Bio-Plex Manager™ MP Software User Guide Version 1.
Bio-Plex Manager™ MP Software User Guide Version 1.
Bio-Rad Technical Support Department The Bio-Rad Technical Support department in the U.S. is open Monday through Friday, 5:00 AM to 5:00 PM, Pacific Time. Worldwide technical support is available on the Web at www.consult.bio-rad.com. Phone: 1-800-424-6723, option 2 Fax: 1-510-741-5802 Email: LSG.TechServ.US@Bio-Rad.com (U.S.) LSG.TechServ.Intl@Bio-Rad.com (International) Web: www.consult.bio-rad.
Table of Contents Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7 Chapter 2 Creating Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9 About Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Navigating to the Protocol Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Creating a Protocol . . . . . . . . . . . . . . . . . . . . . . . . .
Table of Contents Reading the Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Raw Data Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Bead Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Interrupting a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Resuming a Run .
Table of Contents Chapter 5 Analyzing Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Chapter 6 Maintaining the MAGPIX System. . . . . . . . . . . . . . . . . . . . 57 Recommended Routine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 Daily Maintenance Routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Daily Start Up Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Table of Contents Chapter 7 Maintenance Routines . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 Calibration and Verification Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 Clear Bubbles Routine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Daily Start Up Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 Enhanced Maintenance Routine . . . . . . . . . . . . . . .
1 Introduction Bio-Plex Manager™ MP is an application that allows you to run and maintain your MAGPIX instrument. MAGPIX monitors the state of your instrument and recommends routines to keep the instrument in good working order, and it also recommends maintenance routines to resolve problems. With Bio-Plex Manager MP, you do not have to keep track of when to calibrate your instrument or verify the calibration settings. Its easy-to-use interface facilitates creating and running your protocols.
1 | Introduction Bio-Plex Data Pro is an optional software application that allows you to do further analysis of your results: Identify and group biological replicates Determine statistically significant changes Generate and export charts, heat maps, and tables Bio-Plex Data Pro (catalog #171-001513 and #171-001523) is a separate product that can be purchased from Bio-Rad. MAGPIX Operation Data Review and Optimization Bio-Plex Manager MP Bio-Plex Manager 6.
2 Creating Protocols About Protocols A protocol contains the parameters of a Bio-Plex Manager™ MP software run. It includes information about the analytes included in the run, the plate wells to be read, the concentrations of standards, and instrument settings. These parameters are saved in the result along with the data from the reading. You can save a protocol and reuse it or modify it for another reading. Each time you run the protocol, a new result is created and stored in the database.
2 | Creating Protocols Navigating to the Protocol Dialog Box Protocols are created from the protocol dialog box. There are a number of ways you can get to the protocol dialog box. To navigate to the protocol dialog box 10 1. Click Create/Run Protocols in the navigation bar. 2. Do one of the following: Click New. Click New From and select a protocol from the Select Protocol dialog box. With an open protocol in the Create/Run Protocols view, click Edit.
Creating a Protocol Creating a Protocol The following are the steps to create a new protocol. To create a new protocol 1. Click Create/Run Protocols in the navigation bar. 2. Click New to open the New Protocol dialog box. 3. Click the Assay Panel dropdown list and select an assay panel. 4. Select the analytes for your experiment. 5. Click Format Plate. 6. Format the wells to use in the experiment. For more information on formatting wells, see Formatting Plates on page 14. 7.
2 | Creating Protocols About Analytes Bio-Plex Manager MP software groups analytes by panels. Preconfigured panels of analytes that correspond to off-the-shelf Bio-Plex® assays can be selected. These assays include human, mouse, and rat cytokines and phosphoproteins, as well as the newer human angiogenesis, diabetes, isotyping, and acute phase assays.
Selecting Analytes Selecting Analytes After you select the assay panel you want to use in your experiment, you select the analytes you are interested in. To select an analyte 1. From the protocol dialog box, click Select Analytes. 2. From the Assay Panel dropdown list, select an assay panel. 3. Click the checkboxes to select the analytes to include in your protocol or click Select All to select all analytes. 4. Click OK.
2 | Creating Protocols Formatting Plates The array reader uses the plate formatting to identify which wells are to be read and Bio-Plex Manager MP uses it to determine how to analyze the different samples in each well. Note: Only formatted wells are read by the array reader. Undefined wells are not read. To format a plate 1. Navigate to the protocol dialog box. 2. Click Format Plate. 3. Click the button in the toolbar for the type of well you want to format. 4.
Formatting Plates The template diagram in the Create/Run Protocols view displays the formatted wells in your protocol and the raw data table is populated with the well location and sample type.
