Analysis Settings” on page 110. 15.To change the analysis for a single analyte, click the Analysis field for the analyte you wish to modify. The Analysis Settings dialog box opens. 16.Select an analysis method in the Method list. 17.
Using the Software 3. From the Method list, click No Analysis, Cubic Spline, Linear Fit, Logistic 4P, Logistic 5P, Luminex Logistic 4P, or Luminex Logistic 5P. 4. From the Weight list, click None or 1/Y^2. NOTE: The Weight options are only available if the chosen Method is Logistic 4P or Logistic 5P. 5. Check Mark as Intra-Well Normalization Bead if you wish to use a normalization bead. The normalization bead is a microsphere set that is included in the assay as an internal control.
Luminex xPONENT 3.1 Software Manual • To add well commands, highlight the appropriate wells and mark them as unknown, standard, control, background, or wash. You can also delete commands that you’ve added, and change the starting location on the plate. If you wish to run in replicate, change the Replicate Count to the appropriate number and the Grouping to your preferred grouping method. • To add maintenance commands, choose the desired command from the Command list.
Using the Software Edit Protocol 1. 2. 3. 4. 5. 6. 7. Open the Protocols page, then open the Protocols tab. Select a protocol. Click Edit. The Settings tab opens. Define settings and click Next. The Analytes tab opens. Define analytes and click Next. The Plate Layout tab opens. Define the plate layout. Click Save. Lots and Kits You can edit standard and control lot information. Once a lot is used, changing or modifying it will prompt you for a new lot name.
Luminex xPONENT 3.1 Software Manual 3. If the protocol uses standards, type the appropriate information for each standard in the Assay Standard Information section. In each analyte column, type the expected concentration for the analyte. 4. Alternatively, click Apply Std/Ctrl Kit and select a lot from the Select Lot dialog box. Click OK to apply the lot. 5. If your batch uses controls, select Expected, Low, or High from the Show Value options.
Using the Software WARNING: Lack of proper maintenance can lead to inaccurate test results and failure of system components. Please follow all scheduled maintenance routines to ensure proper functioning of equipment. Perform System Calibration Perform system calibration weekly. In addition, recalibrate the system if the delta cal temperature exceeds +/-3ºC. For further information, see “System Initialization” on page 97.
Luminex xPONENT 3.1 Software Manual Run Routine 1. 2. 3. 4. Open the Maintenance page, then open the Cmds & Routines tab. Select a routine to run from the Routine Name list. Click Eject on the status bar. Add the appropriate reagents to the plate, reservoirs, and well strips as indicated in the plate image and set the plate on the plate holder. 5. Click Retract. 6. Click Run. The Routine Message dialog box opens when the routine is complete. 7. Click OK.
Using the Software Shutting Down the Analyzer 1. On the Home page, click Shutdown. The Auto Maint tab opens, with System Shutdown selected. 2. Refer to the Automated Maintenance plate depiction in the lower right of the Auto Maint tab. Fill the well indicated in this depiction with a 10% to 20% household bleach and water solution. 3. Add deionized water to the reservoir. 4. Click Run.
Luminex xPONENT 3.
Glossary 21CFRPart11 21 CFR Part 11 sets the criteria under which the Food and Drug Administration (FDA) considers electronic records, electronic signatures, and handwritten signatures executed to electronic records to be trustworthy, reliable, and generally equivalent to paper records and handwritten signatures executed on paper. agglutination The coalescing of small particles that are suspended in solution; these larger masses are then (usually) precipitated.
Luminex xPONENT3.1 Software Manual two classification dyes. The unique ratio is identified by a unique spectral address. Also sometimes called microsphere set, microsphere region, or test by the software during acquisition. calibration A process used to normalize the settings for the reporter channel, both classification channels, and the doublet discriminator channel for the Luminex System. Calibration ensures optimal and consistent microsphere classifications and reporter readings.
Glossary DD temperature The current temperature of the doublet discriminator avalanche photo diode. dot plot Graphical representation of microsphere analysis classification data displayed by frequency and intensity. doublet discriminator (DD) A classification channel measuring side scatter; used to filter for single bead events based on size. emission spectrum Wavelength range that an excited fluorochrome emits when its electrons fall from a higher to a lower energy state.
Luminex xPONENT3.1 Software Manual multi-analyte microspheres. laser Light Amplification by Stimulated Emission of Radiation. This highly purified source of light is an efficient way to excite fluorochrome electrons. LIS Laboratory Information System; A system for storing sample records and test requests. lot A reagent with specific target values used for analysis or calibration.
Glossary Qual A value that determines a cutoff or threshold. This, in conjunction with ranges using the Lum Qual Formula, Adv Qual Formula, or an edited range specific for your assay, helps to determine qualitative results for unknown samples. qualitative Pertaining to calculations that determine the absence or presence of an analyte. quantitative Pertaining to calculations that determine the precise numerical measurement of an analyte. reagent A substance used to detect or measure other substances.
Luminex xPONENT3.1 Software Manual microspheres, assay. suspension Solution consisting of homogeneously dispersed microspheres in an aqueous medium. system controls Include the xMAP reporter and classification control microspheres. They are used to verify the calibration of the Luminex analyzer. template This is now called a protocol. test Each test represents an analyte and corresponds to a bead set. Each bead set falls into a particular location on the bead map.
Index A account status 93 Acquisition Settings panel 24, 49 Admin System Setup page 71 admin archive 94 Archive page 84 Batch Options page 79, 81, 86, 87 Create New User Account page 78 CSV Options page 83 group setup 92 Group Setup page 75 licensing 95 Licensing page 85 support utility 116 user groups 75 user setup 92 User Setup page 77 Analyte Settings 28, 52 analytes select 27, 51 statistics 35 Application Settings 90 B batch run 24 single step 23, 57 transmit 107 view and print reports 107 view logs 10
Luminex xPONENT 3.
Index third-party software 2 U user permissions 93 V validate standards 105 validation 77 W warmup 97 website 117 127
