Luminex xPONENT 4.2 User Manual

xPONENT® for

FLEXMAP 3D

Software Version 4.2 User Guide

Luminex Corporation, 2012. All rights reserved. No part of this publication may be reproduced, transmitted, transcribed, or translated into any language or computer language, in any form or by any means without prior express, written consent of Luminex Corporation.

LUMINEX CORPORATION

12212 Technology Boulevard

Austin, Texas 78727-6115

U.S.A.

Voice: (512) 219-8020

Fax: (512) 219-5195

xPONENT® for FLEXMAP 3D® Software Verison 4.2 User Manual

89-00002-00-399 Rev. A

July 2012

Luminex Corporation (Luminex) reserves the right to modify its products and services at any time. This guide is subject to change without notice. Although prepared to ensure accuracy, Luminex assumes no liability for errors or omissions, or for any damages resulting from the application or use of this information.

The following are trademarks of Luminex Corporation: Luminex®, xMAP®, xTAG®, xPONENT®, Luminex® SD™, Luminex® XYP™, MAGPIX®, MagPlex® Microspheres, MicroPlex®.

All other trademarks, including ProClin®, Cheminert®, Windows® Pentium® and Dell® are trademarks of their respective companies.

xPONENT® for FLEXMAP 3D ii

Standard Terms and Conditions for Use of Instrument Product

By opening the packaging containing this instrument product ("Product") or by using such Product in any manner, you are consenting and agreeing to be bound by the following terms and conditions. You are also agreeing that the following terms and conditions constitute a legally valid and binding contract that is enforceable against you. If you do not agree to all of the terms and conditions set forth below, you must promptly return the Product for a full refund prior to using them in any manner.

1. Acceptance

ALL SALES ARE SUBJECT TO AND EXPRESSLY CONDITIONED UPON THE TERMS AND CONDITIONS CONTAINED HEREIN, AND UPON BUYER'S ASSENT THERETO. NO VARIATION OF THESE TERMS AND CONDITIONS SHALL BE BINDING UPON LUMINEX CORPORATION ("LUMINEX") UNLESS AGREED TO IN WRITING AND SIGNED BY AN AUTHORIZED REPRESENTATIVE OF LUMINEX.

For purposes of this agreement, "Seller" shall mean either Luminex, if the Product is purchased directly from Luminex, or a Luminex authorized reseller. Buyer, by accepting the Product, shall be deemed to have assented to the terms and conditions set forth herein, notwithstanding any terms contained in any prior or later communications from Buyer and whether or not Seller shall specifically or expressly object to any such terms.

2. Warranties

THIS WARRANTY IS APPLICABLE FOR PARTS AND SERVICE FOR LUMINEX INSTRUMENTS PURCHASED DIRECTLY FROM LUMINEX TO BUYER AND ONLY TO THE EXTENT SUCH INSTRUMENTS ARE LOCATED IN NORTH AMERICA AND THE COUNTRIES THAT COMPRISE THE EUROPEAN UNION. LUMINEX MAKES NO WARRANTY, EITHER EXPRESS OR IMPLIED, WITH RESPECT TO PRODUCTS SOLD, DISTRIBUTED, LOCATED OR USED OUTSIDE OF NORTH AMERICA OR THE COUNTRIES COMPRISING THE EUROPEAN UNION. PRODUCTS SOLD OUTSIDE OF NORTH AMERICA OR THE COUNTRIES COMPRISING THE EUROPEAN UNION ARE SOLD ONLY ON AN "AS IS, WHERE IS" BASIS. NOTWITHSTANDING THE FOREGOING, LUMINEX SHALL PROVIDE BUYER A WARRANTY ON FIELD SERVICE PARTS PROCURED FROM LUMINEX FOR MAINTENANCE OF LUMINEX INSTRUMENTS IN ALL COUNTRIES IN THE WORLD AND PER THE TERMS AND CONDITIONS HEREIN. TO THE EXTENT THAT THE FOREGOING DISCLAIMERS ARE INVALID OR UNENFORCEABLE UNDER THE LAWS OF ANY JURISDICTION, THE WARRANTY, DISCLAIMER, LIMITATION OF LIABILITY AND OTHER PROVISIONS SET FORTH BELOW SHALL THEREUPON BE EFFECTIVE TO THE FULLEST EXTENT PERMITTED BY APPLICABLE LAW.

Notwithstanding Buyer's acceptance thereof, if Product is purchased directly from Luminex, Luminex warrants that for a period of twelve (12) months from date of delivery that the Product shall conform in all material respects with the Product Specifications provided by Luminex with the Product. The warranty provided herein specifically excludes any software or

iii

hardware not provided by Luminex. If Product is purchased from a Luminex authorized reseller, any warranty obligations shall be provided in writing directly by such Luminex authorized reseller to Buyer. THIS WARRANTY IS EXCLUSIVE AND LUMINEX MAKES NO OTHER WARRANTY, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. Seller's warranties made in connection with this sale shall not be effective if Seller has determined, in its sole discretion, that Buyer has misused the Product in any manner, has failed to use the Product in accordance with industry standards or practices, or has failed to use the Product in accordance with instructions, if any, furnished by Seller.

BUYER'S EXCLUSIVE REMEDY WITH RESPECT TO PRODUCT PROVED TO SELLER'S SATISFACTION TO BE DEFECTIVE OR NONCONFORMING, SHALL BE, REPAIR OR REPLACEMENT OF SUCH PRODUCTS WITHOUT CHARGE OR REFUND OF THE PURCHASE PRICE, IN SELLER'S SOLE DISCRETION, UPON THE RETURN OF SUCH PRODUCTS IN ACCORDANCE WITH SELLER'S INSTRUCTIONS BELOW. NEITHER SELLER NOR LUMINEX NOR ANY OF ITS AFFILIATES SHALL IN ANY EVENT BE LIABLE FOR INCIDENTAL, CONSEQUENTIAL OR SPECIAL DAMAGES OF ANY KIND RESULTING FROM ANY USE OR FAILURE OF THE PRODUCT, EVEN IF SELLER OR LUMINEX OR ITS AFFILIATE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING, WITHOUT LIMITATION, LIABILITY FOR LOSS OF WORK IN PROGRESS, DOWN TIME, LOSS OF REVENUE OR PROFITS, FAILURE TO REALIZE SAVINGS, LOSS OF PRODUCTS OF BUYER OR OTHER USE OR ANY LIABILITY OF BUYER TO A THIRD PARTY ON ACCOUNT OF SUCH LOSS, OR FOR ANY LABOR OR ANY OTHER EXPENSE, DAMAGE OR LOSS OCCASIONED BY SUCH PRODUCT, INCLUDING PERSONAL INJURY OR PROPERTY DAMAGE UNLESS SUCH PERSONAL INJURY OR PROPERTY DAMAGE IS CAUSED BY SELLER'S GROSS NEGLIGENCE.

In the event that Product is located outside of North America or the European Union and fails to conform to the warranty set forth herein, during the warranty period: (i) Buyer shall notify Luminex in a timely manner in writing that such Product failed to conform and shall furnish a detailed explanation of any alleged nonconformity; (ii) Buyer, at its expense, will contact either Luminex or a Luminex trained service engineer to assess the issue and identify the defective FS-PART; and (iii) at Luminex's option and election, Buyer shall either return such nonconforming Product to Luminex's manufacturing facility or destroy such Product and provide Luminex with written certification of destruction. In the event that an FS-PART is returned to Luminex's manufacturing facility, Luminex may analyze such FS-PART for defects. In the event that Luminex determines that such FS-PART is not defective, the FSPART shall be shipped to Buyer and Buyer shall be responsible for the payment for such FSPART and related shipping charges. In the event that Luminex determines that such FSPART is defective, Luminex shall be responsible for the payment for such FS-PART and related shipping charges. Except as expressly provided herein, Buyer shall not have the right to return a Product to Luminex without Luminex's prior written consent.

3. Buyer's Use of Product

Buyer shall not use this Product for any commercial purpose, including without limitation, performance of testing services, unless expressly agreed to in writing by Luminex or as specifically authorized by Luminex through a Luminex distributor.

Buyer agrees that no rights or licenses under Luminex's patents shall be implied from the sale of the Product, except as expressly provided herein or as specifically agreed to in writing by Luminex, and Buyer does not receive any right under Luminex's patent rights hereunder. Buyer acknowledges and agrees that the Product is sold and licensed only for use with

xPONENT® for FLEXMAP 3D iv

Luminex's laser based fluorescent analytical test instrumentation. Buyer further acknowledges that the Product has not received approval from the United States Food and Drug Administration or other federal, state or local regulatory agencies and has not been tested by Seller or Luminex for safety or efficacy in food, drug, medical device, cosmetic, commercial or any other use, unless otherwise stated on the Product label or in Seller's technical specifications or material data sheets furnished to Buyer. Buyer expressly represents and warrants to Seller that Buyer will use the Product in accordance with the Product label, if applicable, and will properly test and use any Product in accordance with the practices of a reasonable person who is an expert in the field and in strict compliance with the United States Food and Drug Administration and all applicable domestic and international laws and regulations, now and hereinafter enacted.

BUYER HEREBY GRANTS TO LUMINEX A NONEXCLUSIVE, WORLDWIDE, UNRESTRICTED, ROYALTY-FREE, FULLY PAID-UP LICENSE, WITH THE RIGHT TO GRANT AND AUTHORIZE SUBLICENSES, UNDER ANY AND ALL PATENT RIGHTS IN INVENTIONS COMPRISING MODIFICATIONS, EXTENSIONS, OR ENHANCEMENTS MADE BY BUYER TO THE PRODUCT OR TO THE MANUFACTURE OR USE OF THE PRODUCT ("IMPROVEMENT PATENTS"), TO MAKE, HAVE MADE, USE, IMPORT, OFFER FOR SALE OR SELL ANY AND ALL OF THE PRODUCT; EXPLOIT ANY AND ALL METHODS OR PROCESSES; AND OTHERWISE EXPLOIT IMPROVEMENT PATENTS FOR ALL PURPOSES. NOTWITHSTANDING THE FOREGOING, "IMPROVEMENT PATENTS" SPECIFICALLY EXCLUDES PATENT CLAIMS CONCEIVED AND REDUCED TO PRACTICE BY BUYER CONSISTING OF METHODS OF SAMPLE PREPARATION, METHODS OF CONJUGATING PRODUCT TO ANALYTES, THE COMPOSITION OF MATTER OF THE SPECIFIC CHEMISTRIES OF THE ASSAYS DEVELOPED BY BUYER AND METHODS OF PERFORMING THE ASSAYS (I.E., THE PROTOCOL FOR THE ASSAY).

Buyer has the responsibility and hereby expressly assumes the risk to verify the hazards and to conduct any further research necessary to learn the hazards involved in using the Product. Buyer also has the duty to warn Buyer's customers, employees, agents, assigns, officers, successors and any auxiliary or third party personnel (such as freight handlers, etc.) of any and all risks involved in using or handling the Product. Buyer agrees to comply with instructions, if any, furnished by Seller or Luminex relating to the use of the Product and to not misuse the Product in any manner. Buyer shall not reverse engineer, decompile, disassemble or modify the Product. Buyer acknowledges that Luminex retains ownership of all patents, trademarks, trade secrets and other proprietary rights relating to or residing in the Product and Buyer receives no rights to such intellectual property rights by virtue of its purchase of Product other than as expressly set forth herein. Buyer shall have no right to use any trademarks owned or licensed to Luminex without the express written permission of Luminex.

4. Buyer's Representations, Release and Indemnity

Buyer represents and warrants that it shall use the Product in accordance with Paragraph 3, "Buyer's Use of Product," and that any such use of the Product will not violate any law, regulation, judicial order or injunction. Buyer agrees to release, discharge, disclaim and renounce any and all claims, demands, actions, causes of action and/or suits in law or equity, now existing or hereafter arising, whether known or unknown, against Seller and Luminex, and their respective officers, directors, employees, agents, successors and assigns (collectively the "Released Parties"), with respect to the use of the Product. Buyer agrees to indemnify and hold harmless the Released Parties from and against any suits, losses, claims, demands, liabilities, costs and expenses (including attorney, accounting, expert witness, and

consulting fees) that any of the Released Parties may sustain or incur as a result of any claim against such Released Party based upon negligence, breach of warranty, strict liability in tort, contract or any other theory of law or equity arising out of, directly or indirectly, the use of the Product or by reason of Buyer's failure to perform its obligations contained herein. Buyer shall fully cooperate with the Released Parties in the investigation and determination of the cause of any accident involving the Product which results in personal injury or property damage and shall make available to the Released Parties all statements, reports, recordings, and tests made by Buyer or made available to Buyer by others.

5. Patent Disclaimer

Neither Seller nor Luminex warrants that the use or sale of the Product will not infringe the claims of any United States or other patents covering the Product itself or the use thereof in combination with other products or in the operation of any process.

89-30000-00-186 (Rev C.)

xPONENT® for FLEXMAP 3D vi

End-User License Agreement (EULA) for Luminex xPONENT® Software

This Luminex End-User License Agreement (“EULA”) is a legal agreement between you (either an individual or a single entity, also referred herein as “you”) the end-user and Luminex Corporation (“Luminex”) regarding the use of the xPONENT software product provided to you above, which includes computer SOFTWARE and online or electronic documentation and may include associated media and printed materials (if any) (“SOFTWARE”). The terms also apply to any updates, supplements, web content or internetbased services, such as remote access.

BY USING THE SOFTWARE, YOU ACCEPT THESE TERMS. IF YOU DO NOT ACCEPT THESE TERMS, DO NOT USE THE SOFTWARE. INSTEAD, RETURN IT TO LUMINEX OR THE LUMINEX AUTHORIZED DISTRIBUTOR FROM WHICH YOU PURCHASED THE SOFTWARE FOR A REFUND OR CREDIT. IF YOU COMPLY WITH THESE LICENSE TERMS, YOU HAVE THE RIGHTS TO USE THE SOFTWARE AS SPECIFICALLY SET FORTH BELOW.

1. OVERVIEW. The SOFTWARE is protected by copyright laws and international copyright

treaties, as well as other intellectual property laws and treaties. The SOFTWARE is licensed, not sold.

2. ADDITIONAL LICENSING REQUIREMENTS AND/OR USE RIGHTS.

a. Trial and Conversion. Some or all of the SOFTWARE may be licensed on a trial basis.

Your rights to use trial SOFTWARE are limited to the trial period. The trial SOFTWARE and length of the trial period are set forth during the activation process. The SOFTWARE may be used for evaluation purposes only during the trial period and not for any commercial use, including without limitation to any diagnostic use. You may have the option to convert your trial rights to perpetual rights. Conversion options will be presented to you at the expiration of your trial period.

b. Activation. For certain SOFTWARE, you can activate the SOFTWARE by obtaining a

license key provided by Luminex Technical Support at support@luminexcorp.com or 1-877-785-2323 or 1-512-381-4397.

c. Branding. You may only add additional branding or other graphics to SOFTWARE with

Luminex's express written consent.

d. Upgrades. You may only obtain updates or upgrades for the SOFTWARE from

Luminex Technical Support at orders@luminexcorp.com or authorized resellers. For more information on obtaining updates from authorized resellers, see http:// www.luminexcorp.com.

3. GRANT OF LICENSE. Subject to the terms and conditions of this EULA, Luminex hereby

grants to you a non-exclusive, non-transferable, non-assignable license (without right to sublicense) under Luminex's copyrights and trade secrets to use the SOFTWARE on a single computer running with a single unit of a specific model of Luminex instrument, as such model is identified on the packaging included with the SOFTWARE. You may make one (1) copy of the SOFTWARE for backup or archival purposes only. You may also install the SOFTWARE on up to two (2) additional computers for purposes of performing ancillary tasks (i.e. preparing templates/protocols, performing further analysis or rerunning previous data), provided such computers are at a single location and are NOT connected with a Luminex instrument. In addition, you may purchase the right to use the

vii

SOFTWARE on additional computers, as agreed to in writing with Luminex or its authorized reseller, for purposes of performing ancillary tasks (i.e. preparing templates/ protocols, performing further analysis or re-running previous data), provided such computers are at a single location and are NOT connected with a Luminex instrument. Although no rights or licenses under any of Luminex's patents are granted by or shall be implied from the license of the SOFTWARE or the sale of Luminex instrumentation to you, the purchaser, you may obtain a license under Luminex's patents, if any, to use this unit of Luminex instrumentation with fluorescently labeled microsphere beads authorized by Luminex by purchasing such beads from Luminex or an authorized Luminex reseller.

4. RESTRICTIONS

• SOFTWARE must only be installed and operated on a single computer running with a Luminex instrument, as set forth above.

• You may not use this SOFTWARE for any commercial purpose, including in the performance of testing services, unless expressly agreed to in writing by Luminex or as authorized in writing by Luminex through an authorized reseller of the SOFTWARE.

• You may only use the SOFTWARE with microspheres manufactured by Luminex or with kits developed, manufactured and distributed by licensees authorized in writing by Luminex.

• You must maintain all proprietary notices on all copies of the SOFTWARE.