2 | Creating Protocols Well Types The following are different well types that you can specify on the plate: Blank Standard Control Undefined Unknown Blank Wells In certain types of assays, such as the Bio-Plex phosphoprotein assay, it might be useful to subtract the assay background from the readings of standards, controls, and unknown samples. Prepare blank wells that contain all of the assay components excluding the sample. Blank wells are read along with the rest of the assay.
Formatting Plates Unknown Wells The unknown wells contain samples of unknown concentration. These samples are taken from the subjects of your experiments. Undefined Wells Use the Undefined wells button to remove the definition of a well. Undefined wells are not read by the array reader. Autofilling Well Numbers Use the Autofill feature to quickly define a well type for multiple wells.
2 | Creating Protocols In the following example, Autofill Down was used to create 20 Unknown wells. Note, the numbering of the wells is top to bottom, then left to right. The arrow shows the path of the cursor as it is dragged across the plate template. Defining a Replicate Group You can quickly format a replicate group. To define a replicate group 1. Click Turn Autofill Off. 2. Click and drag your cursor over the wells that contain the same sample. The wells are labeled with the same number.
Formatting Plates 2. Click the Set Replicate Size dropdown list and pick the number of replicates in the group. Note: The maximum size you can specify with the Set Replicate Size dropdown list is eight. Tip: You can create replicate groups that are larger than eight by clicking Turn Autofill Off, setting the replicate size to 1, and selecting the number of wells you want in your replicate group. 3. Click the well type. 4. Click and drag your cursor over the wells on your plate.
2 | Creating Protocols Removing the Well Formatting Removing the formatting of a well returns it to its unformatted state. Unformatted wells are not read by the array reader. To remove the formatting of a well 1. Click Undefined. 2. Click and drag your cursor over the wells you want to clear. The formatting is removed and the wells return to their unformatted state. Changing the Well Formatting You can overwrite the formatting of a well by simply applying another sample type over the wells.
Selecting a Standard Lot Selecting a Standard Lot Before you can select the standard lot to use with your protocol, you must first select your analytes, format the standard wells, and create a standard lot for the assay panel you are using if one has not already been defined for your analytes. To select a standard lot for your protocol run 1. From the protocol dialog box, click Standards Info. The table displays the analytes you selected on the Select Analytes pane.
2 | Creating Protocols Only the standard lots that contain the selected analytes appear in the list. If the list is empty, then there are no defined standard lots that include the analytes you selected and you must create a standard lot. Or if the list does not include the standard lot you are using, then you must create a standard lot definition. For more information on creating standard lots, see Creating New Standard Lots on page 50.
Reusing a Protocol Reusing a Protocol You can use a saved protocol as a template for your experiment. You can make changes to a copy of the saved protocol — for example, you might change the number of unknown samples. To reuse a saved protocol 1. Click New From on the toolbar to open the Select Protocol dialog box. 2. Select the protocol you want to use and click OK. 3. In the protocol dialog box, make any changes to the selected analytes, the plate formatting, and the standards information. 4.
2 | 24 Creating Protocols | Bio-Plex Manager MP Software
3 Running Protocols Once your protocol is created, you are ready to run the protocol. The result is displayed in the raw data table and bead map and it can be exported to Bio-Plex Manager™ 6.x software for analysis. You can interrupt a run at any time, make any necessary changes to the protocol, and resume the run with no loss of data. Bio-Plex Manager™ MP software provides graphical clues and alerts informing you when it detects problems with your run.
3 | Running Protocols Plate Handling Guidelines Before starting the run, note the following plate handling guidelines and warnings: Protect your assay microspheres from light. Once photobleached, the beads are no longer usable. You must care for the microspheres properly to maintain your product warranty. When using a filter plate and wrapping the plate, avoid touching the bottom of the wells. The sample may wick or leak from the well bottom.
Plate Types Plate Types The plate height adjustment procedure adjusts the probe setting for four consumables, the well strip, and the reservoirs in the reagent block. When you run your protocol, you must specify one of the following plate types. Plate Type Compatible Consumable Distance from Platform (mm) * Flat bottom plate Bio-Plex Pro™ flat bottom plate (black plate comes with Bio-Plex Pro assays, catalog #171-025001) 3.94 Filter plate Millipore multiscreen plate (for example, MSBVN1210) 3.
3 | Running Protocols Using the Plate Heater For some experiments, for example nucleic acid testing, you may need to heat and maintain the temperature of the plate with the MAGPIX plate heater. You can turn the heater on from any view in Bio-Plex Manager MP and set the temperature of the plate from 35–60ºC in 0.5º increments. Note: While the plate temperature is being set, you cannot run your protocol. To use the plate heater 1.
Running the Protocol To run your protocol 1. In the Create/Run Protocols view, click Start. The microplate platform automatically ejects. 2. In the Run Settings dialog box, enter the name of the result in the Result Name box. The result name is the name that the data are stored under in the database. This name is case-sensitive and must be unique. Therefore, RESULT 1 is not the same as result 1. 3. (Optional) Enter the Plate ID.
