Bio-Rad Bio-Plex Manager User Manual
Bio-Plex Manager™ MP Software
User Guide
Version 1.0
Bio-Plex Manager™ MP
Software
User Guide
Version 1.0
10032257 Rev A
Bio-Rad Technical Support Department
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By opening the packaging containing this unit of Luminex instrumentation or using this unit of Luminex Instrument
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reverse engineer the Luminex Instrument or any such beads.
The Bio-Plex suspension array system includes fluorescently labeled microspheres and instrumentation licensed to
Bio-Rad Laboratories, Inc. by the Luminex Corporation.
CST antibodies exclusively developed and validated for Bio-Plex
phosphoprotein and total target assays.
Copyright © 2013 by Bio-Rad Laboratories. All rights reserved.
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
About Analytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Selecting Analytes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Formatting Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Well Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Autofilling Well Numbers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Defining a Replicate Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Autofilling Replicate Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Removing the Well Formatting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Changing the Well Formatting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
About Standards. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Selecting a Standard Lot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Reusing a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Editing a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter 3 Running Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Running the Recommended Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Plate Handling Guidelines. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Plate Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Using the Plate Heater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Running the Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
User Guide | iii
Table of Contents
Reading the Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Raw Data Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Bead Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Interrupting a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Resuming a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Encountering and Resolving Low Bead Counts . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Run Results Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
Exporting Data to Bio-Plex Manager 6.x. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Exporting Data from the Create/Run Protocols View . . . . . . . . . . . . . . . . . . . . 40
Exporting Data from the Analyze/Export View . . . . . . . . . . . . . . . . . . . . . . . . .41
Exporting Data Results Multiple Times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Chapter 4 Managing Assay Panels and Standard Lots . . . . . . . . . . . 43
Creating Assay Panels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Customizing an Existing Assay Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Creating an Assay Panel by Combining Existing Panels. . . . . . . . . . . . . . . . . . 45
Importing an Assay Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Creating a New Assay Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Editing an Assay Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Customizing Your Assay Panel List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Sharing Customized Assay Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Restoring an Assay Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
About Standard Lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Creating Standard Lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Creating New Standard Lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Defining a Standard Lot with Custom Concentrations . . . . . . . . . . . . . . . . . . . 52
Creating a Standard Lot from an Existing Lot . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Importing a Standard Lot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Editing Standard Lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Deleting Standard Lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Exporting Standard Lots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
iv | Bio-Plex Manager MP Software
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Enhanced Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Shut Down Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Running a Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Monitoring the Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Setting Up the Reagent Block. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Calibration and Verification Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Importing the Calibration or Verification Values . . . . . . . . . . . . . . . . . . . . . . . . 67
Checking the Status of the Instrument Maintenance . . . . . . . . . . . . . . . . . . . . . . 68
Responding to a Failed Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Calibration Failures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Verification Failures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .70
Interrupting a Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Preparing Your Instrument for Nonuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Adjusting the Probe Height . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Cleaning the Sample Probe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
MAGPIX Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
User Guide | v
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Fluidics Preparation Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Prepare for Storage Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Prime Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Shut Down Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Unclog Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Verification Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Wake from Storage Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Wash Between Plates Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Appendix A License Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Activating the Bio-Plex Manager MP License. . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Activating the License Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Activating the License through Technical Support . . . . . . . . . . . . . . . . . . . . . . . . 91
Generating the Credentials File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Activating the Software with a License File. . . . . . . . . . . . . . . . . . . . . . . . . . 94
Deactivating the Bio-Plex Manager MP License. . . . . . . . . . . . . . . . . . . . . . . . . . 97
Deactivating the License Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Deactivating the License through Technical Support . . . . . . . . . . . . . . . . . . . . . .99
Exporting the Deactivation Certificate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Appendix B Backing Up the Database . . . . . . . . . . . . . . . . . . . . . 103
Backing up the xPONENT Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Backing up the Bio-Plex Manager MP Database . . . . . . . . . . . . . . . . . . . . . . . . 105
Showing Hidden Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Appendix C Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
vi | Bio-Plex Manager MP Software
1 Introduction
Bio-Plex Manager™ MP is an application that allows you to run and maintain your
MAGPIX instrument. MAGPIX monitors the state of your instrument and
recommends routines to keep the instrument in good working order, and it also
recommends maintenance routines to resolve problems. With
Bio-Plex Manager MP, you do not have to keep track of when to calibrate your
instrument or verify the calibration settings. Its easy-to-use interface facilitates
creating and running your protocols. Bio-Plex Manager MP works with any MAGPIX
instrument purchased from any vendor.