• You may not distribute copies of the SOFTWARE to third parties.

• You may not reverse-engineer, decompile, disassemble, or otherwise attempt to derive source code from the SOFTWARE.

• You may not copy (other than one backup or archival copy), distribute, sublicense, rent, lease, transfer or grant any rights in or to all or any portion of the SOFTWARE.

• You must comply with all applicable laws regarding the use of the SOFTWARE.

• You may not modify or prepare derivative works of the SOFTWARE, including modifying any branding or graphics.

• You may not use the SOFTWARE in a computer-based service business or publicly display visual output of the SOFTWARE.

• You may not transmit the SOFTWARE over a network, by telephone, or electronically by any means.

5. TERM AND TERMINATION. Your rights under this EULA are effective until termination. You may terminate this EULA at any time by destroying the SOFTWARE, including all computer programs and documentation, and erasing any copies residing on your computer equipment. Luminex may terminate this EULA upon thirty (30) days written notice to you. Your rights under this EULA automatically terminate without further action on the part of Luminex if you do not comply with any of the terms or conditions of this EULA. Upon any termination of this EULA, you agree to destroy the SOFTWARE and erase any copies residing on your computer equipment.

6. RIGHTS IN SOFTWARE. All rights and title in and to the SOFTWARE and any copies thereof are owned by Luminex or its suppliers. This EULA is not a sale and does not transfer to you any title or ownership interest in or to the SOFTWARE or any patent, copyright, trade secret, trade name, trademark or other intellectual property right therein. You shall not remove, alter, or obscure any proprietary notices contained on or within the SOFTWARE and shall reproduce such notices on any back-up copy of the SOFTWARE. All title and intellectual property rights in and to the content which may be accessed through use of the SOFTWARE is the property of the respective content owner and may

xPONENT® for FLEXMAP 3D viii

be protected by applicable copyright or other intellectual property laws and treaties. This EULA grants you no rights to use such content.

7. EXPORT RESTRICTIONS. You agree that you will not export or re-export the SOFTWARE to any country, person, entity, or end-user subject to U.S.A. export restrictions. You hereby warrant no state or federal agency has suspended, revoked, or denied your export privileges.

8. NO WARRANTY. THE SOFTWARE IS LICENSED "AS IS." ANY USE OF THE SOFTWARE IS AT YOUR OWN RISK. THE SOFTWARE IS PROVIDED FOR USE ONLY WITH LUMINEX PRODUCTS. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, LUMINEX AND ITS SUPPLIERS DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT.

9. LIMITATION OF LIABILITY. IN NO EVENT SHALL LUMINEX OR ITS AFFILIATES OR SUPPLIERS BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR INABILITY TO USE THE SOFTWARE, EVEN IF LUMINEX OR ITS AFFILIATES OR SUPPLIERS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

10. MISCELLANEOUS. This EULA is governed by the laws of the State of Texas, U.S.A., without reference to conflicts of laws principles. You shall not assign or sublicense or otherwise transfer the rights or license granted hereunder, by agreement or by operation of law, without the prior written consent of Luminex, and all assignments in violation of this prohibition shall be null and void. This EULA is the complete and exclusive agreement of Luminex and you and supersedes all other communications, oral or written, relating to the subject matter hereof. No change to this EULA shall be valid unless in writing and signed by the party against whom enforcement is sought. The waiver or failure of Luminex or you to exercise in any respect any right or rights provided for herein shall not be deemed a waiver of any further right hereunder. If any provision of this EULA is held unenforceable, the remainder of this EULA will continue in full force and effect.

89-30000-00-403 Rev. A

xPONENT® for FLEXMAP 3D x

Chapter 1 Introduction .......................................................................................................1

Safety Precautions .......................................................................................................................................1

Elements of the Software .............................................................................................................................1

Home Page ...........................................................................................................................................1

Screen Elements ...................................................................................................................................3

System Monitor .....................................................................................................................................4

Help .......................................................................................................................................................5

Quick Start .............................................................................................................................................5

System Info Tab ....................................................................................................................................6

Basic Procedures .........................................................................................................................................8

StartingxPONENT®...............................................................................................................................8

Adding a New License Key ...................................................................................................................8

Logging On to xPONENT®....................................................................................................................8

Initial Startup .......................................................................................................................................10

Shutting Down the Analyzer ................................................................................................................13

Logging Off and Exiting .......................................................................................................................13

Using Online Help ...............................................................................................................................14

Luminex® Support .....................................................................................................................................15

Viewing the Luminex® Website ...........................................................................................................15

Contacting Technical Support .............................................................................................................15

Software Packages ....................................................................................................................................15

Chapter 2 Running Assays with FLEXMAP 3D®............................................................17

General Guidelines ....................................................................................................................................17

Biological Samples ....................................................................................................................................18

Bead (Microsphere) Handling ....................................................................................................................18

Sample Volume .........................................................................................................................................18

Plates .........................................................................................................................................................19

Chapter 3 Samples Page ..................................................................................................21

Samples Page Overview ...........................................................................................................................21

Creating New Samples ........................................................................................................................22

Editing a Sample List ...........................................................................................................................24

Chapter 4 Batches Page ...................................................................................................27

Batches Page Functionality .......................................................................................................................27

Setting Up Batches ....................................................................................................................................28

Using the Batches Page ............................................................................................................................29

Create a New Batch from an Existing Protocol ...................................................................................29

Create a New Batch from a New Protocol ...........................................................................................35

Create a New Multi-Batch ...................................................................................................................46

Batch Procedures ......................................................................................................................................49

Running a Pending Batch ....................................................................................................................49

Importing a Batch ................................................................................................................................49

Exporting a Batch ................................................................................................................................49

Editing a Batch ....................................................................................................................................50

Deleting a Batch ..................................................................................................................................50

Chapter 5 Results Page ....................................................................................................51

Results Page .............................................................................................................................................51

Performing Analysis ...................................................................................................................................52

Current Batch Tab .....................................................................................................................................53

Saved Batches Tab ...................................................................................................................................59

Replaying a Batch ...............................................................................................................................63

Results Subtab ....................................................................................................................................63

Settings Subtab ..................................................................................................................................66

Log Subtab ..........................................................................................................................................67

Sample Details Subtab ........................................................................................................................68

LIS Results Tab .........................................................................................................................................69

Reports Tab ...............................................................................................................................................70

Generating a Report ............................................................................................................................72

Chapter 6 Protocols Page .................................................................................................73

Protocols Page Functionality .....................................................................................................................73

Protocol Procedures ..................................................................................................................................74

Creating an Allele Call Protocol ...........................................................................................................74

Creating a Quantitative Assay Protocol ...............................................................................................75

Creating a Qualitative Assay Protocol .................................................................................................77

Deleting a Protocol ..............................................................................................................................78

Editing a Protocol ................................................................................................................................78

Exporting a Protocol ............................................................................................................................79

Importing a Protocol ............................................................................................................................79

Adding a New Lot for Protocol .............................................................................................................79

Lots and Kits Procedures ...........................................................................................................................79

Creating a Lot ......................................................................................................................................79

Editing a Lot ........................................................................................................................................80

Deleting a Lot ......................................................................................................................................80

Exporting a Lot ....................................................................................................................................80

Importing a Lot ....................................................................................................................................80

Creating a Kit .......................................................................................................................................80

Protocols Tab .............................................................................................................................................81

Settings Subtab ...................................................................................................................................82

Plate Layout Subtab ............................................................................................................................86

Analytes Subtab ..................................................................................................................................88

Standards and Controls (Stds & Ctrls) Tab ...............................................................................................91

Chapter 7 Maintenance Page ...........................................................................................93

Auto Maintenance (Auto Maint) Tab ..........................................................................................................93

Running Calibration and Verification ...................................................................................................95

Running the Performance Verification Routine ...................................................................................95

Lot Management Tab .................................................................................................................................95

Importing CAL or VER Kits ..................................................................................................................97

Deleting CAL and VER Kit Information ................................................................................................97

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Commands and Routines ..........................................................................................................................97

Creating a New Routine ......................................................................................................................99

Editing a Routine ...............................................................................................................................100

Deleting a Routine .............................................................................................................................100

Running a Routine .............................................................................................................................100

Importing a Routine ...........................................................................................................................100

Exporting a Routine ...........................................................................................................................101

Probe and Heater Tab .............................................................................................................................101

Adjusting the Sample Probe Height ..................................................................................................102

System Info Tab .......................................................................................................................................103

System Status Tab ..................................................................................................................................105

Schedule Tab ...........................................................................................................................................106

Support Utility Tab ...................................................................................................................................107

Sending a Support.zip File ................................................................................................................108

Chapter 8 Admin Page ....................................................................................................109

System Setup Tab ...................................................................................................................................109

Adding an External Analysis Program ...............................................................................................112

Editing an Analysis Program .............................................................................................................112

Removing an Analysis Program ........................................................................................................112

Arranging Main Navigation Buttons ...................................................................................................112

Maintenance Options ........................................................................................................................113

Group Setup Tab .....................................................................................................................................114

User Setup Tab ........................................................................................................................................116

Create User Account Window ...........................................................................................................118

Edit User Account Window ................................................................................................................119

Batch Options Tab ...................................................................................................................................120

Alert Options Tab .....................................................................................................................................122

Alert Options Tasks .................................................................................................................................123

CSV Options Tab .....................................................................................................................................124

Archive Options Tab ................................................................................................................................126

Archive Utility .....................................................................................................................................126

Licensing Tab ..........................................................................................................................................130

Adding a New License Key ...............................................................................................................131

Schedule Tab ...........................................................................................................................................131

Editing Maintenance Schedule Settings ............................................................................................132

Report Options Tab .................................................................................................................................133

Table of Contents

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xPONENT® for FLEXMAP 3D xiv

Chapter 1: Introduction

Safety Precautions

DANGER: Samples and waste fluid can contain biohazardous infectious

agents. Handle them at Biosafety level 2, as recommended for any potentially infectious human serum or blood specimen in the DCE/NIH manual, Biosafety in Microbiological and Biomedical Laboratories, 1984.

CAUTION: Although beads do not contain hazardous or carcinogenic

components at toxic levels, they can be toxic if swallowed. In addition, contact with acids liberates toxic gases. If beads come into contact with skin, wash immediately with copious amounts of water. In case of an accident, seek medical advice immediately and show the product label or container to your medical provider. A material safety data sheet (MSDS) is available upon request.

CAUTION: Luminex® reagents can contain ProClin® as a preservative. This

can cause an allergic reaction in some people. Use personal protective equipment (PPE), including gloves and safety glasses. Check the assay package insert for assay component information.

NOTE: Do not use strong organic solvents with this instrument. Contact

Luminex® Technical Support when in doubt about compatibility of cleaning and decontamination agents or materials.

Elements of the Software

Home Page

Home > Home

The Home page displays a Welcome message, batch creation buttons, Daily Activities shortcuts, and the Installed Protocols list.

Return to the Home page at any time by clicking Home in the Navigation toolbar. This page contains the following:

Click to Create a new Batch using the highlighted Protocol below - Creates a new batch from a new protocol. This allows you to create a new protocol while you are creating the batch. Choose this function if you want to quickly create a batch and run it and you do not already have a protocol that is appropriate for use. This is useful for one time batches you do not expect to rerun frequently. However, you always have the option of saving a protocol once a batch is created.

Click to Create a new Batch using the highlighted Protocol below - Creates a new batch using a selected protocol from the Installed Protocols list.

Installed Protocols - Displays a list of protocols. The list contains the following information about each protocol:

• Name

• Version

• Manufacturer

• Date

Scroll - Use the arrows on the right to move through the list of protocols.

View - Opens the Settings tab of the Protocols page to view the selected protocol. This tab

enables viewing the settings, analytes, and plate layout for the selected protocol.

Daily Activities - Contains shortcut buttons to common commands in the Luminex

xPONENT® software:

xPONENT® for FLEXMAP 3D 2

• System Initialization - Opens the routine specified in the Maintenance Options on the Admin page.

• Shutdown - Opens the System Shutdown command in the Auto Maint tab on the Maintenance page.

• Probe and Heater - Opens the Probe and Heater tab on the Maintenance page.

Sys Info - Opens the System Info tab of the Maintenance page.

Reports - Opens the Reports tab of the Results page.

Screen Elements

This section shows screen elements and the terms used in this book to describe them.

1 Page 2 Tab 3 Subtab

Navigation Elements

Page - Across the top of the window, there is a content pane with page tabs. Click a page to

go to that part of xPONENT®.

Tab - On the left side of the window, along the left side of the content pane, are tabs. Click a tab to go to that subsection of the software.

Subtab -

A tab can have one or more subtabs. These are located below the tab, are smaller, and are identified by the circle on the left end of the subtab. The circle is red when the subtab is open. For some workflows, you must move through the subtabs of a tab sequentially, completing the work on one subtab and clicking Next to move to the next subtab.

Introduction

Right-Click Menu

Certain sections of the software such as tables, lists, and text boxes have right-click option menus. Menus are different depending upon the item you right-clicked.

• Apply Dilution Down - sets the dilution levels for the sample.

• Print All - Prints all sections or cells of the item.

• Print Selection - Prints only the selected section or cell.

• Import - Imports a file.

• Export Grid Contents - Opens a File Dialog dialog box. Use the Browse button to select a location, file name, and file type (either a text or CSV file) for the export. This exports all data from the right-clicked item.

• Cut - Cuts the selected data.

• Copy All - Copies all data.

• Copy - Copies only the selected data.

• Paste - Pastes previously copied text or data into the box.

• Delete - Erases text or data from the selection.

System Monitor

The System Monitor is displayed at the bottom of all xPONENT® windows. It displays the physical state of the Luminex® system. Values are reported directly from the Luminex

system.

1 System Status button 2 Connection Status 3 Check Cal/Ver Ok

4 Command Display 5 Progress Bar and buttons 6 Stop button

7 Pause button 8 Eject button 9 Delta Cal Temp Status

10 Sheath Pressure 11 XY Status 12 Laser Status

13 Region Event Status 14 Total Events Status 15 Warm Up button

System Status Button - This button has two functions: When clicked, it opens the system log. It also displays the current status of the system. If there are no warnings or errors, the System Status button is green with a check mark. If there is a warning, out of calibration condition, or other important user notification, the button is yellow with an exclamation point.

Connection Display - Displays the connection status.

Cal/Ver Ok - This will be lit up if the calibrations and verifications are connected. When you

click the Cal/Ver button, it takes you to Maintenance > System Setup.

xPONENT® for FLEXMAP 3D 4

Command Display - Displays the following:

• The command currently running.

• The system state (i.e. running, idle, etc.).

• Date and time.

Progress - Displays a bar graph showing the progress of the current command or routine; if the command or routine is finished, it displays a full progress bar and the command status as

Complete.

Pause - Pauses the system after the current command completes. Pause does not stop the

system in the middle of running a command. You cannot run another command while the system is paused. Pause the system before stopping it so that it will finish the current command, store the pending batch and then resume exactly where it left off.

Stop - Stops the system, regardless of command status. Use this only if it does not matter whether the data from the current well is lost.

Eject - Ejects the plate. Once the plate is ejected, the Eject button changes to Retract. Retract retracts the plate, and the Retract button changes back to Eject.

Delta Cal Temp - Displays the difference in temperature in degrees Celsius between the current reading and the reading when the system was calibrated. If the temperature is out of tolerance, this shows a high or low arrow. When clicked, it opens the Auto Maint tab.

Sheath Pressure - Displays the sheath pressure in psi. A high or low arrow is displayed if the pressure is trending up or down versus the calibration pressure it turns yellow. When clicked, it opens the System Info tab.

XY Status - Displays the current location of the command and the temperature of the plate heating block in degrees Celsius. When clicked, it opens the Probe & Heater tab.

Laser Status - Displays the laser status, including the time remaining until you must warm up the laser again. The Laser status box is blue. The button turns yellow when the lasers are turned off and about ten minutes before they turn off. Clicking the Warm Up button restarts the active clock for the laser.

Region Events Status - Displays the number of bead events detected per second that are classified in a region.

Total Events Status - Displays the number of total events detected per second.

Warm Up Button - Starts or schedules a warmup.

Help

To display online help for the tab in which you are currently working, click the blue “i” icon at the upper right of the xPONENT® window. This opens a help window with information specific to that tab.

To display system-level help, click the blue question mark at the top of the xPONENT window, then click Contents and Index. The online help opens and you can navigate to any available topic.

To display quick start information, click the blue question mark at the top of the xPONENT window, then click Quick Start.This displays information about the seven basic steps to start the system.

Quick Start

The five steps to starting and using xPONENT® are the following:

Introduction

To Go to Expanded Help

Adjust the sample probe height Home > Probe and Heater Adjusting the Sample Probe

Initialize the system Home > System Initialization Running the System Initialization

Routine

Run an assay Home > Create a new Batch

Analyze Results > Saved Batches Performing Analysis

Print reports Results > Reports Reports Tab

System Info Tab

Maintenance > System Info

from a new protocol, or Home > Create a new Batch using the highlighted protocol below

Create a New Batch from a New Protocol

Create a New Batch from an Existing Protocol

Use this tab to view information and diagnostics about the Luminex instrument.