3 | Running Protocols If you select a pre-run routine, refer to the Reagent Block diagram and fill the appropriate reservoirs with the specified fluids. 6. (Optional) In the Post-Run Routine list, select any routines you want executed after the protocol run. Note: Bio-Rad recommends you run the Wash Between Plates routine after each protocol run to prevent traces of sample or other debris from collecting inside the Bio-Plex® suspension array system.
Running the Protocol Reading the Plate In the template diagram in the Create/Run Protocols view, the blue wells indicate which wells have been formatted. Only formatted wells are read. Each well is read in turn, from top to bottom, then from left to right. A pulsing triangle shows you which well is currently being read. Protocol name Run commands status Template diagram Well E2 The Run Commands status displays information about the well that is currently being read.
3 | Running Protocols Once the reading for a well is complete, the pulsing triangle resolves into one of the following symbols indicating the result of the reading. Symbol Description The bead count for all analytes is 20 or higher. The bead count for one or more analytes is below 20 bead events. No data were found or an error occurred while reading the well. The results are displayed in the Raw Data table and the Bead Map.
Bead Map your analytes. The new analytes, if detected during the run, will then appear in the table. Column Heading Description Well Location of the well on the plate template. Type Identifies the type of well, Blank, Control, Standard, Unknown, and the sample. For example, C1 is the first control sample and S4 is the fourth standard sample. Total Events Total bead events recorded for that well, including unclassified events (events that fall outside the 50 regions).
3 | Running Protocols The x-axis is the Classification 1 channel and the y-axis is the Classification 2 channel. These channels measure the embedded fluorochromes in each bead, which are used to identify the bead set and corresponding analyte. The resulting data point clusters in the map represent the different bead sets in the assay and their associated analytes. Tip: Use Maximize View to expand the bead map to fill the entire window.
Resuming a Run When a sample is being read, the Start button changes to a Stop button. Note: When you click Stop, Bio-Plex Manager MP finishes reading the current well before it stops the run. Therefore, you may have to wait up to a minute before Bio-Plex Manager MP responds to another command. Resuming a Run You can interrupt a run and make changes to your protocol, including changing the analytes you are interested in or correcting the format of your plate.
3 | Running Protocols Encountering and Resolving Low Bead Counts Bio-Plex Manager MP notifies you when a low bead count is detected: The well with the low bead count displays a warning symbol. A warning symbol is displayed for the region in the Raw Data table if a low bead count occurred for that particular analyte. You can specify that Bio-Plex Manager MP stop the run if it encounters three or more consecutive wells with low bead count of less than 20.
Encountering and Resolving Low Bead Counts 1 2 3 LEGEND 1 Warning symbol indicating wells with a low bead count 2 Warning symbol indicating region in which there is a bead count of fewer than 20 beads 3 Asterisk (*) indicating region in which the bead count is lower than the recommended 50 beads Important: Bio-Plex Manager MP will provide warning messages when a low bead count occurs with recommended steps to resolve the problem.
3 | Running Protocols Run Results Table The data from each run are saved as a result in the MAGPIX database. Each result is a row in the run results table. The following table describes the information in the run results table.
Exporting Data to Bio-Plex Manager 6.x Exporting Data to Bio-Plex Manager 6.x Before data can be analyzed in Bio-Plex Manager 6.x, the Bio-Plex Manager MP run result must first be saved to a file. This file can then be exported to Bio-Plex Manager 6.x. You can export your results in either of the following ways: Export your results immediately following a protocol run from the Create/ Run Protocols view. For more information, see Exporting Data from the Create/Run Protocols View on page 40.
3 | Running Protocols Exporting Data from the Create/Run Protocols View You must first export the result to a file before you can analyze the data. To export data from the Create/Run Protocols view 1. From the Create/Run Protocols view, click Export Results. 2. In the Export Results dialog box, navigate to where you want the run result to be saved. 3. Enter the name of the file.
Exporting Data to Bio-Plex Manager 6.x Exporting Data from the Analyze/Export View The result from a protocol reading is stored in the run results table. (See Run Results Table on page 38 for more information.) You can export your run result at a later time from the Analyze/Export view. To export data from the Analyze/Export view 1. Click Analyze/Export in the navigation bar. 2. Click the row of the run result you want to export. 3. Click Export Results. 4. Enter the name of the file.
3 | Running Protocols Exporting Data Results Multiple Times As you analyze your data result in BPM 6.x, you may want to rerun the protocol and generate a new result. As you switch between BPM MP and BPM 6.x, you should be aware of how you name your result files. For example, assume you save your result to a file called Exp. Region 21. After you examine the result in BPM 6.x, you decide you want to make some changes to the protocol and run it again.