You will use two software applications, Bio-Plex Manager MP 1.0 and
Bio-Plex Manager 6.x to run your experiments and analyze your results. Both
software applications are required and are shipped along with the MAGPIX
instrument.
Use Bio-Plex Manager MP to do the following:
Operate the MAGPIX instrument
Maintain the instrument
Define protocol parameters and initiate plate readings
Use Bio-Plex Manager 6.x to do the following:
Review and optimize results
Export results to Microsoft Excel or other third-party analysis software
Export results to Bio-Plex Data Pro™ for analysis of your experiment
(grouping biological replicates and identifying statistically significant
changes)
User Guide | 7
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
Bio-Plex Manager MP
MAGPIX
Data Review
and Optimization
Bio-Plex Manager 6.x
Experimental Analysis
and Interpretation
Bio-Plex Data Pro
8 | Bio-Plex Manager MP Software
2 Creating Protocols
About Protocols
A protocol contains the parameters of a Bio-Plex Manager™ MP software run. It
includes information about the analytes included in the run, the plate wells to be
read, the concentrations of standards, and instrument settings. These parameters
are saved in the result along with the data from the reading.
You can save a protocol and reuse it or modify it for another reading. Each time you
run the protocol, a new result is created and stored in the database.
You set up your protocol from the protocol dialog box. There are three phases to
setting up your protocol that correspond to the three panes in the protocol dialog
box:
Select Analytes – select an assay panel and the analytes for your
experiment.
Format Plate – specify which wells are to be read and the sample type of
each well.
Standards Info – specify the concentrations of your standards.
User Guide | 9
2 | Creating Protocols
Navigating to the Protocol Dialog Box
Protocols are created from the protocol dialog box. There are a number of ways you
can get to the protocol dialog box.
To navigate to the protocol dialog box
1. Click Create/Run Protocols in the navigation bar.
2. 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.
10 | Bio-Plex Manager MP Software
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
7. Click Standards Info.
8. From the Standard Lot dropdown list, select the standard lot you want to use
with this protocol.
Note: If no standard lots appear in the list, you must first create a standard
lot for your assay panel. For more information, see
Lots on page 50.
Formatting Plates on page 14.
Creating a Protocol
Creating New Standard
9. Select the dilution factor from the Dilution Factor dropdown list. For more
information, see
10. Click OK.
11. (Optional) Click Save As to save the protocol.
Note: Save the protocol if you want to run it again at a later time or if you
want to use it as a template for another protocol. For more information on
using the protocol as a template, see
12. (Optional) In the Save Protocol dialog box, enter the protocol name and click
OK.
Note: Protocols created on one computer cannot be exported and used on
another computer running Bio-Plex
Selecting a Standard Lot on page 21.
Reusing a Protocol on page 23.
Manager MP.
User Guide | 1 1
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. The
following assays are currently not available for the MAGPIX instrument: nonhuman
primate diabetes, canine kidney tox, rat and human kidney tox, angiogenesis, and
acute phase. You can add other panels to this list or create custom panels that
include only the analytes you use in your experiments.
Note: After you select the assay panel, you select which analytes you want to
appear in your reports. During a reading, the array reader detects all the
analytes in the sample, including any analytes you excluded from selection.
However, only the selected analytes are included in the final reports and tables.
After the run is completed, you can always edit the protocol, select any
analytes that were previously omitted, and the data for those analytes will
appear in the tables.
Each analyte is listed by name and region. The region number refers to the area of a
fluorescent color map that identifies the analyte’s bead region. Each bead region is
embedded with specific quantities of two fluorescent dyes. The array reader detects
the combination of these fluorochromes and associates the bead region with a
unique region on the color map. Therefore, the location on the map identifies the
bead region and its associated analyte.
Each analyte on a Bio-Rad preconfigured panel is identified by a unique region.
However, analytes on different panels may occupy the same region. If you pick
analytes from more than one panel, only one analyte for a particular region can be
selected. Bio-Plex
12 | Bio-Plex Manager MP Software
Manager MP warns you if there is a conflict.
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.
The following figure shows the MAGPIX Quick Start assay panel with analytes in
r
egions 20, 21, and 25 through 27 selected.
Selecting Analytes
User Guide | 1 3
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 r
ead.
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. Click the wells in the template that you want defined with this well type.