This tab contains the following information:

• Software

• Version

• Operating System

• Licensing

• Instrument Type

xPONENT® for FLEXMAP 3D 6

• Serial Number

• Firmware Version

• XYP Heater Temperature

• Sheath Pressure

• Calibration/Verification Status

• Last F3DCAL1 Calibration

• Last F3DeCAL1 Calibration

• Last F3DCAL2 Calibration

• Last F3DCAL3 Calibration

• Last F3DVER1 Verification

• Last F3DeVER1 Verification

• Last F3DVER2 Verification

• Last Fluidics Test

• Delta Calibration Temp

• System Temperature

• DD Temperature

• CL1 Temperature

• CL2 Temperature

• CL3 Temperature

• CL1 Voltage

• CL2 Voltage

• CL3 Voltage

• DD Voltage

• RP1 Voltage

• Number of Syringes

Items in this list relating to calibration and verification (CAL/VER) have one of the following states:

• Passed - Indicates that the process completed successfully.

• Failed - Indicates that the process was not completed successfully. Failed items appear in red.

• Not Current - Indicates that verifiers are not current. Verifiers are not current if you have not calibrated the system since the last time you ran the verifiers.

• Not Yet Run - Indicates that this process has not yet been run on the machine.

Copy - Copies the system information to the Windows clipboard. You can then paste it into a text editor such as Notepad.

Save - Opens the Save As dialog box to specify a file name and location to save the system information file.

Introduction

Basic Procedures

StartingxPONENT

• On the PC desktop, click the Luminex® xPONENT® icon, or click Start > All Programs > Luminex > xPONENT > Luminex xPONENT.

• If you have a trial license, contact Luminex® Technical Support to obtain a full license, or click OK in the dialog box to continue.

• If this is the first time you have started the software, the User License Agreement may display. Read the license agreement. Select I accept the terms of this license

agreement, then click OK.

NOTE: For safety and legal information, refer to the xPONENT® for

FLEXMAP 3D ® Hardware Version 4.2 User Manual that you received with your instrument.

Adding a New License Key

1. Access the Admin page, then the Licensing tab.

2. Click License (bottom right corner of window).

3. Copy and paste the new key into the License Code field. The License File field remains

blank.

4. Click OK. This closes xPONENT®, applies the license, and restarts xPONENT®.

Contact Luminex® Technical Support if you have any difficulty saving or adding a new license key.

Logging On to xPONENT

If your version of xPONENT® is licensed for 21 CFR Part 11 or Security, an application administrator must set up user IDs (and passwords, if required).

NOTE: Contact Luminex® Technical Support if you have problems logging

xPONENT® for FLEXMAP 3D 8

in. If you want to purchase a license for 21 CFR Part 11 or the security module, contact Luminex® to place an order.

CAUTION: Use of this software by untrained personnel can result in

inaccurate data and test results. Users of xPONENT® must read the documentation thoroughly before operating the software.

1. On the System Login tab, type your user ID.

2. If you are using a secure version of the software, type your password. The Home page

opens.

3. From the Home page, open the Admin page. Open System Setup tab.

NOTE: This allows you to define the System Initialization routine.

Introduction

4. From the Maintenance options drop-down menu you can define the daily startup routine.

Select the check box if you want to Allow running the calibration or verification if the

instrument is not warmed up.

5. You can set how often the system will run the calibration routine.

Initial Startup

When you turn on the system for the first time, perform the following procedures:

1. Adjusting the Sample Probe Height

2. System Initialization

Adjusting the Sample Probe Height

Adjust the sample probe height to ensure that the probe drops far enough into the well to acquire sample.

NOTE: Ensure that there is no liquid in the wells or reservoirs before

NOTE: When you adjust and save the probe height settings for all three

WARNING: Correct sample probe height is critical to successful sample

adjusting the sample probe height.

areas under a plate name, all areas retain the adjustment.

acquisition and calibration. Problems with the sample probe height can lead to fluid leaks and inhibit sample acquisition.

1. On the Home page, click Probe and Heater under Daily Activities. The Probe &

Heater tab opens.

2. Select a plate in the Plate Type list.

• 96-well and 384-well Hard Bottom Plates - No disk is required. Ensure that the well location is selected on the plate image. Use well D6 for the 96-well plate and well H12 for the 384-well plate (a green pin marks the location). To change the well location, click on the desired well in the plate image.

• 96-well Filter or Mylar Bottom Plate - Place one (5.08) alignment disk into a well. Ensure that the well location is selected on the plate image. Luminex® recommends using well D6 for 96-well plates.

• 384-well Filter or Mylar Plate - Use the Probe Height Adjustment Tool (not supplied).

NOTE: You can order the Probe Height Adjustment Tool (P/N CN-0298-01)

at http://www.luminexcorp.com/Products/ORDERING-

INFORMATION

3. Verify that the microtiter is not warped. Warped plates can lead to incorrect probe height adjustment.

4. Click Eject to eject the plate carrier.

xPONENT® for FLEXMAP 3D 10

NOTE: If using a strip-well plate, ensure that a strip is present in the

selected well location, prior to calibration.

5. Place the plate on the plate holder with A1 in the top left corner. Place the off-plate reagent block on the plate carrier. Place a well-strip (provided with the Calibration and the Performance Verification kits) in column S1 of the block.

NOTE: Make sure there is no liquid in the plate or the off plate reagent

block.

6. Click Retract to retract the plate carrier.

7. Type a name for the plate in the Plate Name box, or select a saved plate from the Plate

Name list.

NOTE: If a saved plate is selected the results of the new calibration will

override the previous calibration.

8. In the Plate section, click D6 for the 96-well plate. Click H12 for the 384-well plate.

9. In the Reservoir section, click RB1.

10. In the Strip-Wells section, click SD1.

11. Click Auto Adjust Height. The probe automatically adjusts itself and saves it to the plate you selected.

NOTE: The probe height is automatically set to 0.49 mm. The probe

automatically adjusts this distance from the bottom of the plate or calibration disks.

NOTE: When you adjust and save the probe height settings for all three

under a plate name, all areas retain the adjustment.

Introduction

WARNING: Correct sample probe height is critical to successful sample

acquisition and calibration. Problems with the sample probe can lead to fluid leaks and inhibit sample acquisition.

CAUTION: Ensure that the probe height is set correctly before calibrating

the system.

Revive After Storage Routine

NOTE: The Revive After Storage routine is necessary when the system

has been idle for more than a week.

After you have adjusted the sample probe height, run the Revive After Storage (Luminex) routine.

1. Open the Maintenance page, then the Cmds & Routines tab.

2. Select Revive After Storage (Luminex) from the Routine Name drop-down list. The Revive After Storage routine performs the following commands:

• Warmup

• Backflush (x2)

• Drain RA2 (x3)

• Alcohol Flush RB1 (x2)

• Backflush

• Wash RA1 (x3)

3. Add 70% isopropanol or 70% ethanol to reservoir RB1 on the off-plate reagent block as indicated on the Cmds & Routines tab. Add DI Water to reservoir RA1.

NOTE: The drain reservoir (RA2) should be empty.

4. Click Run.

After the Revive After Storage routine is complete, run the System Initialization routine.

System Initialization

Warm up the lasers to prepare the optics prior to sample acquisition. The system automatically begins warming up when you turn power on; however, you will need to use the Warmup command if the system is idle for four hours or longer. Failure to properly warm up the lasers will affect assay results and system performance.

• On the System Status bar, click the Warm Up button.

• Open the Maintenance page, and then the Cmds & Routines tab. Click Warmup in the

Commands section at the left of the screen, and then click the Run button at the bottom right to begin the procedure. The warmup process takes 30 minutes to complete.

Calibrate the system before use. Open the Maintenance page and then the Auto Maint tab and select the Calibration Verification button and follow the instructions provided on the screen.

xPONENT® for FLEXMAP 3D 12

NOTE: See the Defining the System Initialization section for more

information.

Calibrator xMAP beads are used to normalize the settings for the reporter channel, all classification channels, and the doublet discriminator channel. Verification xMAP beads are used to verify calibration and optical integrity of the system.

If the system is not fully calibrated, a warning message opens.

Once calibrated, the values remain until you recalibrate. You can track system calibration and verification results through the Calibration and Verification report.

Luminex® recommends that you calibrate your system once a week. In addition, recalibrate the system if any of the following things occur:

• The delta calibration temperature exceeds ± 5°C.

• You move the instrument.

• You experience sample acquisition problems.

• The instrument undergoes hardware maintenance, such as replacement of a part.

Luminex® recommends that you verify system performance on a daily basis.

The daily system initialization routine can be set to include calibration and or verification under the Admin page, System Setup tab, Maintenance Options section.

Before you can calibrate or verify the system, you must import FLEXMAP 3D® calibrator and verification bead lot information. Do this using the Lot Management tab of the Maintenance page. This information is available on the CD that accompanies the Performance Verification Kit and the Calibration Kit, and also available on the Luminex website at http:// www.luminexcorp.com/Support/index.htm.

NOTE: Ensure that the Luminex analyzer lasers are warmed up and the

probe height is set correctly before calibrating the system. Do not move the system waste line while calibrating.

Shutting Down the Analyzer

Run the daily shutdown routine to prevent clogs and crystallization of salt in the sample probe. Clogs and crystallization of salt in the sample probe can cause problems with calibration, verification, and data acquisition; they can also cause sample splashing. Shut down the system properly to ensure system integrity.

Logging Off and Exiting

To log off and exit xPONENT®:

1. Click Logoff at the top of the page.

2. When the Confirm dialog box opens, click OK. This opens the Log In page, with Exit on the left tab.

Introduction

3. Click Exit to exit the application.

Using Online Help

English-language help is available at all times while you are using xPONENT®. To display online help for the page or tab in which you are currently working, click the blue “i” icon at the upper-right of the xPONENT® window. This opens a help window with information specific to that page or tab.

To display system-level help, click the blue question mark at the top of the xPONENT window, then click Contents and Index. The online help opens, where you can navigate to any available topic.

To display quick start information, click the blue question mark at the top of the xPONENT window, then click Quick Start. This displays information about the basic steps to start the system.

To display software information, click the blue question mark at the top of the xPONENT window, then click About Luminex xPONENT. The xPONENT information dialog box opens, displaying the software version information.

xPONENT® for FLEXMAP 3D 14

Luminex® Support

Viewing the Luminex® Website

Additional information is available on the Luminex® website. FAQs are available at http://

www.luminexcorp.com/Support/index.htm.

You can access the Technical Support Website using a user name and password at https://

esupport.luminexcorp.com/OA_HTML/jtflogin.jsp.

Contacting Technical Support

Luminex® Technical Support representatives are ready to help you. If the question or problem relates to materials from the assay kit, contact the kit provider directly.

Luminex® Technical Support is available to users in the U.S. and Canada by calling 1-877-785-BEAD (2323). Users outside of the U.S. and Canada can contact us at +1 512-381-4397. Inquiries may also be sent by email to support@luminexcorp.com.

Software Packages

Multiple levels of user access can be licensed for xPONENT®.

Basic - Allows instrument control.

Additional features for which you can obtain a license:

• Secure - Includes all of the Basic functions as well as administrator-controlled user

permission levels.

• 21 CFR Part 11 - Includes all of the Secure package features as well as the option to

require electronic signatures to perform certain tasks. (Electronic signatures are listed in the system log.)

• Automation - Includes the ability to communicate with external hardware.

• Remote Web Monitoring - Enables you to view alerts and system status using a

webpage.

• LIS - Enables the system to communicate with an external Laboratory Information System

(LIS) database. The LIS package enables you to export and import patient result data in ASTM file format.

You must have an instrument control license to operate the instrument.

For more information about purchasing upgraded packages, or to obtain specific package documentation, contact your vendor.

Introduction

xPONENT® for FLEXMAP 3D 16

Chapter 2: Running Assays with

FLEXMAP 3D

General Guidelines

WARNING: Modifying or deleting xPONENT® system files can cause

degradation of system performance. Repair modified or deleted xPONENT® system files by uninstalling and re-installing the xPONENT® software. Luminex ®recommends that you contact Luminex® Technical Support before uninstalling and reinstalling xPONENT®.

WARNING: Using unauthorized third-party software with xPONENT

software can result in corruption or failure of the xPONENT software. Use third-party software at your own risk. The operation of the system software is validated only when it runs alone on the dedicated PC.

NOTE: If you are using a screen saver on the PC on which xPONENT® is

installed, xPONENT® prevents it from activating. A dialog box opens each time xPONENT® is launched, recommending that the screen saver and any power management settings be turned off.

CAUTION: This system contains electrical and mechanical components that,

if handled improperly, are potentially harmful. Adhere to standard laboratory safety practices.

CAUTION: Protection provided by the equipment can be impaired or the

warranty voided if the Luminex® system is used in a manner not specified by Luminex® documentation or Luminex® Corporation.

Biological Samples

CAUTION: Human and animal samples may contain biohazardous

infectious agents. Where exposure to potentially biohazardous material—including aerosol—exists, follow appropriate biosafety procedures and use personal protective equipment such as gloves, gowns, laboratory coats, face shields, or mask and eye protection. Use ventilation devices. Observe all local, state, and federal biohazard handling regulations when disposing of biohazardous waste material.

Dilute concentrated biological samples, such as plasma or serum, at least 1:5 with reagents as part of assay setup or as a final dilution step to reduce the chance of system clogs. If you are running a MagPlex® or MicroPlex®kit, follow the dilution instructions in the kit’s product insert.

Bead (Microsphere) Handling

MicroPlex® and MagPlex® beads come in various configurations. To reduce foaming and precipitation, avoid agitating the beads until you are ready to vortex and use them. Beads settle and must be resuspended by vortexing before use. In addition:

• Multiple pipetting from the original container can affect bead concentrations.

• Protect MagPlex® and MicroPlex® beads from light at all times to prevent photobleaching.

Photobleaching effects are cumulative. To maintain the integrity of the beads, minimize their exposure to light.

• Store MagPlex® and MicroPlex® beads at 2 degrees C to 8 degrees C.

NOTE: Refer to the product information sheet that accompanies your

Sample Volume

Sample volume or sample sizes range from 10 to 200 µL. Ensure that some of the sample remains in the well after aspiration; about 25 µL greater than the sample volume. This amount may vary depending on the type of plate used. After acquisition, the Luminex analyzer washes the sample lines resulting in ejection of approximately 45 µL of sheath fluid back into the well for a 96 and 384-well plate. Ensure that there is room to add this amount to the well without overflowing and contaminating other wells.

The volume restrictions on the assay design can be expounded by the following formula:

Total well volume (µL) - Sample uptake volume (µL) + 45 (µL) <Maximum Well Volume (µL)

• Total well volume = Starting sample volume of a well before the unit samples for

acquisition. Well volume is determined by the consistency of the bead set.

• Sample uptake volume = Uptake volume for acquisition (program this in the protocol as

sample volume).

• 45 (μL) = Volume expelled back into the well.

xPONENT® for FLEXMAP 3D 18

MapgPlex® beads or assay for additional information.

Plates

• Maximum well volume plate = The maximum volume capacity of the wells in a selected 96

and 384-well microtiter plate.

NOTE: This sample volume information is for a 96 and 384-well plate.

Follow the IVD assay manufacturer's instructions for use on the selection of plates. If not specified, follow these guidelines when choosing plates:

• When using uncovered plates, use black opaque plates to reduce photobleaching.

• For heated assays, use CoStar® Thermowell® 96-well or 384-well, thin-wall polycarbonate,

model P plates.

• For unheated assays, use a 96-well plate or a 384-well plate with an overall height no

greater than 0.75 inches (19 mm).

CAUTION: The heater block or plate can be hot and can cause personal

injury when touched. Use care when you are working with it and do not touch it.

See the recommended consumables list on the Luminex® website at http:// www.luminexcorp.com/Support/index.htm and click Recommended Materials from the Support Resources section for more information.

Running Assays with FLEXMAP 3D

xPONENT® for FLEXMAP 3D 20

Chapter 3: Samples Page

Samples Page Overview

Samples > Samples

Use this tab for the following:

Create New Samples - Click to create a new sample.

Protocol - Displays the protocol selected in the Samples tab. If xPONENT® has a Laboratory

Information System (LIS) license enabled, any sample details provided by the LIS also appear in the Sample list.

Version - Displays the protocol version number.

Number of Samples - Displays the number of samples are in the protocol.

NOTE: If a protocol is created using the same name and version as a

previously deleted protocol, previous, or pending are relinked to the added protocol.

Details - Displays the details of the selected protocol.

Create Batch - Creates a new batch from the selected protocol.

Creating New Samples

Follow these steps to create a new sample list.

1. Open the Samples page.

xPONENT® for FLEXMAP 3D 22

2. In the Sample Lists section, select the protocol you are using for the sample list, then click Create New Samples. The Create Sample tab opens.

3. In the ID box, type the sample ID.

WARNING: You will not warned if you create a sample ID that is the same

as another.