4 Managing Assay Panels and Standard Lots In Bio-Plex Manager™ MP software, you can select any of the Bio-Rad assay panels for use in your experiments. These panels can be customized for your experiments and reused or shared with colleagues who are using Bio-Plex Manager MP on other computers or in other locations. Bio-Plex Manager MP makes it easy to manage your standards through predefined standard lots. Standard lots are panels of assays with starting concentrations for Bio-Rad kits.
4 | Managing Assay Panels and Standard Lots Creating Assay Panels You can create assay panels in the following ways from the Manage Assay Panels dialog box: 44 Customize an existing assay panel (Edit button). Create an assay panel by combining one or more existing panels (New From button). Enter your analytes into a new assay panel (New or New From buttons). Import an assay panel (Import button).
Creating Assay Panels Customizing an Existing Assay Panel Bio-Plex Manager MP provides a list of all the assay panels it manufactures along with related analytes. In many instances you will take one of these panels and use it as is. If your experiment uses only a subset of the analytes, Bio-Rad recommends you edit the assay panel and delete any analytes you are not interested in and save the panel with a new name. This customized panel makes it easier to run repeated experiments using the same panel.
4 | Managing Assay Panels and Standard Lots From the protocol dialog box, you can now select this new assay panel from the Assay Panel dropdown list. Importing an Assay Panel The Import feature can be used to share assay panels among users working on different computers or to add new Bio-Rad assay panels. Once the panel is imported, you can edit the panel or select it in your protocol. You import an .xpnl file that contains one or more assay panels.
Editing an Assay Panel Creating a New Assay Panel You can create a new panel by starting with an empty assay panel and entering the details for the assay. To create a new assay panel 1. From the protocol dialog box, click Select Analytes. 2. Click New Assay Panel. 3. In the New Assay Panel dialog box, enter a name for the assay panel. 4. Enter the region and name of each analyte. 5. Click OK. In the protocol dialog box, the new panel is added to the Assay Panel list.
4 | Managing Assay Panels and Standard Lots Use the Add and Delete buttons to add or remove analytes from the list. Tip: Click the number of the analyte to select the entire row. 5. Use the Up and Down buttons to reorder the analytes. When you are done making changes to the panel, click OK. Customizing Your Assay Panel List The Assay Panel list includes all the assay panels provided by Bio-Rad as well as any panels you create.
Restoring an Assay Panel To export an assay panel 1. From the protocol dialog box, click Select Analytes. 2. Click Manage Assay Panels. 3. Select the panel you want to export and click Export. 4. In the Export Assay Panels dialog box, enter the name of the file and click Save. Restoring an Assay Panel You may inadvertently delete an assay panel, or you may want to return to the original version of a Bio-Rad panel that you modified.
4 | Managing Assay Panels and Standard Lots A list of the predefined standard lot definitions and any standard lots you create is displayed in the Manage Standard Lots dialog box. Creating Standard Lots You can start with a blank standard lot and enter the required information for the standard lot definition. However, you are more likely to take an existing standard lot and modify it. You can share standard lot definitions using the export and import features.
Creating Standard Lots Tip: Bio-Rad recommends you include the lot number of the standards. This will help you select the correct standard to use when running your protocol. 5. In the Expiration Date field, enter the expiration date for this standard lot. Tip: Click on the calendar and select a date. 6. From the Assay Panel dropdown list, select the assay panel you are using. 7. Select how the standard lot is defined by choosing one of the Define Standard Lot By options.
4 | Managing Assay Panels and Standard Lots The starting concentrations are specified on a label or product insert in the standard lot kit. Tip: If the starting concentration for all of your analytes is identical, enter the concentration for the first analyte. Select the entire row by clicking in the first column in the table. Right click and select “Apply starting concentration to all analytes” from the menu to populate the starting concentration for all the analytes with the same number.
Editing Standard Lots 4. Enter a new name for the standard lot. 5. Enter the expiration date for the standard lot. Tip: Click on the calendar and select a date. 6. Make any changes to the starting concentration of the analytes. 7. When you are done making your changes, click OK. Importing a Standard Lot You can import an .xstds file that contains one or more standard lots.
4 | Managing Assay Panels and Standard Lots 3. In the Manage Standard Lots dialog box, select a standard lot from the list and click Edit. 4. Make any changes to the name of the standard lot, the expiration date, the method used to dilute the standards, and the starting concentrations of the analytes. When you are done making changes, click OK. Deleting Standard Lots You can delete standard lots you no longer need from the Manage Standard Lots dialog box.
5 Analyzing Results Bio-Plex Manager™ MP is used to create and run your protocols. Once the plate has been read, you can review the fluorescence intensities of the analytes you selected and use the bead map to confirm that the bead sets are correctly selected and identified. Further analysis of your results is done in Bio-Plex Manager 6.x. The Bio-Plex Manager MP results are exported to Bio-Plex Manager 6.x. For more information on exporting your results, see Exporting Data to Bio-Plex Manager 6.
