Bio-Plex Manager MP Software User Guide - Bio-Rad

Bio-Plex Manager MP Software User Guide - Bio-Rad
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
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:
[email protected] (U.S.)
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www.consult.bio-rad.com
Notice
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including photocopy, recording, or any information storage or retrieval system, without permission in writing from
Bio-Rad.
Bio-Rad reserves the right to modify its products and services at any time. This user guide is subject to change
without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or omissions, or for
any damage resulting from the application or use of this information.
Luminex, MAGPIX, and xPONENT are trademarks of Luminex Corporation. Windows is a trademark of Microsoft
Corporation. MaxiSorp, Nunc, and PolySorp are trademarks of Thermo Fisher Scientific.
By opening the packaging containing this unit of Luminex instrumentation or using this unit of Luminex Instrument
in any manner, you are consenting and agreeing to be bound by the following terms and conditions and the terms
and conditions set forth in the End User License Agreement for the Luminex software included with this unit. You
are also agreeing that all such terms and conditions constitute a legally valid and binding contract that is
enforceable against you. If you do not agree to all of such terms and conditions, you must promptly return this unit
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from the sale of this unit of Luminex Instrument or license of Luminex software to you, the purchaser, and you do
not receive any right under Luminex’s patent rights by virtue of your purchase of Luminex Instrument or license of
Luminex software. You agree that the Luminex Instrument and Luminex software are sold only for use with
fluorescently labeled microsphere beads authorized by Luminex and you may obtain a royalty-free license under
Luminex’s patents, if any, to use this unit of Luminex Instrument with fluorescently labeled microsphere beads
authorized by Luminex by purchasing beads authorized by Luminex and registering this unit of Luminex Instrument
with Luminex dealer, in accordance with the instructions accompanying the Luminex Instrument. You agree not to
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
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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
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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
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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
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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)
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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.x
Experimental Analysis
and Interpretation
MAGPIX
8
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Bio-Plex Manager MP Software
Bio-Plex Data Pro
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.
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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.
| Bio-Plex Manager MP Software
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.
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 Creating New Standard
Lots on page 50.
9.
Select the dilution factor from the Dilution Factor dropdown list. For more
information, see Selecting a Standard Lot on page 21.
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 Reusing a Protocol on page 23.
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 Manager MP.
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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 Manager MP warns you if there is a conflict.
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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.
The following figure shows the MAGPIX Quick Start assay panel with analytes in
regions 20, 21, and 25 through 27 selected.
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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.
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.
Control, 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.
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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
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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. Bio-Plex Manager 6.x then subtracts the mean background
reading 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 control 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 standard curve of
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.
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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.
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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.
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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
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.
In the following example, Autofill Across is selected and the replicate size is set to 2.
Eight groups 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.
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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
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 row in the table. There is a column for each standard well
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.
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 protocol.
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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 parentheses is the name of the assay panel and the expiration
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 standard 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
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:

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.
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2 |
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Creating Protocols
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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.
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
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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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 Clear Bubbles Routine on
page 77), then rerun the protocol.

Shake the microplate on a plate shaker for 30 seconds prior to performing
a reading.
For some experiments the temperature of the plate must be maintained at a
particular temperature. See Using the Plate Heater on page 28 for more information.
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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)
3.05
PCR plate
Bio-Rad low-profile unskirted PCR plate
(for example, MLL-9601)
2.79
Auxiliary plate
Nunc PolySorp (for example, 475094),
Nunc MaxiSorp (for example, 445105)
3.30
* This is the distance between the platform and the inside bottom of the plate well.
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. Therefore, 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 probe 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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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 Manager such as
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.
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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.
You can specify anything here that will help you distinguish your experiments
and results.
4.
Specify the type of plate in the Plate Type List.
If you do not see your plate listed here, see Using the Plate Heater on page 28
to determine the equivalent match for your plate type.
5.
(Optional) In the Pre-Run Routine list, select any routines you want executed
before the protocol run.
Note: A Rinse routine is always run before a plate is read. This routine is
run in addition to any pre-run routine specified here.
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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.
If you select a post-run routine, refer to the Reagent Block diagram and fill the
appropriate reservoirs with the specified fluids.
7.
Accept the default for “Stop runs with low bead count” or clear the checkbox if
you do not want the run interrupted.
By default, the run is interrupted if three consecutive wells have a bead count of
less than 20.
8.
Click Create/Run Protocols.
The plate retracts and Bio-Plex Manager MP starts the run.
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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. In the preceding example, Well E2 is being read. The Run Commands
status indicates when the reading begins and ends for the current well.
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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.
Raw Data Table
As the wells are read, the Raw Data table is populated with the results. The table
displays the well location and the well type for all formatted wells. As
Bio-Plex Manager MP completes reading each well, the Raw Data table is
populated with the results for that well. The fluorescence intensities of the analytes
you selected are displayed for each well.
Note: During a reading, the array reader detects all of the analytes in the
sample, including any that you have not selected. However, any analytes that
are not selected in the protocol are not included in the table, even if they are
detected. After a reading you can edit the protocol and change the selection of
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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). This column can be displayed or hidden
using a toggle command.
Total Region
Events
Total bead events recorded within the 50 defined
regions. This column can be displayed or hidden
using a toggle command.
Region_##(##)
When bead region counts are displayed, there are two
numbers. The first number is the fluorescence
intensity for that analyte. The second number, in
parentheses, is the number of bead events for that
region.
If there are low bead counts for any of the selected
analytes, the following symbols appear:
*
There are fewer than the recommended
50 beads for one or more analytes.
There are fewer than 20 beads for one or
more analytes.
Bead Map
The bead color map is a density dot plot of the events in a reading for a selected
well. Different colored dots in the map represent different numbers of events at
those data points. There are 50 available regions in the bead map.
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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.
Once maximized, you can use the Zoom tool to focus further on a particular
area in the bead map.
Note: Each bead set generates a cluster of data points, rather than a single
point, because of minute variations in fluorochrome levels and intensity among
the beads in the set.
The white areas on the map indicate the expected regions of the selected analytes.
When you move your cursor over these areas, the name of the analyte appears in a
tool tip. The data point clusters should fall within these regions. If one or more
clusters do not fall within the white areas, there may be a problem with the beads
such as photobleaching. Or the analyte selections in the protocol may be incorrect.
If all the data clusters have shifted out of the white regions, there may be
microbubbles in the cuvette. The bead map can be used to confirm that the bead
sets are correctly selected, measured, and identified.
Interrupting a Run
The results for each run, whether the run is completed or interrupted, are saved to a
unique result which can later be retrieved and viewed. Any data that were read up to
the point the run is interrupted are saved to the result name you specify in the Run
Settings dialog box. When you are ready to run the protocol again, return to the Run
Settings dialog box.
To interrupt a run