4. Type a patient first name in the First name box (optional).

5. Type a patient last name in the Last name box (optional).

6. Type any comments (optional).

7. Click Save to add the sample to the Sample list.

8. To add more samples, click New. Repeat Steps 3-7 until you have added all of the samples you want in your samples list.

9. Once you have added all the desired samples, click Close.

NOTE: Samples can also be added using an LIS.

Samples Page

Editing a Sample List

1. Open the Samples page.

xPONENT® for FLEXMAP 3D 24

2. In the Samples list section, choose the protocol you want to edit, then click Details. The Edit Samples subtab opens.

3. Click a sample, then use the Move arrows to move it up or down in the sample list, changing the order in which they will be acquired.

4. To add a new sample to the list, click New, then perform the following steps:

a. In the ID box, type the sample ID.

b. Type a patient first name in the First name box if desired

c. Type a patient last name in the Last name box if desired.

d. To add a comment about the sample, type it in the Comment box; this is optional.

e. Click Save to add the sample to the Sample list.

5. To edit an existing sample, click the sample, then click Edit.

6. Once you have completed editing the sample list, click Close.

Samples Page

xPONENT® for FLEXMAP 3D 26

Chapter 4: Batches Page

Batches Page Functionality

Batches > Batches

Options on the Batches tab on the Batches page are:

• Create a New Batch from an existing Protocol

• Create a New Batch from a new Protocol

• Create a New Multi-Batch

NOTE: These tabs (except New MultiBatch) are sequential. You must

complete each screen in a specific order.

The Pending Batches list displays the name of the protocol used with the batch, the protocol version, date, and status for each pending batch. The following buttons only appear if the pending batches have data:

Reacquire - Reacquires the selected batch.

WARNING: Performing this action may result in varying results due to

decreased bead counts, potential carry over effects, and timesensitive reagents.

Save Prtcl. - Saves protocol and/or assay information for a standard/control.

Plate Layout - Opens the Report dialog box, which includes the Batch Plate Layout Report.

Import - Imports a batch not previously run in xPONENT® 4.2 from a folder on the PC into

xPONENT

Export - Exports the batch information in order to move it to another computer, make a copy of the data, and then import it into xPONENT® on another computer.

Delete - Deletes a batch.

Edit - Edits a batch.

Run - Runs a batch.

Setting Up Batches

Batches consist of protocols and samples for acquisition and can span more than one plate. Protocols contain predefined commands that must be included in every batch acquisition.

You can group batches together as a multi-batch. Multi-batches can consist of any number of batches that have been set up from different protocols and are processed consecutively. Multi-batches cannot be run on multiple plates.

NOTE: It is recommended that the manufacturer assay kit controls are

analyzed with each plate.

WARNING: Human and animal samples may contain biohazardous

When setting up a batch, if the number of samples exceeds the number of wells in one microtiter plate, you can add additional plates in the Add and Change Plate secondary window. Additional plates are identified on the bottom of the plate image as Plate a of b, where a is the plate number and b is the total number of plates.

infectious agents. Where exposure (including aerosol) to potentially biohazardous material exists, follow appropriate biosaftey procedures and use personal protective equipment, such as gloves, gowns, laboratory coats, face shields, or mask and eye protection, and ventilation devices. Observe all local, state, and federal biohazard handling regulations when disposing of biohazardous waste material.

xPONENT® for FLEXMAP 3D 28

Using the Batches Page

1. Open the Batches page.

2. Click one of the following:

• Create a New Batch from an Existing Protocol

• Create a New Batch from a New Protocol - if you select this option, you can save

the protocol and/or stds/ctrls information.

• Create a New Multi-Batch

3. Type the batch name in the Batch Name box.

4. Type an optional description of the batch in the Enter Optional Description box.

5. If you are creating a batch from an existing protocol, select the protocol in the list. Click

Next. If the protocol uses standards and/or controls, the Stds & Ctrls tab displays.

NOTE: If you are creating a batch from a new protocol, the next steps do not

apply. You have to add Acquisition Settings and Analysis Settings before moving to the next screen.

6. The Stds & Ctrls tab appears. View the details of the active reagents, apply different assay standards/controls, or manually enter new information. Click Next.

7. On the Plate Layout tab, assign well commands for this batch.

8. Click Run Batch to begin batch acquisition, or click Save to save batch information to the

Pending Batch list to be run at a later time.

NOTE: If the batch spans more than one plate, the tray ejects automatically

when all defined wells have been acquired. A dialog box displays prompting you to insert the next plate.

Create a New Batch from an Existing Protocol

Read the instructions provided with the assay kit you are using.

1. Open the Batches page.

2. Click Create a New Batch from an existing Protocol.

3. Type the batch name in the Batch Name box.

4. Type a description about the batch in the Enter Optional Description box.

5. Click a protocol you wish to use in the Select a Protocol list.

6. Click Next. If the protocol uses standards, controls, or both, the next tab that opens is the Stds & Ctrls tab. View the details of the active reagents or apply different assay standards, controls, or both or manually enter new information. Select Next. If the selected protocol does not use standards, controls, or both, the next tab that opens is the Plate Layout tab.

7. On the Plate Layout tab, assign well commands for this batch. See Plate Layout Tab for a complete description of the commands and options on this tab.

8. Click Run Batch to begin batch acquisition, or click Save to save batch information to the Pending Batch list to be run at a later time.

Batches Page

NOTE: If the batch spans more than one plate, the tray ejects automatically

when all defined wells have been acquired. A dialog box opens, prompting you to insert the next plate.

Protocol Subtab

Batches > Batches > Protocol

Use this tab to name a batch, type a batch description, select a protocol, and view active reagents. This tab contains the following:

Batch Name/Description - Used to name and describe a batch.

Select a Protocol - Contains the protocol name, version, manufacturer, and creation date for

each protocol.

Active Reagents - Displays assay and control lots/kits associated with the selected protocol. The Standard/Ctrls Kit Name - Lot# field displays the assay standard/control kit/ lot name and lot number currently associated with the selected protocol. The Standard Lots and Controls Lots fields display any standard or control lots associated with the selected protocol.

Cancel - Returns to the main Batches tab.

Next - If you have selected a protocol with no standards or controls (displayed as None in

the Active Reagents section), clicking Next continues to the Plate Layout tab. If you have selected a protocol with standards and controls, clicking Next continues to the Stds & Ctrls tab.

Standards and Controls (Stds & Ctrls) Subtab

Batches > Batches > Stds & Ctrls

xPONENT® for FLEXMAP 3D 30

Use this tab to apply a kit or lot to the batch. This tab contains the following:

Apply Std/Ctrl Kit - Opens the Select Std/Ctrl Kit dialog box. The dialog box displays the Std/Ctrl Kit Lot #, Std/Ctrl Kit Name, Expiration, and Manufacturer for the kit. Select a Std/Ctrl kit from the list and then click OK to close the dialog box. The kit information will

display in the boxes to the right of the Apply Std/Ctrl Kit button. The selected kit must be associated with the same analyte names. You can also type information by clicking in the

Name, Std/Ctrl Kit Lot #, Expiration, and Manufacturer boxes and typing the information.

Assay Standard Information - Displays the selected standard reagents in a list. The list

displays the Reagent, Name, Lot #, Expiration, Manufacturer, and expected concentration value of each analyte.

NOTE: Click a Reagent column header to re-sort the order from the highest

number standard to standard number one. This is useful for applying dilutions in which the last standard is the highest standard.

Batches Page

Apply Std Lot - Opens the Select Lot dialog box.

Select a lot from the list and then click OK to apply the lot.

Apply Values - Applies a value across or down the Reagent, Name, Lot #, Expiration, and Analyte fields. Type a value in these fields by double-clicking on them, and then using one of the two Apply Values arrows to apply that value down or across the list of analytes.

Dilution - Contains the following dilution options:

• 1:2 - Halves the standard from each previous iteration.

• 1:10 (Log) - Computes a value of one-tenth of the standard from each previous iteration.

• 1/2 Log - Creates a 1:3.16 dilution, or half of each 1:10 (Log) from each previous iteration.

Apply Dilution - Applies the dilution selected in the Dilution list.

NOTE: The Dilution list and Apply Dilution button are displayed only if a

quantitative analysis has been selected.

NOTE: You can also manually type a number to set your own dilution factor.

It must be a whole number.

Assay Control Information - Lists the selected control reagents. The list displays the Reagent, Name, Lot Number, Expiration, and Manufacturer. Existing control lot information can be applied or new information can be typed manually.

• Apply Ctrl Lot - Opens the Select Lot dialog box. Select a lot from the list and then click

OK.

• Show Concentration - Expected, Low, and High set the expected, lowest, or highest

acceptable concentration of the analyte in the sample.

• Apply Values - Applies a value down or across the list of analytes.

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Cancel - Returns to the Batches tab.

Back - Returns to the previous tab.

Next - Continues to the Plate Layout tab.

Plate Layout Subtab

Batches > Batches > Plate Layout

Use this tab to define commands that apply to one or more wells. You can also define offplate and maintenance commands. This tab contains the following:

Plate Image - This is a representation of the plate. Each well is displayed as a circle on the grid. Well commands appear in the appropriate circles as you assign them to wells on the plate.

Command Sequence - Contains the command sequence for the active plate. The list includes all active wells, the type of command (Unknown, Standard, Control, Background, or assigned maintenance command), ID, and dilution factor. Double-click the ID field to type an ID. Double-click the Dilution field to type a dilution factor.

NOTE: A command's ID and Dilution fields have a blue border around them

if they can be double-clicked to type information.

Move Command - These arrows move a selected command up or down in the Command Sequence list, changing the acquisition order.

Import List - Opens the Open dialog box to import an existing command sequence list.

NOTE: A list of unknowns must be specified before importing a list without

locations specified.

Batches Page

Replicate Count - Defines a quantity of replicate sets from one to nine.

NOTE: Replicate count selection must be made before adding a well

command.

Grouping - Selects the sequence in which the replicates are laid out in plate wells.

NOTE: Grouping selection must be made before adding a well command.

The options are:

• 123123123. . . Lays out one of each replicate set at a time in numerical order.

• 111222333. . . Lays out all the replicates in a set before moving on to the next set in

numerical order.

You can assign the following well commands. Each command is associated with a color. You can click and drag to highlight a series of wells, click a column or row header to highlight the entire column or row, or click and highlight different wells and then click a command below to assign that command to all the highlighted wells.

• Unknown (U): Yellow

• Background (B): Purple

• Control (C): Red

• Standard (S): Green

The Delete and Start at Well commands are also available to assign as well commands. Delete removes the well command for the selected well. The Start at Well command enables you to begin acquisition at a well other than A1.

NOTE: Before adding well commands, delete all standards from the plate

layout if any of the standards need to be rearranged. Delete all controls from the plate layout if any of the controls need to be rearranged.

NOTE: Wells and commands you assign to the protocol plate layout are

saved into the protocol settings and execute each time you use the protocol to run a batch. Standards and controls associated with a given protocol typically remain constant, while the number of unknown wells often varies. You can assign a specific number of unknown wells to the plate when setting up a batch.

Commands and Routines - Allows you to add and delete commands and routines, and to create pre and post batch routines. Select a well and then select the appropriate command:

• Add

• Delete

• Pre Batch Routine

• Post Batch Routine

NOTE: If you select a routine you created, that routine must also exist on

any system to which you import this protocol. The system displays

xPONENT® for FLEXMAP 3D 34

an error when attempting to run a batch on a system where the routine does not exist.

Clicking either Pre Batch Routine or Post Batch Routine opens the Commands and Routines dialog box, where you can select the command or routine you want before or after running the batch. Clicking Add after selecting a well opens the same box for you to select a command or routine for that well. Clicking Delete after selecting a well deletes any commands or routines associated with that well.

Plate - Specifies the plate to display in the plate image in the list. Add Plate adds a new plate to the batch, and Delete Plate deletes the plate highlighted in the list.

Direction - Specifies the direction to run the plate commands. Select either horizontally or vertically. The selected direction also dictates how wells are added to the plate when assigning multiple unknowns, standards, and controls at one time.

Plate Navigation - Displays a smaller plate image for the current batch.

Single Step - Instructs the system to acquire one well and then stop. Use this to ensure the

system is working correctly before you run the whole batch.

Off Plate Area - - Designates an alternate location for maintenance commands in the Commands and Sequence list.

Save Prtcl - Opens the Save Protocol dialog box to save the protocol and/or kit.

• Select Save Protocol and/or Save Std/Ctrl Kit to save the protocol and/or kit.

• Type information in the following boxes and click Save to save the protocol or kit.

• Protocol Name

• Version

• Manufacturer

• Optional Description

• Std/Ctrl Kit Name

• Std/Ctrl kit Lot#

• Expiration

• Manufacturer

• Lots

Save - Saves the information as a pending batch.

Cancel - Returns to the Batches tab.

Back - Returns to the previous window.

Run Batch - Runs the batch and opens the Current Batch tab, where you can monitor the

batch as it runs.

Create a New Batch from a New Protocol

Click this option to create a new batch from a new protocol. This option enables you to create a protocol while you are creating the batch.

1. Open the Batches page.

2. Click Create a New Batch from a new protocol to open the Settings tab.

3. Type a name in the Batch Name box.

4. Type a description in the Description box.

Batches Page

5. Define the settings in the Acquisition Settings section. These are Volume, XY Heater (enable/disable and set temperature), Plate Name, and enable/disable Sample Wash.

NOTE: Final washes are required for proper analysis. If you are not

performing a final wash step on your plate before acquisition on the FLEXMAP 3D® instrument, enable Sample Wash here. This automatically washes each sample.

If you select Qualitative, Quantitative, or Allele Call from the Analysis Type list, you can select Analyze results while acquiring samples to view real-time analysis.

6. Next, complete the Analysis Settings. These include Analysis Type, MFI enable/disable (used for Allele Call analysis), # of standards, # of controls, either Fit all Standards or Mean of Replicates.

7. Click Next. The Analytes tab opens. Click the analytes of interest in the numbered grid. Information about the analytes opens in a list on the right side of the grid. Name the analytes.

8. To change the Default Analysis, click Change. The Analysis Settings dialog box opens.

9. Select the analysis method from the Method list. Click OK to change the default analysis for analytes to be selected. Click Apply to All Analytes to apply the selection to all analytes. The Analysis dialog box closes.

10. Type a unit of measurement in the Units box.

11. Type the desired bead count for each analyte in the Count box.

12. If you click Apply All, this applies to all analytes.

13. To change individual units or counts, change them in the analyte table.

14. Click Next. The Stds & Ctrls tab opens if you selected an analysis type other than None.

• If you are using an assay standard/control kit, click Apply Std/Ctrl Kit. In the Select

Std/Ctrl Kit dialog box, click the kit from the list and click OK. Applying a kit only works for kits already installed, but you can also manually type the information.

• If you are not using a kit, type the appropriate information in the Standard Information

and Control Information sections. The number of standards and/or controls in these sections is defined on the Settings tab in the Analysis Settings section. If your batch uses controls, enter the appropriate values for Expected Values. Click Low Value from the Show list, and enter the low value for each analyte. Click High Value from the Show list, and enter the high value for each analyte. Reagent information is not required for a custom batch unless you want to use the analysis feature.

15. Click Next. The Plate Layout tab opens.

• To add well commands, click the appropriate wells and mark them as unknown,

standard, control, background, or wash. You can also delete commands that you’ve added, and change the starting location on the plate. If you want to run in replicate, change the Replicate Count to the appropriate number and the Grouping to your preferred grouping method.

• As you add commands to your plate, they are listed in the Command Sequence list.

Here you can give each of your wells an ID. You can also import an ID list and move your commands up and down to change the plate location.

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16. Click Single Step to acquire the first well, then pause acquisition.

17. Click Run Batch to start acquisition, or Save to save the batch for a later time. You can also save the protocol and/or standard and control information by clicking Save Prtcl.

NOTE: If the batch spans more than one plate, the tray ejects automatically

when all defined wells have been acquired. A dialog box displays prompting you to insert the next plate.

Settings Subtab

Batches > Batches > Settings

Use this tab to name your new batch and configure acquisition settings. For existing batches, you can view the acquision parameters of the selected saved batch and print the batch settings report.

This tab contains the following:

• Name box and box for description - Type a name and a description in the appropriate

boxes.

• Acquisition Settings - Use this section to set the following:

• Volume - This is the volume the instrument will aspirate into the system for analysis.

Type the desired sample volume in microliters. Use values from 20 to 200 µl. To avoid air intake, add at least 25 µl to the sample well in addition to the sample size. The default value is 50 µl.

• XY heater - Select to enable the XY heater. In the box, type the desired value in

degrees Celsius. The temperature range is 35°C to 60°C.

Batches Page

CAUTION: Acquiring data before the heater has reached the proper

temperature can compromise test results.

• Timeout - Check the Enabled box to enable the Timeout.

• Bead Type - Check the Bead Type box. From the drop down menu you can select

MicroPlex or MagPlex.

• Plate Name - Select the plate name from the drop down menu. Select Current 96-well plate, Current 384-well plate, or a plate that you have created.