5 | Analyzing Results In Bio-Plex Manager MP, there are no gated events. MAGPIX is a CCD, camera-based system and the gating of beads in the assay is accomplished through the software without user input. For more information on analyzing your results in Bio-Plex Manager 6.x, refer to Bio-Plex Manager Software 6.1 User Guide and the online help in the software.
6 Maintaining the MAGPIX System The Maintenance view is used to: Monitor the status of the MAGPIX instrument and to easily identify, at any time, which routines need to be run to keep your instrument operating according to the manufacturer’s specifications Run the maintenance routines, including calibration and verification Import the calibration and verification kits Adjust the probe height User Guide | 57
6 | Maintaining the MAGPIX System Recommended Routine Bio-Plex Manager™ MP software monitors the MAGPIX instrument and identifies what routines need to be run to keep the instrument in good working order. You do not have to keep track of whether you have run the correct routines at the right time. Bio-Plex Manager MP informs you what routine needs to be run in the Recommended Routine section. When all recommended maintenance has been performed, None is displayed.
Daily Maintenance Routines Daily Maintenance Routines Bio-Rad recommends that you run the following routines each day you use the MAGPIX instrument. At the Beginning of the Day Run the routine in the Recommended Routine section. One or both of the following routines are recommended each day: Daily Start Up Enhanced Maintenance Continue to run the recommended routine until maintenance is up to date and None is displayed in the Recommended Routine section.
6 | Maintaining the MAGPIX System Enhanced Maintenance The Enhanced Maintenance routine will be recommended, for example, if calibration or verification failed on the previous day. Once this routine is successfully completed, it is followed with a recommendation to run the Daily Start Up routine.
Running a Routine a. Click the Calibration Kits dropdown arrow to select the correct calibration kit. b. Click the Verification Kits dropdown arrow to select the correct verification kit. Note: The lot number on the MAGPIX Calibration Kit or the MAGPIX Verification Kit CD must match the lot number of the kit to which the reagents belong. For more information on calibration and verification kits, see Calibration and Verification Kits on page 66. 6. Click Start.
6 | Maintaining the MAGPIX System Monitoring the Routine From the Maintenance view, you can monitor the status of the routine in any of several ways. Routine log Routine status Progress bar The following table describes the methods for monitoring the routine status. 62 Routine status The progress of the commands in the routine are displayed here. The status changes, displaying each command as it is being executed. When the routine is finished running, the status displays Completed.
Monitoring the Routine Progress bar The progress bar is a visual display of the duration of the routine. The progress bar fills from left to right as the routine is run. When it is completely filled in, the routine is finished running. The following figure is an example of the Routine Commands dialog box.
6 | Maintaining the MAGPIX System Setting Up the Reagent Block The Reagent Block section of the Maintenance view provides you with the information you need to set up the reagent block before you run your routine.
Setting Up the Reagent Block LEGEND 1 The colored squares indicate which reservoirs to fill and specify the appropriate liquids. 2 The wells are color-coded to correspond to the reagents specified in the reagent block instructions. The colors match the color of the bottle covers of the reagents. 3 Routine name 4 Instructions on which liquids and reagents are required, any preparation required, and the amounts of the liquids and reagents to use.
6 | Maintaining the MAGPIX System To set up the Reagent Block 1. Fill any colored reservoir with the indicated liquid. 2. For each colored well in the well strip, locate the appropriate calibration or verification kit. 3. Vortex each bottle for at least 10 sec. 4. Fill the well with 6 drops of the solution from the bottle with the matching cap color. Calibration and Verification Kits Calibration and verification kits are sold separately.
Calibration and Verification Kits Important: The reagents must be used with the calibration or verification values with the same lot number. If the values and reagents have different lot numbers, the calibration and verification routines will fail. Tip: When you open a new kit, continue to store the bottles in the original box or write the lot number of the kit on each of the reagent bottles. This will make it easier to keep track of which reagents are associated with a particular lot.
6 | Maintaining the MAGPIX System Checking the Status of the Instrument Maintenance The Status section of the Maintenance view displays the status of the following routines: Calibration Verification Fluidics Shut Down The Status section displays information about the last time the routine was run. It shows whether the routine was successfully completed or not (Passed or Failed) and a time stamp.
Responding to a Failed Routine Status also shows the current status of the routine with the following symbols: Symbol Description This routine is current and up to date. This routine is not current or the routine failed. The Shut Down routine is in one of two states: It has either never been run since the software was installed. It has not been run in the current day. This is a reminder to run the Shut Down routine at the end of the day before you turn the instrument off.