34
Click Stop to interrupt a run.
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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. You can run the
protocol again and start where you left off or start from the beginning and read the
entire plate.
To resume a run
1.
From the Create/Run Protocols view, click Start.
2.
In the Run Settings dialog box, either accept the default or enter a different
name in the Result Name field.
By default, the Result Name you entered for the first run is appended with a
number surrounded by square brackets. For example, if the result name you
entered is Test, when you return to the Run Settings dialog box to run the
protocol again, the result name is Test [1]. With each subsequent run, the
number is incremented.
3.
In the Well Selection diagram, specify the wells you want read.
Bio-Plex Manager MP reads only selected formatted wells. A black border
indicates the selected wells. You can:

Read only the wells that were not read on the last run. This is the default,
as shown in the figure that follows. In this example, when the run resumes,
it will start with well A2.

Click Select All to read all the wells.

Click on a subset of the formatted wells to read only those wells.
Tip: Use Shift + Click to select more than one well.
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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. In the Run Settings
dialog box, select “Stop runs with low bead count.” If a low bead count is
encountered, the run is stopped and a dialog box appears with a suggested
solution.
In addition, a warning symbol is displayed in the affected wells in the plate template
and for the applicable analytes in the raw data table.
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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. These
include reviewing your protocol, performing maintenance on the instrument,
and running maintenance routines. It is important that you perform the steps in
the recommended order because this increases the likelihood that the problem
will be resolved.
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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.
Column Name
Description
Name
Name of the result set
Acquisition Time
Time stamp of when the protocol was run
Assay Panel
Assay panel used in the run
# Analytes
Number of analytes selected in the protocol
definition
Description
User-defined description
Tip: Click the column header of any column to sort the table by that column.
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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.

Export your results at a later time from the Analyze/Export view. For more
information, see Exporting Data from the Analyze/Export View on page 41.
Note: You can export your data once the plate reading is completed. If you
select a post-run routine to be run once the run is completed, you do not have
to wait for the routine to complete before exporting your data.
Once the file is saved, it can be viewed in Bio-Plex Manager 6.x in one of the
following ways:

If Bio-Plex Manager 6.x is installed on the same computer where you are
running Bio-Plex Manager MP, then you are prompted to view the result in
Bio-Plex Manager 6.x after the file is saved. If you respond Yes, the result
file is opened in Bio-Plex Manager 6.x.