• DD Gating (Doublet Discriminator) - Use this to set the minimum and maximum DD Gating values. In the first box, type the minimum value. In the second box, type the maximum value. The default is 7500 to 15000.

• Reporter Gain - Select Standard PMT from the drop down menu to decrease the reporter gain.

• Analysis Settings - Displays the analysis type to be used for the batch.

Analysis Type - Use this list to choose from the following analysis types:

• None - No analysis. Select if you have your own data post-processing program and

want to obtain only fluorescent intensity results. You cannot apply standards or controls when you select None. You cannot analyze acquisitions with this setting.

• Qualitative - Qualitative analysis determines results as either positive or negative,

reactive or non-reactive. The software is flexible in defining custom result ranges, such as negative, low positive, or high positive. Determinations are based on a single standard. For qualitative analysis the Luminex software uses a specific algorithm, shown below.

(FIsample)/(FIstandard) = Ki

Where FI = Fluorescent Intensity and Ki = a “Quali” value entered in lot information to determine the value or the qualitative assay standard.

• The “Quali” value determines a cutoff or threshold. This, in conjunction with ranges

using the Lum Qual formula or an edited range specific for your assay, helps to determine qualitative results for unknown samples.

• Two predefined formulas using the algorithm are included in the system. You can use

them as is or edit their range values to meet your requirements.

• Quantitative - Determines the sample concentrations from standard curves using

regression methods Cubic Spline, Linear, Logistic 4P, and Logistic 5P, , and. Type the desired values for standards and controls in the Number of Standards and

Number of Controls boxes. Select either Fit of All Standards or Mean of Replicates for the calculation of the curve fit.

NOTE: Luminex® recommends Fit of All Standards as the most accurate

calculation of the curve fit .

Based on a range of quantitative, numerical results, a threshold range can be applied to a quantitative analysis, for example, high, low, saturated, and expected.

• Allele Call - Sets analysis for an allele call. Analytes must be put in groups of 2, 3, or

4 analytes.

• Min MFI Enabled - Select this box to enable a minimum MFI for the Allele Call

analysis. Type a value in this box to set the minimum MFI for analysis.

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• Number of Standards - Click to type the number of standards for the protocol.

• Number of Controls - Click to type the number of controls for the protocol.

• Fit of all Standards - The standard curve is determined by using each individual

standard replicate when calculating the standard curve. For example, if you run duplicates of a 7-point standard curve, the software will calculate the standard curve by using 14-points.

• Mean of Replicates - The standard curve will be determined by averaging the

individual standard replicates when calculating the standard curve. For example, if you run duplicates of a 7-point standard curve, the software will calculate the standard curve by using 7-averaged points.

• Analyze Results While Acquiring Samples - The software allows for real-time

viewing of the results as the instrument analyzes samples.

• Use External Analysis Program - Select this check box to use a third-party program

to analyze the data. The Analysis Program list becomes active when this is selected.

• Analysis Program - Use this list to select which program to use for data analysis.

• Cancel - Click to return to the main Batches tab.

• Next - Click to advance to the Analytes tab.

Analytes Tab

Batches > Batches > Analytes

Use this tab to select or edit analytes used in the batch or protocol.

This tab contains the following:

Batches Page

Default Analysis - The default analysis changes based on the Analysis Type selected in the Settings tab. You can change the analysis settings for all analytes by clicking Change if this button is enabled in this tab. This displays the Analysis Settings dialog box.

FIGURE 1.

Analysis Settings Dialog Box

If you selected Quantitative on the Settings tab, the default analysis formula is 5P Weighted. To change the default, select one of the following from the Method list:

• No Analysis

• Cubic Spline

• Linear Fit

• Logistic 4P

• Logistic 5P

If you selected Logistic 4P or Logistic 5P, select a weight type of either None or 1/y2.

If you selected Qualitative on the Settings tab, the default analysis is Luminex Qualitative. Change the default value by selecting either Luminex Qualitative or No Analysis.

Click Apply to All Analytes to apply your selection to all selected analytes. Click OK to change the default analysis to the analysis you selected. Click Cancel to close the dialog box without saving. For more information, see the “Analysis Settings” section.

Units - Type the desired units for the analytes in this box.

Count - Type the desired bead count for the analytes by clicking in the Count box. If each

selected bead set does not acquire this number of events, a warning is added to the log that not enough bead events were acquired. If you select bead sets that are not present, the analyzer continues to acquire, trying to reach the number of events per bead for bead sets that are not in the sample. Therefore, choose only the bead sets present in your sample.

Apply All - Applies the information in the Units and Counts boxes to all analytes.

Total Count - Select Stop after bead count reaches: to stop acquisition when the bead count

reaches a certain number determined by the user. Type the desired value in the box. The default value is 100.

You can also specify the minimum allowable bead count per well that the xPONENT

software analyzes. This excludes data from any beads carried over during acquisition.

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Selected Analytes List - Selected analytes appear in a list on the right side of the analyte grid. This list includes the following information:

• Name - The name of the analyte. Click and type to rename the analyte.

• Analysis - To change the type of analysis for an analyte, click this field to open the

Analysis Settings dialog box and select another analysis from the list.

• Select a method from the Method list.

• If necessary, select a weight type from the Weight Type list.

• Apply the analysis to all analytes in the list by clicking Apply to All Analytes.

• Select Mark as Intra-Well Normalization Bead to make the analyte an intra-well

normalization bead.

• Add a range to the analysis by clicking Add Range.

• Select Use Threshold Ranges to enable ranges for the analysis.

• Click Add Range to add a range.

• Type a Range Name, a Low Value, a High Value, and select Inclusive if you wish to include the low and high values in the range. Click OK to exit the dialog box.

• Units - The unit of measurement you specified in the Unit box. Click this box to type a value for the analyte.

Group - If you have selected Allele Call from the Analysis Type in the Settings tab, this button displays. Click Group to group 2, 3, or 4 analytes for the group. Multiple groups can be defined.

Cancel - Click Cancel to return to the Batches tab.

Back - Click Back to return to the Settings tab.

Next - Click to go to the next tab. If the Analysis Type selected in the Settings tab was None or Allele, this takes you to the Plate Layout tab. If the Analysis Type selected was Quantitative or Qualitative, this button takes you to the Stds & Ctrls tab.

Standards and Controls (Stds & Ctrls) Subtab

Batches > Batches > Stds & Ctrls

Batches Page

Use this tab to apply a kit or lot to the batch. This tab contains the following:

• Apply Std/Ctrl Kit - Opens the Select Std/Ctrl Kit dialog box. The dialog box displays the

Std/Ctrl Kit Lot #, Std/Ctrl Kit Name, Expiration, and Manufacturer for the kit. Select a Std/Ctrl kit from the list and then click OK to close the dialog box. The kit information will

display in the boxes to the right of the Apply Std/Ctrl Kit button. The selected kit must be associated with the same analyte names. You can also type information by clicking in the Name, Std/Ctrl Kit Lot #, Expiration, and Manufacturer boxes and typing the information.

• Assay Standard Information - Displays the selected standard reagents in a list. The list displays the Reagent, Name, Lot #, Expiration, Manufacturer, and expected concentration value of each analyte.

NOTE: Click a Reagent column header to re-sort the order from the highest

number standard to standard number one. This is useful for applying dilutions in which the last standard is the highest standard.

• Apply Std Lot - Opens the Select Lot dialog box.

Select a lot from the list and then click OK to apply the lot.

• Apply Values - Applies a value across or down the Reagent, Name, Lot #, Expiration,

and Analyte fields. Type a value in these fields by double-clicking on them, and then using one of the two Apply Values arrows to apply that value down or across the list of analytes.

• Dilution - Contains the following dilution options:

xPONENT® for FLEXMAP 3D 42

• 1:2 - Halves the standard from each previous iteration.

• 1:10 (Log) - Computes a value of one-tenth of the standard from each previous iteration.

• 1/2 Log - Creates a 1:3.16 dilution, or half of each 1:10 (Log) from each previous iteration.

• Apply Dilution - Applies the dilution selected in the Dilution list.

NOTE: The Dilution list and Apply Dilution button are displayed only if a

quantitative analysis has been selected.

NOTE: You can also manually type a number to set your own dilution factor.

It must be a whole number.

• Assay Control Information - Lists the selected control reagents. The list displays the Reagent, Name, Lot Number, Expiration, and Manufacturer. Existing control lot information can be applied or new information can be typed manually.

• Apply Ctrl Lot - Opens the Select Lot dialog box. Select a lot from the list and then

click OK.

• Show Concentration - Expected, Low, and High set the expected, lowest, or highest

acceptable concentration of the analyte in the sample.

• Apply Values - Applies a value down or across the list of analytes.

• Cancel - Returns to the Batches tab.

• Back - Returns to the previous tab.

• Next - Continues to the Plate Layout tab.

Plate Layout Subtab

Batches > Batches > Plate Layout

Batches Page

Use this tab to define commands that apply to one or more wells. You can also define offplate and maintenance commands. This tab contains the following:

• Plate Image - This is a representation of the plate. Each well is displayed as a circle on the grid. Well commands appear in the appropriate circles as you assign them to wells on the plate.

• Command Sequence - Contains the command sequence for the active plate. The list includes all active wells, the type of command (Unknown, Standard, Control, Background, or assigned maintenance command), ID, and dilution factor. Double-click the ID field to type an ID. Double-click the Dilution field to type a dilution factor.

NOTE: A command's ID and Dilution fields have a blue border around them

if they can be double-clicked to type information.

• Move Command - These arrows move a selected command up or down in the Command Sequence list, changing the acquisition order.

• Import List - Opens the Open dialog box to import an existing command sequence list.

NOTE: A list of unknowns must be specified before importing a list without

locations specified.

• Replicate Count - Defines a quantity of replicate sets from one to nine.

NOTE: Replicate count selection must be made before adding a well

command.

• Grouping - Selects the sequence in which the replicates are laid out in plate wells.

NOTE: Grouping selection must be made before adding a well command.

The options are:

xPONENT® for FLEXMAP 3D 44

• 123123123. . . Lays out one of each replicate set at a time in numerical order.

• 111222333. . . Lays out all the replicates in a set before moving on to the next set in

numerical order.

• Unknown (U): Yellow

• Background (B): Purple

• Control (C): Red

• Standard (S): Green

NOTE: Before adding well commands, delete all standards from the plate

layout if any of the standards need to be rearranged. Delete all controls from the plate layout if any of the controls need to be rearranged.

NOTE: Wells and commands you assign to the protocol plate layout are

Commands and Routines - Allows you to add and delete commands and routines, and to create pre and post batch routines. Select a well and then select the appropriate command:

• Add

• Delete

• Pre Batch Routine

• Post Batch Routine

NOTE: If you select a routine you created, that routine must also exist on

any system to which you import this protocol. The system displays an error when attempting to run a batch on a system where the routine does not exist.

• Plate - Specifies the plate to display in the plate image in the list. Add Plate adds a new plate to the batch, and Delete Plate deletes the plate highlighted in the list.

• Direction - Specifies the direction to run the plate commands. Select either horizontally or vertically. The selected direction also dictates how wells are added to the plate when assigning multiple unknowns, standards, and controls at one time.

Batches Page

• Plate Navigation - Displays a smaller plate image for the current batch.

• Single Step - Instructs the system to acquire one well and then stop. Use this to ensure the system is working correctly before you run the whole batch.

• Off Plate Area - Designates an alternate location for maintenance commands in the Commands and Sequence list.

• Save Prtcl - Opens the Save Protocol dialog box to save the protocol and/or kit.

• Select Save Protocol and/or Save Std/Ctrl Kit to save the protocol and/or kit.

• Type information in the following boxes and click Save to save the protocol or kit.

• Protocol Name

• Version

• Manufacturer

• Optional Description

• Std/Ctrl Kit Name

• Std/Ctrl Kit Lot#

• Expiration

• Manufacturer

• Lots

• Save - Saves the information as a pending batch.

• Cancel - Returns to the Batches tab.

• Back - Returns to the previous window.

• Run Batch - Runs the batch and opens the Current Batch tab, where you can monitor the batch as it runs.

Create a New Multi-Batch

Batches > Batches > New Multibatch

Use the Create a New Multi-Batch button to add or remove batches to the multi-batch set up and to run a multi-batch.

You must ensure that the batches fit on one plate. After you add each batch, the software automatically adds the next batch to the first well of the next column or row (depending on your plate orientation) as long as space is available on the plate. You can also select a well first, which places the next batch in your chosen location. If space limitations create an overlap, an error message appears. Results for each batch are saved as individual batch files.

NOTE: You cannot add a batch that forces multiple plates to a multi-batch

operation. When creating or adding batches, ensure your batches fit on one plate. All batches must use the same plate name previously defined and adjusted.

This tab contains the following:

Select Pending Batch - Contains a list of all pending batches. The list includes name, protocol, protocol version, date, and status information for each pending batch. Select the batch you want to add to the plate. Click OK. A plate layout diagram automatically populates the wells for the batch. Click Add to open this box again and add additional batches.

xPONENT® for FLEXMAP 3D 46

Multi-Batch - Lists pending batches selected for the multi-batch. The list includes name and “Start at” well.

Plate Layout - Opens the Multi-batch Report dialog box that contains:

• Page - Use these arrows to scroll through the report pages.

• Zoom - Select from the list to change the report magnification.

• Print - Prints report.

• Save - Saves report.

• Close - Closes report dialog box.

Multi-batch Plate Layout Report - includes the multi-batch plate layout, command number, plate location, command type, sample ID and dilution. The report is date and time stamped.

New Batch - Opens the Create New Batch tab. Create your new batch. Click Save to return to the New Multi-batch tab.

Add - Opens the Select Pending Batch box. Add a batch from the available options, including batches newly created. The selected batch then appears on the plate layout. If the batches selected do not fit on the plate, a Multi-Batch error dialog box opens, indicating you must edit one or more of the selected batches. The Multi-batch feature will automatically set the batches side-by-side if space remains on the plate. After you add each batch, the software automatically adds the next batch to the first well of the next column or row (depending on the plate direction). You can also select a well first, which places the next batch in your chosen location.

Remove - Removes a selected batch in the Multi-Batch list. The batch still remains in the Pending Batches section This button is displayed only if you have added a batch to the Multi-Batch list and selected the batch from the list.

Cancel - Returns to the main Batches tab without saving.

Save - Saves the batch.

Run - Runs the batch

Creating a New Multi-Batch

Use the Create a New Multi-Batch button to add or remove batches to the multi-batch set up and to run a multi-batch.

1. Select the pending batch from the Select Pending Batch dialog box.

Batches Page

2. Once you've selected a batch click Ok.

3. On the next screen, select a well location for the next batch and click Add.

xPONENT® for FLEXMAP 3D 48

4. Once the batches are created, click Run.

After creating a multi-batch, you can save it to the Select Pending Batch list. When saved to this list, the protocol appears as “Multibatch.”

To save a Multi-Batch:

1. Create a new Multi-Batch.

2. Select a pending batch.

3. Type the name for the Multi-Batch Name field.

4. Click Save. You are returned to the Batches page, and the multi-batch is added to the

pending batches list.

NOTE: Batches saved to a multi-batch cannot be edited or deleted unless

they are removed from the multi-batch. However, you can edit the multi-batch itself. To remove a batch from a multi-batch, click a well in the plate layout, and click Remove.

Batch Procedures

Running a Pending Batch

Open the Batches page. Select the pending batch that you want to run, then click Run.

NOTE: If the batch spans more than one plate, the tray ejects automatically

when all defined wells have been acquired. A dialog box displays prompting you to insert the next plate.

Importing a Batch

You only need to import batches to the system once. You must type lot information for the standard and control reagents as specified in the protocol. This lot information is used for every batch set up using the protocol, until it is changed.

To import a batch:

1. Open the Batches page.

2. Click Import. The Import Batch dialog box opens. Batch files are MDF files.

3. Click Browse to open the Select File dialog box. Navigate to the batch file you want to

import, then click Open.

4. Click OK in the Import Batch dialog box. The batch displays in the Pending Batches

list.

Exporting a Batch

1. Open the Batches page.

2. In the Pending Batches section, click the batch you want to export, then click Export.

The Export Batch dialog box opens.

3. Click Browse. The Select File dialog box opens.

Batches Page

4. Navigate to the location to which you want to save the file, then click Save.

5. Click OK in the Export Batch dialog box.

NOTE: When exporting a large batch and including the LXB files, such as a

batch with hundreds of wells or hundreds of analytes, the export process may take ten minutes or more.

Editing a Batch

1. Open the Batches page.

2. Click the batch you want to edit, then click Edit. The Protocol tab opens.

3. Edit the information as needed on the Protocol, Std & Ctrls, and Plate Layout tabs.

4. Click Save on the Plate Layout tab.

Deleting a Batch

You can only delete unprocessed batches. Batches are deleted from the Open Batch list and moved to the Open Incomplete Batch list.

To delete a batch:

1. Open the Batches page.

2. In the Pending Batches section, click the batch you want to delete, then click Delete.

The Delete Pending Batch dialog box opens.