6 | Maintaining the MAGPIX System Calibration Failures If the calibration routine fails, Bio-Rad recommends you perform the following steps in the order shown. Performing the steps in order increases the likelihood that when you run the calibration routine again, it will succeed. To correct a calibration failure 1. Check that the beads are in the correct wells. 2. Check that the correct calibration control values are being used. 3. Clean the sample probe. 4.
Interrupting a Routine 7. Run the Calibration and Verification routine. If verification fails a second time, contact Bio-Rad Technical Support. Interrupting a Routine You can interrupt a maintenance routine before it has finished, for example, if you forgot to fill the reagent block with the necessary liquids and reagents. To interrupt a maintenance routine Click Stop. Note: When you click on the Routine Log link while a routine is running, the Routine Commands window opens.
6 | Maintaining the MAGPIX System Adjusting the Probe Height The probe must be calibrated in order to work correctly with the different plate types. Adjust the probe height in the following situations: After you set up the MAGPIX instrument and the computer, you must first adjust the probe height before you run any protocols. After you remove and clean the probe, you must adjust the probe height. If you experience sample problems, adjusting the probe height may resolve these errors.
MAGPIX Maintenance Cleaning the Sample Probe To clean the sample probe 1. Turn off the MAGPIX instrument and unplug the power cord. 2. Remove the sample probe. 3. Use either or both methods to clean the sample probe: Bath sonicator — place the tip of the sample probe in the bath sonicator for 2–5 min. 10 ml syringe — force distilled water through the tip of the sample probe to its large end. 4. Replace the sample probe. Screw the black fitting on top of the sample probe until it clicks. 5.
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7 Maintenance Routines The maintenance routines keep the MAGPIX instrument in good working order and operating according to the manufacturer’s specifications. Bio-Rad recommends that you run the recommended routine at the start of each day to minimize having to keep track of running the correct routines at the right time. In addition to running the recommended routine, you can run any of the maintenance routines as necessary.
7 | Maintenance Routines Estimated Run Time 10 minutes To Run the Calibration and Verification Routine Before you run the Calibration and Verification routine, you must import the calibration and verification kit information. For more information, see Calibration and Verification Kits on page 66. 76 1. Navigate to the Maintenance view. 2. In the Select Routine section, select Calibration and Verification from the Additional Routines dropdown list. 3.
Clear Bubbles Routine Clear Bubbles Routine Description of Routine The Clear Bubbles routine performs a series of fluidics operations to force out air bubbles that may be trapped in the cuvette. When to Run this Routine If you suspect there is air in the MAGPIX system, run the Clear Bubbles routine. Estimated Run Time 3 minutes To Run the Clear Bubbles Routine 1. Navigate to the Maintenance view. 2. In the Select Routine section, select Clear Bubbles from the Additional Routines dropdown list. 3.
7 | Maintenance Routines Daily Start Up Routine Description of Routine Daily Start Up prepares your instrument for daily use. It runs different routines depending on the state of the instrument. Daily Start Up may include the Calibration and Verification, Verification, and Wake From Storage routines. When to Run this Routine Run Daily Start Up each day you use the instrument before you run any protocols.
Enhanced Maintenance Routine Enhanced Maintenance Routine Description of Routine The Enhanced Maintenance routine clears any bubbles from the system and clears any clogs from the probe and fluidics. When to Run this Routine This routine is recommended when a low bead count occurs during a protocol run or when calibration or verification fails. Estimated Run Time 14 minutes Before Running the Routine Before you run the Enhanced Maintenance Routine, Bio-Rad recommends that you check the following: 1.
7 | Maintenance Routines Fluidics Preparation Routine Description of Routine The Fluidics Preparation routine prepares the fluidics system for daily use. When to Run this Routine Run the Fluidics Preparation routine when you replace an empty drive fluid container or if the drive fluid line is not aspirating drive fluid because the line has become dislodged. Estimated Run Time 2 minutes To Run the Fluidics Preparation Routine 80 1. Navigate to the Maintenance view. 2.
Prepare for Storage Routine Prepare for Storage Routine Description of Routine The Prepare for Storage routine clears all fluids from the instrument. When to Run this Routine Run the Prepare for Storage routine if you will not be using the instrument for more than two weeks or before you ship the instrument to Bio-Rad. Estimated Run Time 6 minutes To Run the Prepare for Storage Routine 1. Navigate to the Maintenance view. 2.
7 | Maintenance Routines Prime Routine Description of Routine The Prime routine primes the fluidics system by forcing drive fluid through the fluidics lines. When to Run this Routine If the Unpack MAGPIX routine fails during the initial instrument set up, then run the Prime routine. Estimated Run Time 1 minute To Run the Prime Routine 82 1. Navigate to the Maintenance view. 2. In the Select Routine section, select Prime from the Additional Routines dropdown list. 3. Click Start.