If Bio-Plex Manager 6.x is not installed on your computer, then you must
copy the saved file to a computer where Bio-Plex Manager 6.x is installed
and import it into the software.
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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.
The default file name is the Result Name assigned in the Run Settings dialog
box, followed by a time stamp of the time of the export. For example,
Experiment 2013-02-12 13.04.08. You can accept the default name or enter a
different name for the file.
4.
Click Save.
A message appears informing you that the result file has been exported.
If Bio-Plex Manager 6.x is installed on the same computer where you are
running Bio-Plex Manager MP, you are also asked if you want to open the
result in Bio-Plex Manager 6.x
5.
In the Export Results dialog box, click Yes.
Bio-Plex Manager 6.x is launched and the run result appears in the Raw Data
table.
Note: You are now in the Bio-Plex Manager 6.x application.
Bio-Plex Manager MP continues to run and you can switch back and forth
between the two application windows.
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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.
The default file name is the run result name, followed by the time stamp of the
time of the export. For example, Experiment 2013-02-12 13.04.08. You can
accept the default name or enter a different name for the file.
5.
Click Save.
A message appears informing you that the result file has been exported.
If Bio-Plex Manager 6.x is installed on the same computer where you are
running Bio-Plex Manager MP, you are also asked if you want to open the
result in Bio-Plex Manager 6.x
6.
In the Export Results dialog box, click Yes.
Bio-Plex Manager 6.x is launched and the data result appears in the Raw Data
table.
Note: You are now in the Bio-Plex Manager 6.x application.
Bio-Plex Manager MP continues to run and you can switch back and forth
between the two application windows.
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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. You return to BPM MP, edit the protocol, rerun the protocol, and export
the result a second time. When you are prompted to save the result, if you use
the same file name that you used for the first run (that is, Exp. Region 21) you
will overwrite the result file from the first run.
Note: Before you export your result from BPM MP to BPM 6.x, you must
close the Report Table view for Exp. Region 21 in BPM 6.x. If you do not
close the Report Table view for the first result file, BPM 6.x does not
recognize the new result file as an updated version of what is currently
displayed, and it does not load the new file. Therefore, you will continue to
see the old result.
Tip: Give your result files unique names to avoid running into this
problem. By default, a time stamp is appended to the end of the name of
the result file, making it unique.
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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. You can use the standard lot as provided or customize it to your
experiment. Standard lots can be shared with colleagues.
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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).
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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. For more information on editing an existing
assay panel, see Editing an Assay Panel on page 47.
Creating an Assay Panel by Combining Existing
Panels
You can create a new assay panel by combining existing panels. Once this panel is
created, you can cull the list and delete any analytes you are not interested in.
To create a new assay panel by combining existing panels
1.
From the protocol dialog box, click Select Analytes.
2.
Click Manage Assay Panels.
3.
In the Manage Assay Panels dialog box, select the panels from the Assay Panel
list.
Note: You can select up to four assay panels.
4.
Click New From.
5.
In the New Assay Panel dialog box, enter a name for your assay panel.
6.
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.
7.
Use the Up and Down buttons to reorder the analytes.
8.
When you are done making changes to the panel, click OK.
In the Manage Assay Panels dialog box, the new panel appears at the top of
the list.
9.
Click Close.
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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. If the imported
panel has the same name as an existing panel, Copy is appended to the name to
distinguish the imported assay panel from the existing one; for example, Assay
Panel - Copy.
To import an assay panel
1.
From the protocol dialog box, click Select Analytes.
2.
Click Manage Assay Panels.
3.
From the Manage Assay Panels dialog box, click Import.
4.
In the Import Assay Panels dialog box, navigate to the file you want to import.
5.
Select the file and click Open.
A message informs you of the number of panels that were successfully
imported; for example, “Successfully imported 3 assay panels.” The imported
panels appear at the top of the Manage Assay Panels list.
6.
Click Close.
From the protocol dialog box, you can now select any imported assay panels
from the Assay Panel dropdown list.
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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.
Tip: You can also create a new assay panel from the Manage Assay Panels
dialog box.
Editing an Assay Panel
You can make changes to an existing assay panel.
To edit an assay panel
1.
From the protocol dialog box, click Select Analytes.
2.
Click Manage Assay Panels.
3.
Select the panel you want to edit and click Edit.
4.
In the Edit Assay Panel dialog box, you can make the following changes:

Rename the assay panel.
Tip: Bio-Rad recommends you give the edited panel a new name.
This preserves the original Bio-Rad assay panel, and it eliminates
problems with overwriting your edited panels if you use the Restore
command or import updated panels from Bio-Rad.
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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. You may want to delete assay panels from the list because
you use only a subset of the published assays. If you delete a Bio-Rad assay panel,
you can always return it to the Assay Panel list using the Restore command. For
more information on restoring an assay panel, see Restoring an Assay Panel on
page 49.
To delete an assay panel
1.
From the protocol dialog box, click Select Analytes.
2.
Click Manage Assay Panels.
3.
From the Manage Assay Panels dialog box, select one or more assay panels
and click Delete.
Sharing Customized Assay Panels
If there are multiple users of Bio-Plex Manager MP in your environment, you can
customize an assay panel for your environment once and share it with other users.
Export the assay panel to a file and have your users import the panels into
Bio-Plex Manager MP on their computers. You can also use the Export feature to
archive assay panels that you no longer need.
Note: You can export any number of assay panels at a time. All selected assay
panels are exported to a single file. When the file is imported, all panels are
imported. Users will not be able to selectively import panels from the file.
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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. In these instances, you can
restore the assay panels that were originally distributed with the
Bio-Plex Manager MP software using the Restore command. Any assay panels you
created are not affected.
WARNING! If any of the Bio-Plex Manager MP assay panels provided by
Bio-Rad have been modified, these will be overwritten with the Restore
command. If you want to save these edited panels, rename the panels first
before you use the Restore command.
To restore the Bio-Plex Manager MP assay panels
1.
From the protocol dialog box, click Manage Assay Panels.
2.
Click Restore.
About Standard Lots
Standard lots are definitions of analytes and their starting concentration for a
particular assay panel. When you create a protocol, you select one of the defined
standard lots. The standard lot definitions can be reused, thus eliminating the
tedious task of entering the standards each time you run an experiment.
Bio-Plex Manager MP comes with a set of predefined standard lots.
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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 New Standard Lots
To create a new standard lot
50
1.
From the protocol dialog box, click Standards Info.
2.
Click Manage Standard Lots.
3.
In the Manage Standard Lots dialog box, click New.
4.
In the New Standard Lot dialog box, enter a name for the standard lot.
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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.
In most instances, you will be using a serial dilution. For information on defining
custom concentrations, see Defining a Standard Lot with Custom
Concentrations on page 52.
8.
Specify the starting concentration for the analytes.
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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.
Defining a Standard Lot with Custom Concentrations
There may be times when you want to customize the dilutions of your standards.
For example, you might start with a dilution factor of 4 for the first three wells, then
dilute the standard in smaller increments for the next three wells.
To define custom concentrations for the analytes
1.
In the New Standard Lot dialog box, select Custom for “Define Standard Lot
By.”
The table displays a column for each standard well.
2.
Select the number of standard wells in your protocol.
3.
For each analyte, enter the concentration values for each standard.
4.
When you are done, click OK.
Creating a Standard Lot from an Existing Lot
You can create a new standard lot from an existing lot. This is useful if you use the
same assay panel repeatedly because it saves the time of reentering the starting
concentration values.
To create a new standard lot from an existing lot
52
1.
From the protocol dialog box, click Standards Info.
2.
Click Manage Standard Lots.
3.
In the Manage Standard Lots dialog box, select a standard lot from the list and
click New From.
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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. If the imported
standard lot has the same name as an existing lot, Copy is appended to the name to
distinguish the imported standard lot from the existing one; for example, Standard
Lot - Copy.
To import a standard lot from a file
1.
From the protocol dialog box, click Standards Info.
2.
Click Manage Standard Lots.
3.
In the Manage Standard Lots dialog box, click Import.
4.
Navigate to where the standard lot file is, select the file, and click Open.
Note: The file must have an .xstds extension.
A dialog box appears informing you that the standard lot is successfully
imported and the imported standard lot appears in the list.
Editing Standard Lots
You can make changes to an existing standard lot.
To edit an existing standard lot
1.
From the protocol dialog box, click Standards Info.
2.
Click Manage Standard Lots.
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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. Once deleted, you will not be able to select the lot to use with your
protocol.
To delete a standard lot
From the Manage Standard Lots dialog box, select the lots you no longer need and
click Delete.
Exporting Standard Lots
You can export standard lots to a file, which can then be transferred to another
computer and imported into another copy of Bio-Plex Manager MP.
Note: You can export a single standard lot or multiple standard lots at one
time. In both instances, the lots are exported to a single file. When the file is
imported, all the standard lots are imported. You cannot selectively import
standard lots from a file.
To export a standard lot to a file
1.
From the protocol dialog box, click Standards Info.
2.
Click Manage Standard Lots.
3.
In the Manage Standard Lots dialog box, select a standard lot from the list and
click Export.
In the Export Standard Lots dialog box, enter the name of the file and click Save.
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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.x
on page 39.
Note: Analysis of Bio-Plex Manager MP results is supported only with Bio-Plex
Manager 6.0 or higher. Earlier versions of Bio-Plex Manager are not supported.
The following are differences between Bio-Plex Manager MP and
Bio-Plex Manager 6.x:

The Bio-Plex Manager MP results cannot be viewed in a histogram or bead
map in either software application. (Bio-Plex Manager 6.x results can be
viewed in both a histogram and bead map in the Bio-Plex Manager 6.x
software application.)

Region events are calculated differently in Bio-Plex Manager MP and
Bio-Plex Manager 6.x.

In Bio-Plex Manager MP, the total region events includes all beads within
the 50 regions whether or not they were selected for analysis.

In Bio-Plex Manager 6.x, the total region events includes only beads in the
selected regions.
The same data result will reflect this difference in total region events when
viewed in the two software programs.
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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.
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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
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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.
Best Practice
58

At the start of each day of operation, Bio-Rad recommends that you run
the recommended routine.