3. Click Yes.

NOTE: You can remove a batch that includes results only through the

Archive Utility. See Archive Utility.

xPONENT® for FLEXMAP 3D 50

Chapter 5: Results Page

Results Page

Once data is collected in a batch, observation and analysis take place in the Results page. This page contains the following tabs:

Current Batch - View statistics for the current run and progress per well.

Saved Batches - View information about already processed batches and if necessary, replay

them or recalculate their data.

• From the Saved Batches tab, select the Open button located at the bottom right of the screen. Four subtabs will open:

• Results - Shows the results of a new or saved batch.

• Settings - Shows the report type you selected.

• Log - Information about acquisition.

• Sample Details - Details about the sample.

• From the Saved Batches tab, select the Replay button located at the bottom right of the screen. A dialog box will display Recalculate data and Replay batch. Select either Replay batch or Recalculate data. Three subtabs will open:

• Protocols

• Stds & Ctrls

• Plate Layout

LIS Results- View a batch or transmit a batch that contains LIS results.

Reports - This enables you to select a report to view.

From the Report drop-down box you can choose the Type of report to view.

• Batches Reports

• Data Interpretation

• Batch Settings

• Plate Layout

• Batch Audit

• Patient Report

• Protocol Reports

• Protocol Settings

• Plate Layout

• Protocol Audit

• Calibration and Verification Reports

NOTE: Calibration and Verification Reports gives you Dates fields to

select which dates to view the report.

• All

• F3DCAL1

• F3DeCAL1

• F3DCAL2

• F3DCaL3

• F3DVER1

• F3DeVER1

• F3DVER2

• Fluidics

• Performance Verification Reports

NOTE: Performance Verification Reports gives you Dates fields to select

which type of report you want to view between specified dates. You can specify the Type of report you want from the drop-down menu. You can choose from:

• Condensed

• Detailed

• System Log Reports

• All

• Maintenance

• Security

• Warning and Errors

• Advanced Reports

User Report

Performing Analysis

You may direct the system to acquire samples in replicate regardless of batch type.

For qualitative batches, qualitative results for replicates are averaged and the reported interpretation is determined from this replicate average.

For Quantitative batches, quantitative results can be viewed on the Standard Curve.

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Current Batch Tab

Results > Current Batch

Use this tab to view results, statistics, and log information related to the current batch, and to perform statistical analysis on batch results. This tab offers real-time monitoring of batch sampling during acquisition through a display of sample bead statistics and analytes, and dot plot data. The statistics available on this tab are intrawell bead statistics. They do not describe replicate well assay results.

There are four maximize buttons in this window, one for each major pane. Click the appropriate one to maximize the pane. After clicking, the clicked button becomes a minimize button. Click minimize to return the pane to its standard size.

NOTE: The buttons on this tab change based on settings chosen on other

application pages.

Results Page

The Current Batch tab has the following features:

• Statistic - To view a particular statistic for analytes in a batch, select one of the options on the drop-down list. The statistical options displayed change according to the type of analysis.

• Median (MFI) - The point is a data set where there are as many values occurring above

it as there are below it.

• Net MFI (Median Background) - Net MFI median background.

• Count - Gated events, if gates are set.

• % CV of microspheres - The measure of relative dispersion within the distribution.

%CV = 100 x Std Dev / Mean

• Standard Deviation - For calculating sample variability or dispersion, Luminex uses the

standard deviation formula.

• Peak - The value that is equal to the largest number of data points within the distribution.

For example, in data set {1,2,2,3,3,3,4,5}, 3 is the peak because it occurs the most frequently in the distribution list.

• Trimmed Count

• Trimmed % CV of Microspheres

• Trimmed Standard Deviation

• Trimmed Peak

* Trimmed statistics remove the lower and upper five percent of the extreme statistic values, then use the remaining values for the Standard Deviation, or %CV calculations.

The statistics displayed change according to the analysis type selected.

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• Analyte - Contains a list of analytes run in the batch. Select an analyte to view all statistics for that analyte.

• Well(s) to View

• Current Well - Displays the statistics of the well currently being displayed. (This

changes to Displayed Well if viewing a batch using the Open button of the Saved Batches tab.)

• Single Step - Instrument analyzes one well at a time. Click to turn function on or off.

This is useful to run prior to running an entire batch to confirm that the system is set up correctly.

• Results pane - Displays statistics related to the batch. Use the up, down. left and right arrow buttons to move through the table, or use the scroll bars. The maximize/minimize toggle button expands the batch table and returns it to the standard size.

Plate - Select the plate you want to view, if there is more than one plate.

WARNING: If using multiple plates, ensure that plates are used in the proper

order. Failure to do so can result in inaccurate data and test results.

Well Report pane - This pane displays a representation of the plate and the status of acquired wells. Each well displays one of three possible states:

• Histogram/Dot Plot - Displays real-time monitoring of batch sampling during acquisition.Both the histogram and the dot plot have buttons that enable you to change the default view:

• Click the maximize button to maximize the graph to fill the whole window. In the

maximized view, use sliders to zoom in or zoom out. To return to the standard view, click the minimize button. If the histogram or dot plot display have been changed to another view (e.g. Progress, Well Report), click Default to return to the default histogram and dot plot displays.

• The dot plot default display when using 1 to 100 bead regions Classification 1 and

Classification 2. When running regions greater than 100 beads, the default is Classification 2 and Classification 3 axes, and radio buttons are displayed on the right

for the Classification 1 axis slices. To view the dot plot, you must use the default axis. To display the bead set information, hover over the desired region. Click the upper view classification button immediately below the maximize button to change the display to show Classification 2 and Classification 3. This view displays a series of radio buttons on the right side of the dot plot. When one of the radio buttons is clicked, the bead regions in view are those in a fixed range of CL1 values plotted against CL2 and CL3. Click the bottom view classification button to change back to the default classification display.

• Histogram - The default location of the histogram is the lower left section of the Current Batch tab. The Doublet Discriminator (DD) displays on the X axis. Events display on the Y axis. Doublets appear when two beads stick together, creating undesired results. When you select the gate, two vertical dashed red lines appear. These represent gate positions determined by the protocol. Once the gate is set, everything outside of it is ignored. For batches created using an existing protocol, the gate cannot be changed while running the batch. For new batches created from new protocols, the gate can be changed while running the batch. Any changes made to the gate while running new protocol batches immediately affect the visual display of the dot plot and histogram. In addition, changes made to the gate while running new protocol batches affect the acquisition for all wells initiated after the change is made. When viewing saved batch data, the gate can be

Results Page

changed to visually inspect the effect. Only the visual display of the dot plot and histogram is affected for saved batches, not the acquired data.

NOTE: Gate positions are dependant upon buffer composition. Any changes

made to you assay buffer composition may result in a different optimal gate location.

Right click inside the histogram area to access the following options:

X Axis - Use this function to change the X axis to the following: Doublet Discriminator, Reporter 1, Classification 1, Classification 2, and Classification 3. Doublet Discriminator is the default.

NOTE: You can change the X axis of the histogram for troubleshooting

purposes. Use only the default settings in all other instances.

• Gate - Show, create, delete, or move the gate. You can also move the gates by clicking

and dragging the red lines on the histogram.

• Autoscale - Click to automatically adjust the maximum number of events shown on the

Y axis. Click during acquisition to readjust the Y axis scale.

• Set Scale - The Set Scale dialog box displays. Set the maximum number of events and

click OK. The default number of events is 60.

• View- You can choose to view all events or only gated events.

• Display Mode - Opens the Histogram Options dialog box. Click either Logarithmic or

Linear display. Logarithmic display is the default. Select the Zoom check box for a magnified view of the histogram.

• Dot Plot - The default location of the dot plot is the lower-right section of the Current Batch tab. The dot plot is a graphical display of real-time data collection. Luminex recommends using the default settlings to collect data.

Right-click inside the dot plot area to access the following options:

• X Axis - Changes the X axis to the following: Doublet Discriminator, Reporter 1,

Classification 1, Classification 2, and Classification 3.

NOTE: You can change the X axis of the dot plot for troubleshooting

purposes. Use only the default settings in all other instances.

• Y Axis - Changes the Y axis to the following: Doublet Discriminator, Reporter 1,

Classification 1, Classification 2, and Classification 3.

• View - Choose to view all events or only gated events.

• Display Mode - Select either Logarithmic or Linear display. The software defaults to

Logarithmic display. Click maximize for a magnified view of the dot plot.

• Plot Type - Select either Density Plot or Decaying Plot. The software defaults to

Density Plot, which displays a constant accumulation of events. Contrasting colors indicate increasing density. The Decaying Plot plots only the last 100 events.

NOTE: The Density Plot allows the visual elimination of data values that are

determined to be insignificant to the display. Luminex recommends collecting data in Density Plot mode to observe all collected events. You can only view the Decaying Plot during batch acquisition.

Right-click inside the dot plot area to access the following options:

• Log - Displays a log of system processes. The log includes the following information:

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• Date

• Message

• Code

Log entries indicating warnings are highlighted ion yellow. Errors are highlighted in red. Other log entries are not highlighted. Click the maximize button to maximize the log. The log expands to fill the whole window. Click minimize to return to the standard size.

• Save Image - Opens a Save As dialog box to save a screen capture.

• Details - Opens the Results tab, enabling more analysis and results.

• Progress - Click to display real-time progress of the well acquisition. Analyte counts are displayed in a dynamic bar graph as they are acquired. The scroll bar at the bottom of the Progress displays scrolls through the analyte list.

• Maximize - Maximizes the Progress display to fill the window.

• Zoom - Enable a closer look at the analyte progress.

• Save Image - Opens a Save As dialog box to save a screen capture.

• Default - Returns to the histogram and dot plot display.

• Well Report - Displays a representation of the plate and the status of acquired well. Wells will display one of three possible states:

• Yellow - Well acquired, but the system detects a possible problem (select the Log tab for

more information).

• Green - Well acquired successfully.

• Red - Well acquisition unsuccessful, the system may have stopped, depending on the

circumstances (select Log tab for more information).

• 3D View

The 3D view enables a three dimensional look at the batch results. This view can be manipulated in a variety of ways to view regions, specific events, and results outside expected parameters.

NOTE: The 3D View must be enabled in the Admin > System Setup

screen.

Move the green, purple, and red balls to display only a selection of Classification 3, 2, and 1 data. As you move the balls, a square forms in the middle of the 3D view and excludes data outside that range.

Results Page

• 3D BeadMap - The main display is the 3D BeadMap. The display shows the CL1, CL2, and CL3 axes. Left-click and drag your mouse to move the display for better viewing of a particular section. Right-click anywhere in the display to select from the following viewing options.

Select the Settings button at the bottom to display:

• Show Regions

• 3D

• CL1/CL3 Plane

• CL2/CL3 Plane

• CL1/CL2 Plane

• Show Beads

• 3D

• CL1/CL3 Plane

• CL2/CL3 Plane

• CL1/CL2 Plane

• View

• Show Cursors

• Show Region Labels

• Show 3D Region View Box

• Display Mode

• Logarithmic

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• Linear

• Display Position

• 3D View

• CL1/CL3 Plane

• CL2/CL3 Plane

• CL1/CL2 Plane

• View

• All Events

• Gated Events

• Show Cursors

• Show Region Labels

• Show 3D Region View Box

• 3D Region View - This view in the upper right of the window displays a small 3D representation of the regions. The three axes are shown in the bottom left corner of the display and can be manipulated by left-clicking and dragging the mouse. Move the slider on the right to zoom in or out. Enable the 3D View Box by clicking Settings for an easier way to manipulate the viewing angles.

• Region - A list that enables viewing of specific region.

• View - A list with the options to Show All Events, or Show Gated Events.

• Histogram - A smaller histogram display identical to the histogram display in the 2D view.

• Save Image - Displays the Save As dialog box to save a screen capture of the 3D display.

• Settings - Opens the 3D Settings dialog box the following options:

These settings are also available on the toolbar of the main 3D display:

• Save Image - Saves the current 3D image.

• Settings - Saves the settings to view different angles.

• All Regions - Displays all regions of the batch.

• 2D - Returns to the default display.

Saved Batches Tab

Results > Saved Batches

Results Page

Use this tab to open a batch that has been run and view its details, and to export, approve, or replay a batch.

Select a Completed Batch and click Open to view the batch details.

The Saved Batches tab has 4 subtabs:

• Click the Results subtab to view statistical information about the batch.

• Click the Settings subtab to view the batch settings report.

• Click the Log subtab to view a log for the activity that occurred during acquisition of the selected batch.

• Click the Sample Details tab to view sample details for each sample in the batch.

When the Saved Batches tab opens, it includes the following features:

Filter - Click Filter to open the Filter Setup dialog box.

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This dialog box lets you choose the saved batches you want to display in the Completed Batches list, based on options you select or clear in these check boxes:

• Batch Name

• Protocol

• Batch Status

• Lot ID

• Kit ID

• Analyte

• Sample ID

• First Name

• Last Name

• User ID

• Date

• Reset - Clears all check boxes.

• OK - Closes the dialog box and applies any changes you made.

• Cancel - Closes the dialog box and cancels any changes that you made. When you fill in the Filter Setup box and click OK, the message Filter is on is displayed on the Saved Batches page. To turn off the filter, click Clear.

Completed Batches table - This displays a list of completed batches, including the Name, Protocol, Protocol Version, Date, Status, and User information for each batch. This list

does not include batches that have not been run.

There are more Results options at the bottom of the Saved Batches screen.

Reacquire - Allows you to reacquire any set of wells from a completed or partial batch.

WARNING: Performing this action may result in varying results due to

decreased bead counts, potential carry effects, and timesensitive reagents.

• Save Prtcl - Opens the Save Protocol dialog box, displaying the kit information for the selected batch.

Results Page

• Plate Layout - Opens the Report dialog box, which contains the Batch Plate Layout Report.

• Approve - Opens the Batch Approval Confirmation dialog box to approve the selected batch.

Only approved batches can be transmitted to the LIS. If your software is licensed for LIS use, you can transmit batches to the LIS from the Sample Results tab. After you have approved a batch, the status of the batch changes to Approved in the Complete Batches list.

• Exp Results - Opens the Save As dialog box to choose an export destination for the .CSV file containing your results.

• Import - Opens the Open dialog box so you can select a batch file (.mdf) to import. Select Include Raw Files (LXB) to include raw files in the import. Select Overwrite to overwrite existing files.

• Export - Opens the Export Batch dialog box, where you can choose a location for the file you selected to export. Select Include Raw Files (LXB) to include raw files in the export. Select Overwrite to overwrite existing files.

• Replay - Opens the Select Replay Mode dialog box. This box enables you to use the data stored in the run files from the initial acquisition to reprocess a batch, creating a new batch output file. A batch can be reprocessed multiple times. When you replay or recalculate a batch, you perform the same steps to create the batch as you did when you created the batch the first time. This sequence varies based on whether or not you created a new batch from a new protocol or a new batch from an existing protocol. The initial batch data and output file always remain intact and unchanged. Each time you replay a batch, the system handles it as if it is new data, and creates a separate batch entry and output file.

• Replay batch - Use to replay raw bead data files. The bead data files are replayed

using the gate, analyte, analysis settings, and plate layout that were selected in the new or updated protocol. Settings such as bead type, volume, timeout, XY heater, and report gain have no effect on the replayed results.

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• Recalculate data - Reanalyze the batch results using only the batch MFI values. The

batch MFI values are recalculated using the analysis settings and plate layout selected in the new recalculated batch or protocol. Settings such as bead type, volume, timeout, XY heater, and report gain have no effect on the replayed results. Because only the MFI values are reanalyzed, no data is displayed in the dot plot.

• OK - Saves your changes.

• Cancel - Cancels your changes and closes the box.

• - Opens the Results tab. Use this tab to view the saved batch results for the selected batch. When you click Open, the Results subtab opens.

Replaying a Batch

Replay batch uses the raw bead data files from the initial acquisition to reprocess the batch,

and creates a new batch output file. The bead data files are replayed using the analyte, analysis settings, and plate layout selected in the new batch or protocol. Settings such as bead type, Volume, and XY Heater have no effect.

Results from replaying a batch are generated in the usual manner, with new .lxb and .csv files.

Replaying or recalculating a large batch can take 1 hour or more to complete. Batch replay cannot be stopped while in progress. Allow adequate time for the operation to complete. The operation is complete when all progress bars have disappeared.

A batch can be reprocessed multiple times. If the system crashes but the plate finished, the data can be recovered by replaying the batch.

The initial batch data and output file always remain intact and unchanged. Each time you replay or recalculate a batch, the system handles it as if it is a new batch, creating a separate batch entry and output file.

If you select to replay or recalculate a batch that was originally run without a saved protocol, you have to modify the settings on the following subtabs:

• Settings

• Analytes

• Stds & Ctrls

• Plate Layout

These subtabs appear under the Saved Batches tab. After you have completed them in order, click Replay Batch on the Plate Layout subtab to perform the replay or recalculate procedure.

Results Subtab

Results > Saved Batches > Results

Results Page

This subtab displays the following features:

There are three maximize buttons in this window, one for each major pane. Click the appropriate one to maximize the pane. After clicking, the clicked button becomes a minimize button. Click minimize to return the pane to its standard size.