Shut Down Routine Shut Down Routine Description of Routine The Shut Down routine cleans the fluidics lines and prevents a buildup of debris within the system. When to Run the Routine Bio-Rad recommends that you run the Shut Down routine at the end of each day that you use the instrument. Refer to the Shut Down entry in the status section in the Maintenance view to determine whether the Shut Down has been run that day. Estimated Run Time 2 minutes To Run the Shut Down Routine 1.
7 | Maintenance Routines Unclog Routine Description of Routine This procedure performs a series of fluidics operations to remove possible obstructions from the fluidics lines. When to Run this Routine If you suspect there is an obstruction in the MAGPIX system, run the Unclog routine. Estimated Run Time 2 minutes To Run the Unclog Routine 84 1. Navigate to the Maintenance view. 2. In the Select Routine section, select Unclog from the Additional Routines dropdown list. 3.
Verification Routine Verification Routine Description of Routine The Verification routine ensures that the calibration settings are valid and ensures that well-to-well cross talk does not occur. When to Run this Routine Run the Verification routine when its status in the Maintenance view is not up to date. Bio-Plex Manager MP adds verification to the Daily Start Up routine in accordance with the manufacturer’s recommendation.
7 | Maintenance Routines Wake from Storage Routine Description of Routine The Wake from Storage routine prepares the instrument to be used after it has been idle for a long period of time. When to Run this Routine Run the Wake from Storage routine if the instrument has been idle for 2 weeks or longer or if it has been prepared for storage. Bio-Plex Manager MP adds Wake From Storage to the Daily Start Up routine if it detects that the instrument has been idle for 2 weeks or longer.
Wash Between Plates Routine Wash Between Plates Routine Description of Routine The Wash Between Plates routine performs a series of fluidics operations to prevent traces of sample or other debris from collecting inside the Bio-Plex® suspension array system. When to Run this Routine Bio-Rad recommends that you wash the fluidics lines after each plate reading. Note: In the Run Settings dialog box, the default is to run the Wash Between Plates routine after the reading.
7 | 88 Maintenance Routines | Bio-Plex Manager MP Software
A License Activation To have access to all of the features of Bio-Plex Manager™ MP software, you must activate the product with a valid product license. You will need a separate license for each computer on which you install Bio-Plex Manager MP. Note: If you purchased a new MAGPIX instrument, the computer included with the instrument comes with the software already activated. Therefore, you can skip this step.
A | License Activation 2. If the product license has not been activated, the Product Activation Required window appears. 3. Select Activate Bio-Plex Manager MP Online and click Continue. 4. Enter your activation code in the text box and click Activate. Note: The activation code can be found in the CD folder.
Activating the License through Technical Support The Activation Successful window appears confirming that the software has been activated. 5. Click OK to exit the activation software and start Bio-Plex Manager MP. Activating the License through Technical Support If the computer on which Bio-Plex Manager MP is installed does not have an Internet connection, you can request a product license from Bio-Rad Technical Support to activate the software. This is a two-phase process: 1.
A | License Activation Generating the Credentials File To generate the credentials file 92 1. Start the Bio-Plex Manager MP software. 2. If the product license has not been activated, the Product Activation Required window appears. 3. Select Activate Bio-Plex Manager MP through Technical Support and click Continue.
Activating the License through Technical Support 4. Select Send credentials to Technical Support and click Continue. 5. Enter your activation code in the text box and click Save. Note: The activation code can be found in the CD folder. 6. In the Save Licensing Credentials to a File dialog box, enter the name of the file and click Save.
A | License Activation The File Successfully Saved window appears with instructions on how to send the credentials file to Technical Support. 7. Move the credentials file to a computer where you can send email, and email the file to Bio-Rad Technical Support (LSG_Software_Act@bio-rad.com). Activating the Software with a License File Technical Support will generate a file with the license and email the file to you.
Activating the License through Technical Support To activate Bio-Plex Manager MP with the license file 1. Start the Bio-Plex Manager MP software. 2. In the Product Activation Required window, select Activate Bio-Plex Manager through Technical Support and click Continue. 3. Select “Import license file and activate product” and click Continue.
A | License Activation 4. Click Activate. 5. Navigate to where the license file is located, select the file, and click Open. The Activation Successful window appears confirming that the software has been activated. 6. 96 Click OK to exit the activation software and start Bio-Plex Manager MP.
Deactivating the Bio-Plex Manager MP License Deactivating the Bio-Plex Manager MP License You may want to deactivate the Bio-Plex Manager MP license for one of the following reasons: You want to move the license from one computer to another. This can occur, for example, if you are replacing your computer. You must first deactivate the license from the first computer and then activate it on the second computer. You want to remove the license from the computer.
A | License Activation 4. Enter your activation code and click Deactivate. Note: The Activation Code field will be populated with the activation code. If the field is empty, you can find the activation code in the CD folder. The Deactivation Successful window appears confirming the software has been deactivated. 5. 98 Click Exit.