Before you run a protocol, check to see that all maintenance is up to date
and the Recommended Routine section displays None.
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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.
At the End of the Day
At the end of each day, run the Shut Down routine before you shut down the
instrument.
Daily Start Up Routine
The Daily Start Up routine runs different procedures depending on the state of the
instrument. Bio-Plex Manager MP detects whether the instrument needs to be
verified, calibrated, or both, and it runs the appropriate commands as part of Daily
Start Up. This routine can take 4–12 minutes.
Note: When you turn on the MAGPIX instrument, Daily Start Up is generally the
routine that is recommended. However, there may be times when Enhanced
Maintenance is recommended, for example, if calibration and verification
previously failed. Run whatever routines are recommended until maintenance is
up to date and no routines appear in the Recommended Routine section.
Tip: If verification, calibration, or both routines fail after successive attempts,
contact Bio-Rad Technical Support for assistance.
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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.
Shut Down Routine
If you do not run the Shut Down routine at the end of the previous day, when you
start up the instrument the next day, the Status section in the Maintenance view
shows that Shut Down is not current. Run the Shut Down routine first. This routine
takes 2 minutes. Once that routine has successfully completed, then run the routine
in the Recommended Routine section.
Running a Routine
In addition to running the recommended routines as part of daily maintenance, all
routines may be selected and run at any time.
To run a routine
1.
From the Maintenance view, select the routine from the Select Routine list.
2.
If the routine does not appear in the list, click the Additional Routines dropdown
list and select the desired routine.
3.
Fill the reservoirs as indicated in the Reagent Block.
The Reagent Block is colored with the reservoirs and wells that need to be filled
for the selected routine. For more information on filling the reservoirs, see
Setting Up the Reagent Block on page 64.
4.
If indicated in the Reagent Block, fill the well strip with the appropriate
reagents.
For more information on filling the well strip, see Setting Up the Reagent Block
on page 64.
5.
60
If the routine involves calibration and/or verification, select the kit in the Select
Kit section.
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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.
Once the routine is completed, a dialog box appears informing you that the
routine is completed.
Note: You cannot run a protocol while a routine is running. You must wait for
the routine to complete.
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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.
Routine log
Click the Routine Log link to open a
Routine Commands dialog box
displaying a complete list of all the
commands in the routine, the reagents
used, and the status of the commands.
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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.
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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.
1
2
3
4
5
6
5
6
1
7
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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.
5
Calibration or verification kit lot numbers
6
Reagent lot numbers
7
Description of the routine. Click the arrow to show or hide the description.
There is a diagram of the MAGPIX reagent block and well strip.
Important: The reservoirs and wells in the diagram correspond to those in the
MAGPIX reagent block and well strip as seen when you stand facing the
ejected plate.
When you select a maintenance routine, one or more reservoirs and wells are filled
in.
The Reagent Block section displays the lot number of the calibration kit and
verification kit currently selected. It also displays the lot numbers of the reagents
that belong to the calibration and verification kits. Use this information to ensure
that you are using the correct reagents.
Important: Do not mix reagents from different verification kits. All of the
reagents must belong to the same lot.
If you select a different kit from the Select Kit section, the lot information in the
Reagent Block section automatically updates with the new kit information.
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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. Each calibration kit comes with
the following:

1 bottle of MAGPIX calibrator

1 calibration kit CD

1 pack of well strips
Each verification kit comes with the following:

1 bottle of MAGPIX verifier

1 bottle of MAGPIX fluidics 1

1 bottle of MAGPIX fluidics 2

1 verification kit CD

1 pack of well strips
About Kit Lot Numbers
The lot number on the box identifies the kit. Use this lot number to coordinate the
reagents with the calibration or verification values (on the CDs). The bottle for each
reagent is not identified with the lot number for the kit. Each bottle is identified with
its own lot number, but this number is different from the lot number for the kit.
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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.
Importing the Calibration or Verification Values
The calibration kit CD and the verification kit CD contain values required to calibrate
the MAGPIX instrument and verify the results. Only one set of calibration values and
one set of verification values can be used at a time.
Best Practice

Import the calibration or verification values as soon as you open a new kit.
To import the calibration or verification values
1.
Navigate to the Maintenance view.
2.
In the Select Kit section, click Import Kit.
3.
Load the kit by doing one of the following:

If you have the CD, place the calibration or verification kit CD in the DVD
drive and click Load from CD.

If the file is on your computer, navigate to where it is located on the
computer, select the file, and click Open.
The lot number of the calibration kit or the verification kit appears in the Reagent
Block section of the Maintenance view. Use this number to verify that you are using
the correct calibration or verification values with your reagents.
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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.
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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.
If the Calibration, Verification, or Fluidics routines display the hourglass icon, then
run all routines in the Recommended Routine section. Once the routine is
successfully completed, the routines in the Status pane will display as current.
If the Shut Down routine displays the hourglass icon, then run the Shut Down
routine before running any recommended routines.
Responding to a Failed Routine
A routine may fail due to instrument problems or user error. When failure occurs,
follow the instructions in any messages that appear and perform the recommended
routines.
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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.
Check that the waste container is not full.
5.
Run the Adjust Probe Height procedure.
6.
Run the recommended maintenance routine.
7.
Run the Calibration and Verification routine.
If calibration fails a second time, contact Bio-Rad Technical Support.
Verification Failures
If the verification 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 verification routine again, it will succeed.
To correct a verification failure
70
1.
Check that the beads are in the correct wells.
2.
Check that the correct verification and/or calibration control values are being
used.
3.
Clean the sample probe.
4.
Check that the waste container is not full.
5.
Run the Adjust Probe Height procedure.
6.
Run the recommended maintenance routine.
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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. You must close the Routine Commands
window before you will be able to click Stop to interrupt the routine.
Preparing Your Instrument for Nonuse
When the MAGPIX instrument is not used for a period of time, microbes may grow
in the water reservoir and traces of liquids and reagents in the lines can crystallize.
Therefore, if you do not plan to use your instrument for 14 or more days, Bio-Rad
recommends you prepare your instrument for a period of nonuse. Taking these
steps before the instrument is idle will minimize the maintenance required when you
resume using it.
To prepare your instrument for nonuse
1.
Run the Prepare for Storage maintenance routine.
2.
Remove the drive fluid container from the instrument.
3.
Remove and empty the waste container.
4.
Empty any liquids from the reagent block. Wash and dry the reagent block.
5.
Empty any liquids from the well strip.
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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.
To adjust the probe height
1.
From the Maintenance view, click Adjust Probe Height.
The Adjust Probe Height dialog box appears.
2.
Empty the reagent block and the well strip.
The rightmost reservoir in the reagent block and the rightmost well in the well
strip must be empty.
3.
Insert the MCV plate, well strip, and reagent block.
4.
Click Adjust Probe Height.
When the calibration is completed, a dialog box appears confirming that the
adjust probe height procedure is completed.
5.
Click OK.
Weekly Maintenance
Clean the sample probe once a week to keep it free of any debris. Whenever you
remove the sample probe from the probe assembly, you must recalibrate the probe
before you read another plate. Therefore, cleaning the sample probe must always
be followed up with running the Adjust Probe Height maintenance routine.
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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.
From the Maintenance view, run the Adjust Probe Height procedure.
MAGPIX Maintenance
Within the first year of use, Bio-Rad recommends that you perform the 6-month and
12-month maintenance. The maintenance kits are:

Bio-Plex® MAGPIX™ 6-Month Preventive Maintenance Kit — cleans the air
filters and replaces the syringe seals (catalog #171-012010).

Bio-Plex MAGPIX 12-Month Preventive Maintenance Kit — replaces the
sample probe tube and the drive fluid filter (catalog #171-012012).
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74
Maintaining the MAGPIX System
| Bio-Plex Manager MP Software
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.
Calibration and Verification Routine
Description of Routine
Calibration normalizes the operation of the MAGPIX analyzer when it acquires data.
Once calibrated, the values remain until you recalibrate. Verification verifies the
operation of the MAGPIX analyzer.
When to Run this Routine
Bio-Plex Manager™ MP software adds calibration and verification to the Daily Start
Up routine once a week in accordance with the manufacturer’s recommendation.
Therefore, if you run the Daily Start Up routine daily, you will be running the
Calibration and Verification routine as recommended.
In addition, recalibrate the system if the any of the following is true:

The delta calibration temperature exceeds ±5ºC.

The instrument has been moved.

The instrument undergoes hardware maintenance, for example, a part
replacement.
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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.
Add 5 ml 70% isopropanol to the appropriate reservoir in the reagent block.
4.
Vortex CAL, VER, Fluidics1, and Fluidics2 each for 10 sec.
5.
Add 6 drops each of CAL, VER, Fluidics1, and Fluidics2 to the indicated wells.
6.
Click Start.
| Bio-Plex Manager MP Software
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.
Add 5 ml distilled or deionized water and 5 ml 70% isopropanol to the
appropriate reservoirs in the reagent block.
4.
Click Start.
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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.
You do not need to keep track of the calibration and verification status if you run this
routine at the start of each day.
Estimated Run Time
4–12 minutes
To Run the Daily Start Up Routine
78
1.
Navigate to the Maintenance view.
2.
In the Select Routine section, select Daily Start Up.
3.
Fill the reservoirs and the well strip with the solutions indicated in the Reagent
Block diagram.
4.
Click Start.
| Bio-Plex Manager MP Software
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.
Check that the correct calibration and control lots are being used.
2.
Clean the sample probe.
3.
Check that the waste container is not full.
4.
Run the Adjust Probe Height procedure.
To Run the Enhanced Maintenance Routine
1.
Navigate to the Maintenance view.
2.
In the Select Routine section, select Enhanced Maintenance.
3.
Add 5 ml distilled or deionized water, 5 ml 70% isopropanol, and 5 ml 0.1N
NaOH to the appropriate reservoirs in the reagent block.
4.
Click Start.
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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.
In the Select Routine section, select Fluidics Preparation from the Additional
Routines dropdown list.
3.
Add 5 ml 70% isopropanol to the appropriate reservoir in the reagent block.
4.
Click Start.
| Bio-Plex Manager MP Software
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.
In the Select Routine section, select Prepare for Storage from the Additional
Routines dropdown list.
3.
Add 5 ml distilled or deionized water, 5 ml 0.1N NaOH, and 5 ml 10% bleach to
the appropriate reservoirs in the reagent block.
4.
Click Start.
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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.
| Bio-Plex Manager MP Software
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.
Navigate to the Maintenance view.
2.
In the Select Routine section, select Shut Down.
3.
Add 5 ml distilled or deionized water and 5 ml bleach to the appropriate
reservoirs in the reagent block.
4.
Click Start.
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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.
Add 5 ml distilled or deionized water and 5 ml 0.1N NaOH to the appropriate
reservoirs in the reagent block.
4.
Insert the plate in the microplate platform and click Start.
| Bio-Plex Manager MP Software
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. Therefore, if you run the Daily
Start Up routine daily, you will be running the Verification routine as recommended.
Estimated Run Time
4 minutes
To Run the Verification Routine
Before you run the Verification routine, you must import the verification kit
information. For more information, see Calibration and Verification Kits on page 66.
1.
Navigate to the Maintenance view.
2.
In the Select Routine section, select Verification from the Additional Routines
dropdown list.
3.
Add 5 ml 70% isopropanol to the appropriate reservoir in the reagent block.
4.
Vortex VER, Fluidics1, and Fluidics2 each for 10 sec.
5.
Add 6 drops each of CAL, VER, Fluidics1, and Fluidics2 to the indicated wells.
6.
Click Start.
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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. Therefore, if you run
the Daily Start Up routine daily, you will be running this routine as recommended.
Estimated Run Time
2 minutes
To Run the Wake From Storage Routine
86
1.
Navigate to the Maintenance view.
2.
In the Select Routine section, select Wake From Storage from the Additional
Routines dropdown list.
3.
Add 5 ml distilled or deionized water and 5 ml 70% isopropanol to the