Formatted wells are colored blue with a specific shape to identify the well type.
Contr
ol, Standard, and Unknown wells are numbered. Blank wells are specified
with the letter B. For more information on the well types, see Well Types on
page 16.
14 | Bio-Plex Manager MP Software
Formatting Plates
The template diagram in the Create/Run Protocols view displays the formatted wells
in your protocol and the raw data table is populated with the well location and
sample type.
Create/Run Protocols view
Formatted wells
Name of assay panel
Raw data table
User Guide | 1 5
2 | Creating Protocols
Well Types
The following are different well types that you can specify on the plate:
Blank Standard Undefined
Control Unknown
Blank Wells
In certain types of assays, such as the Bio-Plex phosphoprotein assay, it might
be useful to subtract the assay backgr
ound from the readings of standards,
controls, and unknown samples. Prepare blank wells that contain all of the
assay components excluding the sample. Blank wells are read along with the
rest of the assay. Bio-Plex Manager 6.x then subtracts the mean background
r
eading of these wells from the fluorescence intensity values of the wells
containing standards, controls, and unknowns.
Control Wells
Control wells contain samples of known concentration. The observed
concentration of the contr
ol wells is compared to the expected concentration
and calculated at the end of the reading.
Standard Wells
Standard wells contain analytes of known concentration. A series of known
concentrations of an analyte is used to generate a standar
fluorescence intensity compared to analyte concentration. The regression
equation for the curve is used to calculate the concentration of analytes in the
unknown samples and controls.
16 | Bio-Plex Manager MP Software
d curve of
Formatting Plates
Unknown Wells
The unknown wells contain samples of unknown concentration. These samples
are taken from the subjects of your experiments.
Undefined Wells
Use the Undefined wells button to remove the definition of a well. Undefined
wells are not read by the array reader.
Autofilling Well Numbers
Use the Autofill feature to quickly define a well type for multiple wells.
Autofill Across numbers the wells sequentially from left to right, then top to
bottom
Autofill Down numbers the wells sequentially from top to bottom, then left
to right
To use Autofill to format the plate
1. In the New Protocol window, click Format Plate.
2. Click Autofill Across or Autofill Down.
3. Click the well type.
4. Click and drag your cursor in the plate over the wells you want to format.
User Guide | 1 7
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.
Autofilling Replicate Groups
You can quickly format multiple replicate groups at one time.
To format a replicate group
1. Click Autofill Across or Autofill Down.
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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
dr
opdown list is eight.
Tip: You can create replicate groups that are larger than eight by clicking
T
urn 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.
In the following example, Autofill Across is selected and the replicate size is set to 2.
Eight gr
oups of replicates of Unknown well type were created. Each row represents
a replicate group. The arrow shows the path of the cursor as it is dragged across the
plate template.
User Guide | 1 9
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.
To change the formatting of a well
1. Click the button for the sample type you want to use.
2. Click and drag your cursor over the wells whose format you want to change.
The wells are now formatted with the new well type.
About Standards
Standards are analytes of known concentration. Standards are used to generate a
standard curve of values using one of the several regression methods included in
Bio-Plex
Manager 6.x. This curve is used to calculate concentrations of your
unknowns.
In Bio-Plex Manager MP, you define your standard lot, including the starting
concentration for each of the analytes. This definition is stored and it can be reused
each time you run a plate with those analytes.
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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. Each
analyte appears as a r
you defined on the Format Plate pane. In this example, eight standard wells
were selected on the Format Plate pane, and therefore, there are eight
columns: S1, S2, and so on.
ow in the table. There is a column for each standard well
Selecting a Standard Lot
Note: The Standards Info pane is disabled until you select your analytes
and format your standard wells.
2. From the Standard Lot dropdown list, select the standard lot you want to use
with this pr
otocol.
User Guide | 2 1
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.
Note: The predefined standard lots are identified by their lot numbers.
Included in par
date. In the example, 5029511 [Bio-Rad Pro Hu Group 27-Plex] Exp
2016-03-30, 5029511 is both the name of the standard lot and its lot
number.
3. Select the dilution factor from the Dilution Factor dropdown list.
The table autopopulates with the concentrations using the starting
concentration specified for that standar
entheses is the name of the assay panel and the expiration
d lot and the dilution factor.
Note: Use Most Concentrated Standard to specify whether the first well or
the last well contains the highest concentration of the analyte.
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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. When you are done making changes, click OK.