Deactivating the License through Technical Support Deactivating the License through Technical Support If the computer on which Bio-Plex Manager MP is installed does not have an Internet connection, you can deactivate your license through Bio-Rad Technical Support. This is a two-phase process: 1. Generate a deactivation certificate file and email it to Technical Support. 2. Technical Support informs you that the license has been deactivated.
A | License Activation 4. In the Export Deactivation Certificate window, click Save. A dialog box appears asking you to confirm the deactivation. 100 | 5. Click Yes. 6. In the File browser, navigate to where you want to save the deactivation certificate. 7. Enter the name of the file and click Save.
Deactivating the License through Technical Support The File Successfully Saved window appears with instructions on how to send the deactivation certificate file to Technical Support. 8. Click OK. 9. Move the deactivation certificate file to a computer where you can send email, and email the file to Bio-Rad Technical Support (LSG_Software_Act@bio-rad.com). Technical Support will reply with an email informing you that the license has been deactivated.
A | 102 | License Activation Bio-Plex Manager MP Software
B Backing Up the Database There are two databases that need to be backed up on a regular basis: xPONENT database Bio-Plex Manager™ MP database User Guide | 103
B | Backing Up the Database Backing up the xPONENT Database Bio-Rad recommends that you back up the xPONENT database on a regular basis. You can manually back up the xPONENT database or you can schedule automatic backups. The default is manual backups. Database backups are managed with the Archive Utility.
Backing up the Bio-Plex Manager MP Database You can specify the frequency with which you receive reminders to back up the database or you can schedule automatic database backups. For more information on the Archive Utility, see xPONENT for MAGPIX 4.2 Software User Manual available on the Luminex web site. Backing up the Bio-Plex Manager MP Database It is a best practice to back up the database frequently and keep the backup copies in a safe location. A USB or network hard drive is a good backup solution.
B | Backing Up the Database 106 | Bio-Plex Manager MP Software
C Troubleshooting Problem Possible Cause Solution Instrument is not connected. The connection to the MAGPIX instrument has been lost. Try each of these suggestions in order until you reconnect to the instrument: Region Selection/ Severe Clog One or more of the analytes selected has little or no data. 1. Confirm that the instrument is turned on. 2. Reconnect to the instrument. From the Instrument menu, select Reconnect Instrument. 3. Turn off the instrument and exit Bio-Plex Manager™ MP.
C | Troubleshooting Problem Possible Cause Solution Low Bead Count Three or more consecutive wells have bead counts lower than the recommended number. Perform the following steps: You empty the waste container but continue to see the following error message: The waste container is full. Empty the waste container and replace it with a dry waste container. 108 | The instrument detects some moisture in the waste container and triggers an alert. Bio-Plex Manager MP Software 1. Stop the run. 2.
Problem Possible Cause Solution A Windows security alert dialog box appears with the message: Windows Firewall has blocked some features of this program. The user’s profile and permissions are set such that the user must grant access to xPONENT. Click “Allow access.
C | 110 | Troubleshooting Bio-Plex Manager MP Software
Index A Analytes, definition 12 Analytes, excluding 12 Analytes, selecting 13 Analyzing results in Bio-Plex Manager MP 55 Assay panel list, customizing 48 Assay panel lists, customizing 48 Assay panels, combining existing 45 Assay panels, creating 44 Assay panels, creating new 47 Assay panels, customizing 45 Assay panels, editing 47 Assay panels, exporting 48 Assay panels, importing 46 Assay panels, naming 47 Assay panels, restoring Bio-Rad 49 Assays, exposure to light 26 Autofill across, definition 17 Auto
Index Flat Bottom plate 27 Fluidics Preparation routine 80 Fluidics, checking status of 68 I Instrument not connected error message 107 L License activation, offline 91 License activation, online 89 License deactivation, offline 99 License deactivation, online 97 Lot numbers 66 Low bead count 36 Low Bead Count error 108 M Maintenance of instrument, checking status of 68 Maintenance routine, failed 69 Maintenance routines, beginning of the day 59 Maintenance routines, daily 59 Maintenance routines, end o
Index Software activation, Product activation code 89 Software deactivation 97 Software deactivation, offline 99 Software deactivation, online 97 Standard curve 20 Standard lots, creating 50 Standard lots, creating from existing lots 52 Standard lots, definition 49 Standard lots, deleting 54 Standard lots, editing 53 Standard lots, exporting 54 Standard lots, importing 53 Standard lots, naming convention for 22 Standard lots, selecting 21 Standard wells 16 Standards Info pane, disabled 21 Standards, defini
Index 114 | Bio-Plex Manager MP Software
Bio-Rad Laboratories, Inc. Web site www.bio-rad.