appropriate reservoirs in the reagent block.
4.
Click Start.
| Bio-Plex Manager MP Software
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.
Estimated Run Time
6 minutes
To Run the Wash Between Plates Routine
1.
Navigate to the Maintenance view.
2.
In the Select Routine section, select Wash Between Plates from the Additional
Routines dropdown list.
3.
Add 5 ml distilled or deionized water, 5 ml 70% isopropanol, and 5 ml 0.1N
NaOH to the appropriate reservoirs in the reagent block.
4.
Click Start.
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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.
Activating the Bio-Plex Manager MP License
You can activate the product either online (if you have access to the Internet) or
through Technical Support (if you do not have Internet access).
Note: To activate your license, you will need the product activation code,
which can be found in the Bio-Plex Manager MP CD folder.
Activating the License Online
Follow the procedure below if the computer on which Bio-Plex Manager MP is
installed has an Internet connection. With this method, the software uses your
activation code to automatically activate your software.
To activate Bio-Plex Manager MP online
1.
Start the Bio-Plex Manager MP software.
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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.
90
| Bio-Plex Manager MP Software
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.
Generate a credentials file and email it to Technical Support.
Technical Support uses the credentials file to generate a license and emails the
file back to you.
2.
Use the license file to activate your software.
The procedures that follow describe this two-phase process.
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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.
| Bio-Plex Manager MP Software
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.
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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 ([email protected]).
Activating the Software with a License File
Technical Support will generate a file with the license and email the file to you. When
you receive the email, transfer the file to the computer where Bio-Plex Manager MP
is installed. The file can be copied to a local hard drive, flash drive, or network drive.
94
| Bio-Plex Manager MP Software
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.
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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.
| Bio-Plex Manager MP Software
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.
Deactivating the License Online
To deactivate Bio-Plex Manager MP online
1.
Start Bio-Plex Manager MP.
2.
From the Help menu, click Manage License.
3.
Select Deactivate Bio-Plex Manager MP Online and click Continue.
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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.
| Bio-Plex Manager MP Software
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.
Important: Until Technical Support sends you a confirmation that the license is
deactivated, you will not be able to move the license to another computer or
reactivate it on the current computer.
Exporting the Deactivation Certificate
To export the deactivation certificate
1.
Start Bio-Plex Manager MP.
2.
From the Help menu, click Manage License.
3.
Select Deactivate Bio-Plex Manager MP through Technical Support and click
Continue.
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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.
Bio-Plex Manager MP Software
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
([email protected]).
Technical Support will reply with an email informing you that the license has been
deactivated. Once you receive this email, the license has been removed from the
computer. You have the option to reuse the license and activate it on any computer.
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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
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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.
Unless you specify otherwise, you will get the following reminder to back up your
database:
Please initiate a Scheduled Archive or you will eventually run out of disk space and
not be able to run Batch in xPONENT. Click Yes to open the Archive tool.
You can also run the utility by navigating to the application.
To open the Archive Utility
104 |
1.
Navigate to the following location: All Programs\Luminex\Common
2.
Click xPONENT Archive to start the utility.
Bio-Plex Manager MP Software
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. Keep in
mind that it can take several minutes to back up a large database.
To back up the database
1.
Exit the Bio-Plex Manager MP software.
2.
Navigate to C:\ProgramData\Bio-Rad\Bio-Plex Manager MP.
Note: If you do not see the ProgramData directory, the directory may be
hidden and you must show the hidden files. See Showing Hidden Files on
page 105.
3.
Copy the database file, BioPlexManagerMP_214.db3, to a backup location.
Showing Hidden Files
If you do not see the directory specified in the database path, the cause may be that
the directory is hidden from view. You must display the hidden directory before you
can back up your database.
To display hidden files
1.
Go to the Windows Start menu, select Settings, and select Control Panel.
2.
Click Folder Options.
3.
In the Folder Options dialog box, click the View tab.