This tab has the following features:

• Statistic - To view a particular statistic for analytes in a batch.

NOTE: The statistics displayed change according to the analysis type

selected.

• Median (MFI) - The value (detected signal) that is in the middle of the microsphere

population when sorted by reporter value lowest to highest. The median value is much less sensitive than the mean value to outliers and carryover.

• Test Result - The calculated analysis value for quantitative or qualitative assays derived

from standards with known values.

• Count - Gated events, if gates are set.

• Net MFI (Median Background) - Net MFI median Background.

• % CV of microspheres - The measure of relative dispersion within the distribution.

%CV = 100 x Std Dev / Mean

• Standard Deviation - For calculating sample variability or dispersion, Luminex uses the

standard deviation formula.

• Peak - The value that is equal to the largest number of data points within the distribution.

For example, in data set {1,2,2,3,3,3,4,5}, 3 is the peak because it occurs the most frequently in the distribution list.

• Trimmed Count

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• Trimmed%CV of microspheres

• Trimmed Standard Deviation

• Trimmed Peak

• %CV of Replicates

• % Recovery

• Expected Result - The known or expected test result value for a standard or control.

• Control Range - Low - The lowest value for an assay control used to determine pass/

fail criteria for an assay.

• Control Range - High - The highest value for an assay control used to determine pass/

fail criteria for an assay.

• Normalized New Median

• Units

• Analyte - Contains a list of analytes run in the batch. Select an analyte to view all statistics for that analyte.

• Displayed Well - Displays the number of the well whose contents currently appear in the graph.

• Results pane - Displays statistics related to the batch.

• Use the up, down, left, and right arrow buttons to move through the table, or use the

scroll bars.

• Plate - Select the plate you want to view, if there is more than one plate.

CAUTION: If using multiple plates, ensure that plates are used in the proper

order. Failure to do so can result in inaccurate data and test results.

• Save Image

• Formula - Opens the Change Analysis dialog box with a list of analytes used in the batch. Click an analyte to open the Analysis Settings dialog box from which you can select a new analysis setting for the analyte.

• Default - Returns to the default view.

• Edit Patients - Updates patient information.

• 3D - Ability to look at a region map in three dimensions.

NOTE: The 3D option must be enabled on the Admin > System Settings

page.

• Approve - Opens the Batch Approval Confirmation dialog box, which contains the data for analytes selected in the Results tab. Click Yes to approve the batch. The dialog box confirms the approval.

• Validate - Validates an entire selected row or cell in the Results table. Average rows or cells cannot be selected. If you haven't selected an item or the item you selected does not need to be validated, a warning dialog box displays. Your xPONENT® system administrator must give you privileges to invalidate standards if you are using the Secure xPONENT

package.

• Invalidate - Invalidates an entire selected row or cell in the Results table. The selection will turn red when invalidated. Select the same item and click Validate to remove the invalidation status.

Results Page

• Close - Closes the batch and reopens the Saved Batches tab.

• Save - Saves the batch. This button only appears if a change has been made to the batch.

• Analyze - Analyzes data that has been invalidated. This button only appears if you have clicked Invalidate on a portion of the data, or if you have clicked Validate on an invalidated portion of the data. This will analyze the data again with the invalidated standard removal.

Validate Standards

Your xPONENT® system administrator must give you privileges to validate standards if you are using the Secure xPONENT® package. All standards are assumed to be valid unless explicitly invalidated.

1. Open the Results page.

2. Open the Saved Batches tab.

3. Click the batch name, then click Open. The Results tab opens.

4. Click the square area next to left of the standard you wish to validate, then click Validate.

For information on assay controls and guidelines regarding accepting or rejecting control values, contact the assay kit manufacturer.

Invalidate Standards and Controls

NOTE: It is possible to invalidate or remove a control in data analysis.

However, Luminex does not recommend invalidating controls.

For information on assay controls and guidelines regarding accepting or rejecting control values, contact the assay kit manufacturer.

To invalidate standards and controls:

1. Open the Results page, then open the Saved Batches tab.

2. Open the Saved Batches tab.

3. Click the batch name, then click Open. The Results tab opens.

4. Click the square area to the left of the well you wish to invalidate, then click Invalidate.

The whole row turns red.

Settings Subtab

Results > Saved Batches > Settings

Use this tab to view the acquisition parameters of the selected saved batch and print the batch settings report.

Page - Scrolls through the Batch Settings report.

Save - Opens the Save As dialog box to save the Batch Settings report. Select a location and click OK to save the file. The default save type is a .pdf file.

Print - Prints the report.

Close - Returns to the Saved Batches tab.

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Viewing Batch Settings

1. Open the Results page, then open the Saved Batches tab.

2. Click Saved Batches, then click the batch for which you want to view details.

3. Click Open, then click the Settings tab.

4. Click the left and right Page arrows to view the pages of the batch settings report.

5. Click Save to open the Save As dialog box. Navigate to the location where you want to

save the batch settings report, and click Save.

Log Subtab

Results > Saved Batches > Log

This tab displays a log of the activity which occurred during the acquisition of the selected batch; you can print the log.

The following information is displayed about each activity:

• Date

• Message

• Code

Log entries display yellow if a well was acquired but there was a possible problem, and red if acquisition failed.

• Print - Prints the log.

Results Page

• Export - Opens the Save As dialog box to save the batch log file. Select a location and click Save.

• Close - Reopens the Saved Batches tab.

Viewing Batch Logs

1. Open the Results page, then open the Saved Batches tab.

2. Click Saved Batches, then click the batch for which you want to view details.

3. Click Open. The Results tab opens.

4. Click Log to open the Log tab.

Sample Details Subtab

Results > Saved Batches > Sample Details

The following information is shown on this tab:

• SampleID

• Samples Status

• Analyte

• < and > Arrows - Scroll left to right through the sample details.

• ^ and v Arrows - Scroll up and down through the sample details.

• Transmit - For systems configured for LIS transmission, select a single analyte or the entire sample and click Transmit to send the results.

• Close - Reopens the Saved Batches tab.

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Viewing Sample Details

1. Open the Results page, then open the Saved Batches tab.

2. Click Saved Batches, then click the batch for which you want to view details.

3. Click Open, then click Sample Details. The Sample Details tab opens. If you are using

an LIS licensed package of the software, click Transmit to transmit sample details to the LIS database. You can transmit either a single analyte per sample or the entire sample.

LIS Results Tab

This tab displays information about saved batches that contain LIS samples.

Results > LIS Results

• Filter - Opens the Filter Setup dialog box.

Batch-Specific Details

• Batch Name

• Protocol

• Batch Status

• Lot ID

• Kit ID

• Analyte

Sample Details

• Sample ID

• First Name

• Last Name

Results Page

Others

• User ID

• Date

• Reset

• OK / Cancel

• Clear - Click to turn off the filter.

• Completed Samples - Displays Name, Protocol, Sample Count, Date, Status, and User information for each batch displayed in this list.

• Transmit - Transmits a batch to a LIS if xPONENT® is connected to one.

• Details - Opens the Sample Details tab to view sample results.

Reports Tab

Results > Reports

Use this tab to view, generate, and print reports.

Report and Type lists - Report lists the categories of reports. The selections in the Type list change depending on the selection you made from the Report list. Depending on the choice you make, various other changes occur on the Reports tab:

Batch Reports - A list of batches appears below the Type list. This includes Name, Protocol, Protocol Version, Date, Status, and User information. Chose from the

following reports:

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• Data Interpretation

• Batch Settings

• Plate Layout

• Batch Audit

• Patient Report

If you choose Data Interpretation, a Select Analysis section appears on the right and displays a list of the analytes in the batch. Select the analytes you want to include in the report. Select All to select all the analytes in the list. Select Clear to clear all the analytes in the list.

A series of new buttons appears when you click Generate Report.

• Analyte arrows - This feature is directly below the Report list. Use the left and right arrows to display information for individual analytes of those selected for the report.

• Page arrows - Use the arrows to scroll through the pages being displayed.

• Save All - Click to open the Browse For Folder dialog box. Select a location to save the file, and click OK. This file includes all selected analytes.

• Print All - Click to print the analyte information for all the analytes in the report.

• Save - Click to open the Save As dialog box. Select a location and click Save. This saves only the analyte information currently displayed.

• Print - Click to print the analyte information currently being viewed.

• New Report - Click to return to the main Reports window.

NOTE: If running a data interpreation of an allele call batch, be aware that

when choosing analytes from the Select Analytes list, selecting one analyte will select all analytes in that group.

• Protocol Reports - A list of protocols displays. Choose from the following reports:

• Protocol Settings

• Plate Layout

• Protocol Audit

Select a protocol and then click Generate to generate the report.

• Calibration and Verification Reports - Displays a list of calibrations and verifications. Choose from the following selections:

• All

• F3DCAL1

• F3DeCAL1

• F3DCAL2

• F3DCAL3

• F3DVER1

• F3DeVER1

• F3DVER2

Select a calibration componenet, a date from the Date list, and click Generate to generate

the report.

Results Page

Perfomance Verification Reports - Displays two report types. Choose either of the following:

• Condensed

• Detailed

Select a report type, a date range from the Date list, and then click Generate to generate

the report.

System Log Reports - Displays a list of system log reports. Choose from the following

selections:

• All

• Maintenance

• Security

• Warnings and Errors

Select a system log report, a date from the Date list, and then click Generate to generate

the report.

Advanced Reports - Enables a single option, User Report, in the list.

Click Generate to generate the report.

Generating a Report

1. Open the Results page, then the Reports tab.

2. In the Report drop-down list, select the category of report: batch, protocol, calibration

and verification, performance verification, system log, or advanced. Depending on what you choose in the Report list, the content of the Type list changes and other features can be displayed in the window.

3. Select the specific report from the Type list.

4. If you selected either a batch report or a protocol report, select the specific batch or

protocol from the list.

5. If the report you selected requires a date range (calibration and verification, performance

verification, and system log), use the calendars available when you click the Start and Through buttons to establish the date range.

6. If the report you selected requires a choice of analytes, select them from the Select

Analytes box. Select them all using the All button; clear your selections using the Clear button.

7. Click Generate.

If the report includes multiples analytes, use the arrows above the report to move through the list of analytes.

If the report is lengthy, use the Page arrows to scroll through the pages in the report.

Use the Zoom button to focus on a particular part of the report.

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Chapter 6: Protocols Page

Protocols Page Functionality

Protocols > Protocols

The Protocols page enables you to create or import a new protocol, or select an existing protocol from the Installed Protocols list.

The following installed protocol information is shown on this page:

• Name

• Version

• Manufacturer

• Date

Click the Create New Protocol button or click Stds/Ctrls to move to those pages.

There are action buttons at the bottom of the page. Most of these buttons are not displayed unless you are working with a saved protocol. While you are creating a protocol, only Cancel and Next buttons are displayed. After saving a protocol or opening a saved protocol, the following buttons are displayed:

• New Std/Ctrl

• Plate Layout

• Delete

• Import

• Export

• Edit

• View

NOTE: The buttons are only visible when there is an existing protocol in the

system. If no protocols have been created or imported, then only the

Import button is visible

Protocol Procedures

Creating an Allele Call Protocol

Protocols > Protocols > Create New Protocol

This protocol contains no standards or controls. An allele call protocol compares groups of two, three, or four analytes to identify genotypes.

To create an allele call protocol:

1. Open the Protocols page, then open the Protocols tab. Click Create New Protocol.

The Protocol Settings tab opens.

2. In the Name box, type the name of the protocol.

3. In the Description box, type a description of the protocol.

4. In the Version box, type the version of the protocol.

5. In the Manufacturer box, type the manufacturer information for the protocol.

6. Define the settings in the Acquisition Settings section.

NOTE: Final washes are required for proper analysis. If you are not

performing a final wash step on your plate before acquisition on the FLEXMAP 3D® instrument, enable Sample Wash here. This automatically washes each sample.

7. Define settings in the Analysis Settings section, selecting Allele Call as the analysis

type.

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8. Click Next. The Analytes tab opens.

9. Click the desired analyte (bead ID) in the numbered grid. Information about the analytes

is displayed in a list on the right side of the grid. For an allele call analysis, you must select a group of two, three, or four analytes.

10. Click Group to group analytes for the allele call. The grouped analytes display in a list to

the right. Select more analytes and then click Group again if you want to add another group to the analysis.

11. Click and type an analyte name in the Allele column to the right of the analyte grid.

12. In the Count box, type the desired bead count for each analyte. Click Apply All.

13. To set a bead count and the units for a single analyte, click in the Units and Count

columns directly to the right of the analyte grid, and type a units value and bead count.

14. Click in the Call % column and type a value to set an individual analyte's call percentage.

15. Click Next. The Plate Layout tab opens.

• To add well commands, select the appropriate wells and mark them as unknown, standard, control, background, or wash. You can also delete commands that you've added and change the starting location on the plate. If you want to run in replicate, change the Replicate Count to the appropriate number and the Grouping to your preferred grouping method.

• Delete a command by clicking the well, and clicking Delete. The Delete Options dialog box opens. Select Delete just the selected wells to delete a single well command, or Delete all wells containing these samples to delete all wells with the same command.

NOTE: The Post Batch routine runs after the batch is complete. This routine

is selected by default when the protocol or batch is set up. The default Post Batch routine can be changed in the Batch Options tab of the Admin page.

NOTE: For more information about the commands and settings on the Plate

Layout tab, see the Plate Layout Tab.

Creating a Quantitative Assay Protocol

The protocol must contain multiple standards. The standards are assigned lot value information for each test. A standard curve is generated according to the lot values. Including controls in the protocol is optional, but recommended for judging the acceptability of batch results.

To create a quantitative assay protocol:

1. Open the Protocols page, then open the Protocols tab. Click Create New Protocol. The Settings tab opens.

2. In the Name box, type the name of the protocol.

3. Type a description in the box to the right of the Name box.

4. In the Version box, type the version of the protocol.

5. In the Manufacturer box, type the manufacturer information for the protocol.

6. Define settings in the Acquisition Settings section.

7. Define settings in the Analysis Settings section, selecting Quantitative as the analysis type.

Protocols Page

NOTE: The protocol for a quantitative assay must have at least two or more

standards. The number of controls are optional.

8. Click Next. The Analytes tab opens.

9. Click the desired analytes (bead ID) in the numbered analyte grid. Information about the analyte displays to the right side of the grid.

10. Click and type an analyte name in the Name column to the right of the analyte grid.

11. Click and type the desired unit of measurement in the Units box to the left of the Apply All button.

12. Click and type the desired bead count for each analyte in the Count box. Click Apply All.

13. To set a bead count and the units for a single analyte, click in the Units and Count columns directly to the right of the analyte grid, and type a bead count and units value.

14. To change the default analysis for all analytes, click Change. The Analysis Settings dialog box opens.

15. In the Analysis Settings dialog box, select the analysis method from the Method list, and the weighting in the Weight Type list. Click Apply to All Analytes to apply the selection to all analytes.

16. To change the analysis for a single analyte, click the Analysis field for the analyte you want to modify. The Analysis Settings dialog box opens.

• Select an analysis method in the Method list.

• Select a weight type in the Weight Type list (Weight Type may not display, depending

on the analysis method selected in the Method list).

Select a single analyte to view the Analysis Settings for that analyte. This will open up a dialog box.

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• Check Mark as Intra-Well Normalization Bead if you want to use the analyte as a

normalization bead.

NOTE: The normalization bead is a microsphere set that is included in the

assay as an internal control. It controls for sample variation and can be used to normalize data between samples in a run.

• Check Use Threshold Ranges if you want to use a range for the analysis.

• Click Add Range to setup the threshold range.

• Type a name for the range in the Range Name field.

• Type low and high range values in the Low Value and High Value fields.

• Select the check box in the Inclusive column to include the value in the range, or

leave it clear to make the range value one unit higher than the low value, and one unit lower than the high value.

• Highlight a range and click Delete Range to delete the range.

• Click OK to apply the new settings to the analyte first clicked, or Apply to All

Analytes to apply them to all the analytes in the protocol.

17. Click Next. The Plate Layout tab opens.

• To add maintenance commands, choose a command from the list. Highlight the well

that you want to apply it to, and then choose Pre Batch Routine or Post Batch Routine. The Commands and Routines dialog box opens. If you are working with more than one plate, click Add Plate to select plates to display in the Plate list.

• Delete a command by clicking the well, and clicking Delete. The Delete Options

dialog box opens. Select Delete just the selected wells to delete a single well command, or Delete all wells containing these samples to delete all wells with the same command.

• As you add commands to your plate, they appear in the Command Sequence list.

Type a well ID in the ID field. Here, you can give each of your wells an ID. You can also import a patient file by clicking Import List.

• Move commands up or down in the sequence by highlighting a command and using

the Move Command arrows to move the command up or down in the list.

18. Click Save.

Creating a Qualitative Assay Protocol

You define each Qualitative assay protocol using a single kit. The kit must contain one standard. The standard is assigned a “Quali” value for each test. Controls are optional, but are recommended for judging the acceptability of batch results.