Editing a Protocol
The Edit command opens the protocol dialog box for the protocol currently
displayed in the Create/Run Protocols view. You might want to edit a protocol in the
following situations:
Reusing a Protocol
You make changes to a saved protocol to match the changes in your
experiment. The most common change is to the number of unknown
samples in the experiment.
You run a protocol and discover that there is a low bead count, indicating
that the wrong analytes might have been selected. You can change the
selection of analytes in the protocol dialog box.
User Guide | 2 3
2 | Creating Protocols
24 | Bio-Plex Manager MP Software
3 Running Protocols
Once your protocol is created, you are ready to run the protocol. The result is
displayed in the raw data table and bead map and it can be exported to
Bio-Plex
Manager™ 6.x software for analysis. You can interrupt a run at any time,
make any necessary changes to the protocol, and resume the run with no loss of
data. Bio-Plex
informing you when it detects problems with your run.
Running the Recommended Routine
Run the routine in the Recommended Routine section of the Maintenance view each
day you use the MAGPIX instrument. This keeps the instrument free of bubbles and
ensures that it is operating according to specifications.
To run the recommended routine
1. Navigate to the Maintenance view.
2. In the Recommended Routine section, click Select to select the routine.
3. Fill the reservoirs and the well strip with the solutions indicated in the Reagent
Manager™ MP software provides graphical clues and alerts
Block.
4. Click Start.
5. When the routine is completed, a dialog box displays indicating that the routine
is successfully completed.
You can monitor the progress of the routine; for more information, see Monitoring
the Routine on page 62.
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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.
Should this occur, it can cause problems when reading the plate.
Make sure you have added at least 125 µl of sample to all the wells
specified in your plate template before starting a protocol run. If the array
reader attempts to draw sample from an empty well, air is sucked into the
sample loop and injected into the flow chamber. When this happens,
bubbles form in the cuvette and interfere with the analysis. Should this
occur, perform a Clear Bubbles procedure (see
page 77), then rerun the protocol.
Shake the microplate on a plate shaker for 30 seconds prior to performing
a reading.
Clear Bubbles Routine on
For some experiments the temperature of the plate must be maintained at a
particular temperature. See
26 | Bio-Plex Manager MP Software
Using the Plate Heater on page 28 for more information.
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 Types
Plate Type Compatible Consumable Distance
from Platform
(mm) *
Flat bottom
plate
Filter plate Millipore multiscreen plate (for example,
PCR plate Bio-Rad low-profile unskirted PCR plate
Auxiliary plate Nunc PolySorp (for example, 475094),
* This is the distance between the platform and the inside bottom of the plate well.
Bio-Plex Pro™ flat bottom plate (black
plate comes with Bio-Plex Pro assays,
catalog #171-025001)
MSBVN1210)
(for example, MLL-9601)
Nunc MaxiSorp (for example, 445105)
3.94
3.05
2.79
3.30
For other plate types, check the manufacturer’s specifications to determine the
distance from the surface of the MAGPIX platform to the bottom of the well.
The probe backs off 1 mm after it makes contact with the probe height adjustment
plate. Ther
efore, you need to add 1 mm to the distance in the table to get the
correct probe height.
For example, if the specification for your plate type is 3.4 mm, you can use the
auxiliary plate (3.3 mm) because the actual setting, after running the pr
obe height
adjustment, is 4.3 mm. This gives an allowance of 0.9 mm above the plate’s well
bottom for sample aspiration.
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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. In the dashboard, select the “Plate heater off” checkbox to turn the heater on.
The “Turning on” message appears. When the heater is turned on, Set Temp is
displayed.
2. Use the left- and right-pointing triangles to set the plate temperature.
The temperature can be set from 35–60ºC in 0.5º increments.
When the temperature of the plate falls within range of the set temperature, the
thermometer turns green.
3. When you are done, select Set Temp to turn the heater off.
Running the Protocol
After you create your protocol, you are ready to run it. Refer to Chapter 2, Creating
Protocols for more information on creating protocols.
Note: You can run only protocols created in Bio-Plex Manager MP. You cannot
run protocols created in other versions of Bio-Plex
Bio-Plex
Manager 6.1.
The data from each run are stored as a result in the Bio-Plex Manager MP database.
Result names must be unique. You can retrieve the data by exporting the result to
Bio-Plex
Manager 6.x.
28 | Bio-Plex Manager MP Software
Manager such as
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