4.
Under Advanced Settings, click Show hidden files, folders, and drives.
5.
Click OK.
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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. Turn the
instrument on and restart the
software.
4.
Restart the computer. Restart
Bio-Plex Manager MP.
Perform the following steps:
1.
Stop the run.
2.
Review your data and verify that
you have selected the correct
analytes in the protocol definition.
Make any necessary changes to
the selected analytes.
3.
Clean the probe and run the
Enhanced Maintenance routine.
4.
Run the protocol again.
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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.
Clean or replace the sample
probe.
3.
Perform the Adjust Probe Height
procedure.
4.
Perform the Enhanced
Maintenance routine.
5.
Run the protocol again.
When emptying the waste container,
replace it with a different waste
container that is dry. The sensors on
the emptied waste container may not
be completely dry, causing the
instrument to incorrectly detect the
waste container as full.
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.”
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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
Autofill down, definition 17
Autofilling wells 17
Auxiliary plate 27
B
Bead map 33
Bead map, white areas of 34
Bio-Plex Manager 6.1, running protocols in 28
Bio-Plex Manager 6.x, region events in 55
Bio-Plex Manager MP, differences between
Bio-Plex Manager 6.x and 55
Bio-Plex Manager MP, region events in 55
Blank wells 16
C
Calibration and Verification routine 75
Calibration kit, description of contents 66
Calibration kit, importing values 67
Calibration kit, lot numbers of 66
Calibration routine failure 70
Calibration, checking status of 68
Clear Bubbles routine 77
Control wells 16
Custom concentrations, specifying 52
D
Daily Start Up routine 78
Daily Start Up routine, recommended routine
59
Dilution Factor parameter 22
E
Editing protocols 23
Enhanced Maintenance routine 79
Exporting data from Analyze/Export view 41
Exporting data from Create/Run Protocols
view 40
Exporting data multiple times 42
Exporting data to Bio-Plex Manager 6.1 39
F
Filter plate 27
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| 111
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 of the day 59
Maintenance routines, interrupting 71
Maintenance routines, monitoring 62
Maintenance routines, running 60
Maintenance view 57
Most Concentrated Standard parameter 22
N
New From 23
Nonuse, preparing instrument for 71
P
PCR plate 27
Plate formatting 14
Plate heater, temperature range of 28
Plate heater, using 28
Plate types 27
Plate types, calculating probe height 27
112 |
Bio-Plex Manager MP Software
Plates, formatting 14
Plates, guidelines for handling 26
Post-run routine 30
Prepare for Storage routine 81
Pre-run routine 29
Prime routine 82
Probe height, adjusting 72
Protocol dialog box 10
Protocol dialog, navigating to 10
Protocol run, interrupting 34
Protocol run, resuming 35
Protocol setup, overview of 9
Protocol, definition of 9
Protocols, editing 23
Protocols, reusing 23
Protocols, running 28
Protocols, running in Bio-Plex Manager 6.1 28
Protocols, saving 11
R
Raw data table, description 32
Reagent block, description of 64
Reagent block, setting up 64
Recommended routine 58
Recommended routine, running 25
Region Selection/Severe Clog error 107
Replicate groups, autofilling 18
Replicate groups, defining 18
Result name, default 40
Run results table, description 38
Run Settings dialog box 29
S
Saving protocols 11
Selecting analytes 13
Set Replicate Size 19
Shut Down routine 83
Shut Down, checking status of 68
Software activation, offline 91
Software activation, online 89
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, definition 20
Stop beads with low bead count parameter 30
Wash between Plates routine 87
Waster container is full error 108
Well formats, removing 20
Well formatting, changing 20
Well types 16
Wells, autofilling 17
Wells, blank 16
Wells, control 16
Wells, standard 16
Wells, undefined 17
Wells, unknown 17
T
Troubleshooting MAGPIX 107
Troubleshooting, Resolving Unstable
Instrument Problem 109
U
Unclog routine 84
Undefined wells 17
Unknown wells 17
V
Verification kit, description of contents 66
Verification kit, importing values 67
Verification kit, lot numbers of 66
Verification routine 85
Verification routine failure 70
Verification, checking status of 68
W
Wake from Storage routine 86
User Guide
|
113
Index
114 |
Bio-Plex Manager MP Software
Bio-Rad
Laboratories, Inc.
Web site www.bio-rad.com USA 800 424 6723 Australia 61 2 9914 2800 Austria 01 877 89 01
Belgium 09 385 55 11 Brazil 55 11 5044 5699 Canada 905 364 3435 China 86 21 6169 8500
Czech Republic 420 241 430 532 Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65
Germany 089 31 884 0 Greece 30 210 9532 220 Hong Kong 852 2789 3300 Hungary 36 1 459 6100
India 91 124 4029300 Israel 03 963 6050 Italy 39 02 216091 Japan 03 6361 7000 Korea 82 2 3473 4460
Mexico 52 555 488 7670 The Netherlands 0318 540666 New Zealand 64 9 415 2280 Norway 23 38 41 30
Poland 48 22 331 99 99 Portugal 351 21 472 7700 Russia 7 495 721 14 04 Singapore 65 6415 3188
South Africa 27 861 246 723 Spain 34 91 590 5200 Sweden 08 555 12700 Switzerland 026 674 55 05
Taiwan 886 2 2578 7189 Thailand 800 88 22 88 United Kingdom 020 8328 2000
Life Science
Group
10032257 Rev A
US/EG
13-0782
0413
Sig 1212
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