To create a Qualitative Assay Protocol:

1. Open the Protocols page, then open the Protocols tab. Click Create New Protocol. The Settings tab opens.

2. In the Name box, type the name of the protocol.

3. In the Version box, type the version of the protocol.

4. In the Manufacturer box, type the manufacturer information for the protocol.

5. Define settings in the Acquisition Settings section.

Protocols Page

6. Define settings in the Analysis Settings section, selecting Qualitative as the analysis type.

NOTE: The protocol for a qualitative assay contains a single standard. The

number of controls are optional.

7. Click Next. The Analytes tab opens.

8. Click the desired analytes (bead IDs) in the numbered grid. Information about the analyte displays in a list on the right side of the grid.

9. To change the Default Analysis, click Change. The Analysis Settings dialog box opens.

10. In the Analysis Settings dialog box, click the analysis method from the Analysis

Method list. Click OK to change the default analysis to a single analyte. Click Apply to All Analytes to apply the selection to all analytes. Skip this step if you do not want to

change the default analysis or if you chose No Analysis on the Settings tab.

11. In the Units box, type the desired unit of measurement.

12. In the Count box, type the desired bead count for each analyte. Click Apply All.

13. Click Next. The Plate Layout tab opens.

• To add well commands, highlight the appropriate wells and mark them as unknown,

• To add maintenance commands, choose a command from the list. Highlight the well

that you want to apply it to, and then choose Pre Batch Routine or Post Batch Routine. The Commands and Routines dialog box opens.

If you are working with more than one plate, choose Add Plate. Here, you can add a plate, change the order of the plates, and scroll through all plates.

14. Click Save.

Deleting a Protocol

1. Open the Protocols page, then open the Protocols tab.

2. Select a protocol.

3. Click Delete. The Delete Protocol dialog box opens.

4. Click Yes.

Editing a Protocol

1. Open the Protocols page, then open the Protocols tab.

2. Select a protocol.

3. Click Edit. The Settings tab opens.

4. Define settings and click Next. The Analytes tab opens.

5. Define analytes and click Next. The Plate Layout tab opens.

6. Define the plate layout.

7. Click Save.

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Exporting a Protocol

1. Open the Protocols page, then open the Protocols tab.

2. Select a protocol.

3. Click Export. The Save as dialog box opens.

4. Select a location to export the file to, and click Save.

Importing a Protocol

1. Open the Protocols page, then open the Protocols tab. Click Import.

2. In the Open dialog box, navigate to the protocol file you want to import, then click Open.

3. The imported protocol displays in the Installed Protocols list.

Adding a New Lot for Protocol

1. Open the Protocols page.

2. Click the Stds & Ctrls tab.

3. Click Create New Std/Ctrl Lots and select a protocol from the drop down list in the Select Protocol dialog box, then click OK. The Std/Ctrl Details tab opens.

4. Click Apply Std/Ctrl Kit to associate a kit with the protocol. If you are not using a kit, type the appropriate Standard and Controls information in the Assay Standard Information and Assay Control Information sections.

5. Click Save.

Lots and Kits Procedures

You can edit standard and control lot information. Once a lot is used, changing or modifying it will prompt you for a new lot name.

For assay reagents specified in protocols, you can create new lots, edit lot information, select pre-existing lots for reuse, import lots, and export lots.

Assay kits include standards and/or controls. Once you enter the assay kit information, it can be used in multiple protocols. However, you should create separate kits specific for use with each protocol.

Once a lot is used, changing or modifying it will prompt you for a new lot name.

Creating a Lot

To create lots, you must use a protocol that uses either Quantitative or Qualitative analysis settings.

To create a lot:

1. Open the Stds & Crtls tab from the Protocols page, then open the Create New Std/Ctrl Lots button.

2. In the Select Protocol dialog box, select the protocol you want to use for this lot, then click OK. The Std/Ctrl Details tab opens.

Protocols Page

3. If the protocol uses standards, type the appropriate information for each standard in the Assay Standard Information section. In each analyte column, type the expected concentration for the analyte.

4. Alternatively, click Apply Std/Ctrl Kit and select a lot from the Select Lot dialog box. Click OK to apply the lot.

5. If your batch uses controls, select Expected, Low, or High from the Show Value options. Use the Apply Values arrows to apply values down or across the range of analytes.

6. Click Save.

Editing a Lot

To edit a lot:

1. Open the Protocols page, then open the Stds & Ctrls tab.

2. In the Installed Kits And Lots section, select a lot and then click Edit. The Std/Ctrl

Details tab opens. Change the lot information as appropriate.

Deleting a Lot

To delete a lot:

1. Open the Protocols page, then open the Stds & Ctrls tab.

2. In the Installed Kits And Lots section, click the lot you want to delete, then click Delete.

Exporting a Lot

NOTE: Lots and kits can only be exported if the protocol they were originally

created with exists within the system. If the protocol has been deleted, the lot or kit cannot be exported.

To export a lot:

1. Open the Protocols page, then open the Stds & Ctrls tab.

2. In the Installed Kits And Lots section, click the lot you want to export, then click Export. The Save As dialog box opens.

3. Navigate to the location you want to export the file to, then click Save.

Importing a Lot

1. Open the Protocols page, open the Stds & Ctrls tab, and then click Import.

2. In the Open dialog box, navigate to the file, then click Open.

Creating a Kit

To create a kit:

1. Open the Protocols page, then open the Protocols tab.

2. Select the protocol that you want to use for the kit, then click New Std/Ctrl. The Std/Ctrl Details tab opens.

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3. Type the name of the kit in the Name box, the lot number in the Std/Ctrl Kit Lot# box, the expiration date using MM/DD/YYYY format in the Expiration box, and the manufacturer in the Manufacturer box.

4. Click Apply Std Lot if you want to apply a standard lot. The Select Lot dialog box opens. Click a lot and select OK.

5. Click Apply Ctrl Lot to apply a control lot. The Select Lot dialog box opens. Select a lot and click OK.

6. Alternatively, type the appropriate information in the Assay Standard Information and Assay Control Information sections. The number of standards, controls, or both in these sections is defined in the protocol. If your batch uses controls, select Expected, Low or High from the Show Value options. Use the Apply Values arrows to apply values down or across the range of analytes.

7. Click Save.

Protocols Tab

Protocols > Protocols

Use this tab to create, export, or delete a protocol. You can also add new assay standard and or control information using one of the installed protocols.

This tab contains the following:

Create New Protocol - Opens the Settings tab to create a new protocol. For more information, see "Settings Tab".

Protocols Page

Installed Protocols - Displays installed protocols. The list includes Name, Version, Manufacturer, and Date information for each protocol.

New Std/Ctrl - Opens the Std/Ctrl Details tab.

Plate Layout - Open the Report dialog box, which includes the Plate Layout Report.

Delete - Opens the Delete Protocol dialog box to delete a protocol selected in the Installed Protocol list. Click Yes to delete the selected protocol.

Import - Opens the Open dialog box to select a protocol (.lxt file) to import. Navigate to the protocol file you wish to import and click Open..

Export - Opens the Save As dialog box to export a selected protocol. Choose an export destination and name, and select Save.

Edit - Opens the Settings tab to edit a selected protocol.

View - Opens the Settings tab to view the protocol. Click Next to advance the tab, and Next

again to advance to the Plate Layout tab. Click Close at any time of the three tabs to return to the main Protocols tab, or Back to return to a preceding tab. The View option does not allow any changing of the protocol settings.

Settings Subtab

Protocols > Protocols > Settings

Click Create a New Protocol on the Protocols tab to open the Settings subtab.

Name and description boxes - Type the name and description in the appropriate box.

Acquisition Settings

• Volume - This is the volume the instrument aspirates into the system for analysis. Type the

desired sample volume in microliters. Use values from 10 to 200 µl. To avoid air intake,

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add at least 25 µl to the sample well in addition to the sample size. The default value is 45 µl.

• XY heater - Select Enabled to enable the XY heater. In the box type the desired value in

degrees Celsius. The temperature range is 35° C to 60° C.

CAUTION: Acquiring data before the heater has reached the proper

temperature can compromise test results.

• Timeout - Check the Enabled box to enable the Timeout.

• Bead Type - Check the Bead Type box. From the drop down menu you can select

MicroPlex or MagPlex.

• Plate Name - Select the plate name from the drop down menu. Select Current 96-well

plate, Current 384-well plate, or a plate that you have created.

• DD Gating (Doublet Discriminator) - Use this to set the minimum and maximum DD Gating

values. In the first box, type the minimum value. In the second box, type the maximum value. The default is 7500 to 15000.

• Reporter Gain - Select Standard PMT from the drop down menu to decrease the reporter

gain.

Analysis Settings - Use this section to set the analysis type, set the number of standards and controls, select an external analysis program, and choose whether or not to analyze results while acquiring samples.

• Analysis Type - Use this list to choose from the following analysis types:

• None - No analysis. Select if you have your own data post-processing program. You cannot apply standards or controls when you select None. You cannot analyze acquisitions with this setting.

•

• Qualitative - Qualitative analysis determines results as either positive or negative, reactive or non-reactive. The software is flexible in defining custom result ranges, such as negative, low positive, or high positive. Determinations are based on a single standard. For qualitative analysis the Luminex software uses a specific algorithm, shown below.

(FIsample)/(FIstandard) = Ki

Where FI = Fluorescent Intensity and Ki = a “Quali” value entered in lot information to determine the value or the qualitative assay standard.

Two predefined formulas using the algorithm are included in the system. You can use them as-is or edit their range values to meet your requirements.

• The “Quali” value determines a cutoff or threshold. This, in conjunction with ranges using the Lum Qual formula or an edited range specific for your assay, helps to determine qualitative results for unknown samples.

• Quantitative - Determines the sample concentrations from standard curves using regression methods. Cubic Spline, Linear, Logistic 4P, and Logistic 5P. Type the desired values for standards and controls in the Number of Standards and Number of Controls boxes. Select either Fit of All Standards or Mean of Replicates for the calculation of the curve fit.

Protocols Page

NOTE: Luminex recommends Fit of All Standards as the most accurate

calculation of the curve fit.

Based on a range of quantitative, numerical results, a threshold range can be applied to a quantitative analysis, for example, high, low, saturated, and expected.

• Allele Call - Sets analysis for an allele call. Analytes must be put in groups of 2, 3, or 4.

• Number of Standards - Click to type the number of standards for the protocol. Applies

only to qualitative and quantitative analysis.

• Number of Controls - Click to type the number of controls for the protocol. Applies only to

qualitative and quantitative analyses.

• Fit of all Standards - The standard curve will be determined by using each individual

standard replicate when calculating the standard curve. For example, if you run duplicates of a 7-point standard curve, the software will calculate the standard curve by using 14points. Applies only to quantitative analysis.

• Mean of Replicates - The standard curve will be determined by averaging the individual

standard replicates when calculating the standard curve. For example, if you run duplicates of a seven-point curve, the software calculates the standard curve by using 7-averaged points. Applies only to quantitative analysis.

• Min MFI Enabled - Select this box to enable a minimum MFI for the Allele Call analysis.

Type a value in this box to set the minimum MFI for analysis.

• Analyze results while acquiring samples - The software allows real-time viewing of the results as the instrument analyzes samples. This feature is not available if you select None as your analysis type.

• Use External Analysis Program - Select this check box to use a third-party program to analyze the data. The Analysis Program list becomes active when this is selected. Applies only to qualitative and quantitative analysis. Use this list to select which program to use for data analysis.

Cancel - Returns you to the main Batches tab.

Next - Click to advance to the Analytes tab.

Editing Qualitative Analysis Settings

1. Open the Protocols page, then open the Protocols tab. Select a protocol and click Edit.

2. In the Settings tab, enter a new version number before clicking the Analytes subtab.

3. From the Analytes sub tab, click on any analyte in the Analysis field to open the

Analysis Settings dialog box.

4. From the Method list, click Luminex Qualitative or No Analysis. Check Mark as Intra-

Well Normalization Bead if you want to use a normalization bead. The normalization bead is a microsphere set that is included in the assay as an internal control. It controls for sample variation and can be used to normalize data between samples in a run. An analyte used as a normalization bead will appear blue in the analyte grid.

5. From the Formulas list, click Lum Qual or Adv Qual.

6. Type a new name for the edited formula in the Formula Name box.

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7. If you selected Lum Qual in the Formulas list, edit the values for each range under

Negative, Low Positive, or High Positive. If you selected Adv Qual in the Formulas list, edit Negative, Low Positive, Moderate Positive, or Strong Positive. Select the check box in the Inclusive column to include the value in the range. If you clear the check box, the value will be one unit higher than the low value, and one unit lower than the high value.

8. Click Add Range if you want to add a new range. Type a Range Name, Low Value,

High Value, and check or clear the Inclusive check boxes.

9. If you want to delete a range, click a range to highlight it, and click Delete Range.

10. Type a name for the new formula in the Formula Name box.

11. Click Save Formula. The new formula displays in the Formulas list.

12. Click Apply to All Analytes to apply the new formula to all analytes in the list, or click

OK to apply the new formula to the single analyte you first clicked.

Editing Quantitative Analysis Settings

To edit quantitative analysis settings:

1. Open the Protocols page, the Protocols tab opens. Select a protocol and click Edit.

2. The Settings - subtab opens.

NOTE: Update the version of the protocol before opening the Analytes

subtab.

3. From the Analytes tab, click on any analyte in the Analysis field to open the Analysis

Settings dialog box.

4. From the Method list, click No Analysis, Cubic Spline, Linear Fit, Logistic 4P, or

Logistic 5P.

• No Analysis

• Cubic Spine

• Linear Fit

• Logistic 4P

• Logistic 5P

5. From the Weight list, click None or 1/Y^2.

NOTE: The Weight options are only available if the chosen Method is

Logistic 4P or Logistic 5P.

6. Check Mark as Intra-Well Normalization Bead if you want to use a normalization bead.

The normalization bead is a microsphere set that is included in the assay as an internal control. It controls sample variation and can be used to normalize data between samples in a run.

7. Check Use Threshold Ranges if you want to use a range for the analysis.

8. Click Add Range to setup the threshold range.

9. Type a name for the range in the Range Name field.

10. Type low and high range values in the Low Value and High Value fields.

11. Select the check box in the Inclusive column to include the value in the range, or leave it

clear to make the range value one unit higher than the low value, and one unit lower than the high value.

Protocols Page

12. Highlight a range and click Delete Range to delete the range.

13. Click OK to apply the new settings to the analyte first clicked, or Apply to All Analytes

to apply them to all the analytes in the protocol.

Plate Layout Subtab

Protocols > Protocols > Plate Layout

• Plate Image - This is a representation of the plate. Each well appears as a circle on the grid. Well commands appear in the appropriate circles as you assign them to wells on the plate. The Plate Navigation section in the lower right part of the window can be used to display all the wells in the plate image. Click and drag in the Plate Navigation box to display different portions of the plate.

NOTE: A command’s ID and Dilution fields have a blue border around them

• Move Command - These arrows move a selected command up or down in the Command Sequence list, changing the acquisition order.

• Import List - Opens the Open dialog box to import an existing command sequence list.

NOTE: The import feature allows you to import patient information into

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if they can be double clicked to type information.

unknown wells or wells with specified locations.

Luminex xPONENT 4.2 User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Table of Contents

Safety Precautions

Elements of the Software

Home Page

Screen Elements

System Monitor

Help

Quick Start

System Info Tab

Basic Procedures

Adding a New License Key

Initial Startup

Adjusting the Sample Probe Height

Revive After Storage Routine

System Initialization

Shutting Down the Analyzer

Logging Off and Exiting

Using Online Help

Luminex® Support

Viewing the Luminex® Website

Contacting Technical Support

Software Packages

General Guidelines

Biological Samples

Bead (Microsphere) Handling

Sample Volume

Plates

Samples Page Overview

Creating New Samples

Editing a Sample List

Batches Page Functionality

Setting Up Batches

Using the Batches Page

Create a New Batch from an Existing Protocol

Protocol Subtab

Standards and Controls (Stds & Ctrls) Subtab

Plate Layout Subtab

Create a New Batch from a New Protocol

Settings Subtab

Analytes Tab

Standards and Controls (Stds & Ctrls) Subtab

Plate Layout Subtab

Create a New Multi-Batch

Creating a New Multi-Batch

Batch Procedures

Running a Pending Batch

Importing a Batch

Exporting a Batch

Editing a Batch

Deleting a Batch

Results Page

Performing Analysis

Current Batch Tab

Saved Batches Tab

Replaying a Batch

Results Subtab

Validate Standards

Invalidate Standards and Controls

Settings Subtab

Viewing Batch Settings

Log Subtab

Viewing Batch Logs

Sample Details Subtab

Viewing Sample Details

LIS Results Tab

Reports Tab

Generating a Report

Protocols Page Functionality

Protocol Procedures

Creating an Allele Call Protocol

Creating a Quantitative Assay Protocol

Creating a Qualitative Assay Protocol

Deleting a Protocol

Editing a Protocol

Exporting a Protocol

Importing a Protocol