Luminex xPONENT 4.0 User Manual

xPONENT® 4.0 SP1™

Lum/nex

Software Manual

© Luminex Corporation, 2001-2009. All rights reserved. No part of this publication may be reproduced, transmitted, transcribed, or translated into any language or computer language, in any form or by any means without prior express, written consent of:

LUMINEX CORPORATION

12212 Technology Boulevard

Austin, Texas 78727-6115

U.S.A.

Voice: (512) 219-8020

Fax: (512) 219-5195

Luminex® xPONENT® Software Manual

PN 89-00002-00-185 Rev. C

September 2009

REP

MDCI Ltd. Arundel House 1 Liverpool Gardens, Worthing West Sussex BN11 1SL United Kingdom

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 registered trademarks of Luminex: Luminex®, FLEXMAP 3D™, xMAP®, xPONENT®, xTAG® Microspheres.

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

Standard Terms and Conditions For Use of Product

By opening the packaging containing this 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 the Luminex authorized reseller that sells the Product to Buyer. 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.

Warranties - Any warranty obligations for the Product shall be exclusively provided in writing to

Buyer directly by Seller. LUMINEX MAKES NO WARRANTY WHATSOEVER REGARDING THE PRODUCT AND LUMINEX SPECIFICALLY DISCLAIMS ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. NEITHER SELLER NOR LUMINEX 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 HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE 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.

Buyer's Use of Product - 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, 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 Luminex's standard fluorescently dyed microspheres. Buyer further acknowledges that the Product have not received approval from the United States Food and Drug Administration or other federal, state or local regulatory agencies and have 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 in Luminex or Seller's technical specifications or material data sheets furnished to Buyer. Buyer expressly represents and warrants to Luminex that Buyer 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 PRODUCT; EXPLOIT ANY AND ALL METHODS OR PROCESSES; AND OTHERWISE EXPLOIT IMPROVEMENT PATENTS FOR ALL PURPOSES. NOTWITHSTANDING THE FOREGOING, "IMPROVEMENT PAT-

ENTS" SPECIFICALLY EXCLUDES PATENT CLAIMS CONCEIVED AND REDUCED TO PRACTICE BY BUYER CONSISTING OF METHODS OF SAMPLE PREPARATION, METHODS OF CONJUGATING PRODUCT TO ANALYTES, THE COMPOSITION OF MATTER OF THE SPECIFIC CHEMISTRIES OF THE ASSAYS DEVELOPED BY BUYER AND METHODS OF PERFORMING THE ASSAYS (I.E., THE PROTOCOL FOR THE ASSAY).

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 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.

Buyer's Representations, Release and Indemnity - Buyer represents and warrants that it shall

use the Product in accordance with Paragraph 2, "Buyer's Use of Product," and that any such use of 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.

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.

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

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

BY USING THE SOFTWARE, YOU ACCEPT THESE TERMS. IF YOU DO NOT ACCEPT THEM, DO NOT USE THE SOFTWARE. INSTEAD, RETURN IT TO LUMINEX OR THE LUMINEX AUTHORIZED THIRD PARTY 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. You can activate the SOFTWARE by obtaining a license key provided by Luminex

Technical Support at support@luminexcorp.com

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 updates from authorized resellers, see http://www.luminexcorp.com

or authorized resellers. For more information on obtaining

or 1-877-785-2323 or 1-512-381-4397.

3. GRANT OF LICENSE. Subject to the terms and conditions of this EULA, Luminex hereby grants to you a nonexclusive, nontransferable, nonassignable 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 three (3) additional computers 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. In addition, You may purchase the right to use the 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 rerunning 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 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 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 HAS 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.

Table of Contents

Introduction .......................................................................................................................... 1

Software Packages ......................................................................................................... 1

About This Guide ............................................................................................................ 2

Warnings, Notes and Symbols........................................................................................ 2

General Guidelines ......................................................................................................... 3

Biological Samples .................................................................................................... 3

Bead Handling ........................................................................................................... 3

Limitations ............................................................................................................ 3

Safety Precautions ............................................................................................... 4

Bead Concentration................................................................................................... 4

Repetitive xMAP Bead Measurements...................................................................... 4

Classification and Reporter Fluorochromes .............................................................. 4

Sample Volume ......................................................................................................... 5

Sample Dilution ......................................................................................................... 5

Reagents ................................................................................................................... 6

Gating ........................................................................................................................ 6

Plates......................................................................................................................... 6

Touring the Software............................................................................................................ 7

Log In .............................................................................................................................. 7

Help................................................................................................................................. 8

Log Off ............................................................................................................................ 8

Exit .................................................................................................................................. 8

Screen Elements............................................................................................................. 9

System Monitor ............................................................................................................. 10

Home ............................................................................................................................ 12

Samples ........................................................................................................................ 13

Samples Tab ........................................................................................................... 14

Create Sample Tab ................................................................................................. 15

Batches ......................................................................................................................... 16

Batches Tab ............................................................................................................ 16

Create a New Batch from an existing Protocol........................................................ 18

Protocol Tab....................................................................................................... 18

Stds & Ctrls Tab ................................................................................................. 19

Plate Layout Tab ................................................................................................ 21

Create a New Batch From a New Protocol.............................................................. 24

Settings Tab ....................................................................................................... 24

Analytes Tab ...................................................................................................... 27

Stds & Ctrls Tab ................................................................................................. 31

Plate Layout Tab ................................................................................................ 32

Create a New MultiBatch......................................................................................... 33

Results .......................................................................................................................... 37

Luminex xPONENT 4.0 Software Manual

Current Batch Tab .................................................................................................... 37

3D View............................................................................................................... 41

Saved Batches Tab .................................................................................................. 43

Results Tab......................................................................................................... 48

Settings Tab........................................................................................................ 49

Log Tab............................................................................................................... 50

Sample Details Tab............................................................................................. 51

LIS Results Tab........................................................................................................ 52

Reports Tab.............................................................................................................. 52

Protocols ........................................................................................................................ 55

Protocols Tab ........................................................................................................... 55

Settings Tab........................................................................................................ 56

Analytes Tab ...................................................................................................... 59

Plate Layout Tab................................................................................................. 62

Stds & Ctrls Tab ....................................................................................................... 65

Std/Ctrl Details Tab ............................................................................................. 67

Maintenance .................................................................................................................. 68

Auto Maint Tab ......................................................................................................... 69

Lot Management Tab ............................................................................................... 70

Cmds & Routines Tab .............................................................................................. 71

Probe and Heater Tab.............................................................................................. 75

System Info Tab ....................................................................................................... 77

System Status Tab ................................................................................................... 79

Schedule Tab ........................................................................................................... 80

Support Utility Tab.................................................................................................... 80

Admin............................................................................................................................. 82

System Setup Tab.................................................................................................... 82

Application Settings............................................................................................. 82

LIS Settings......................................................................................................... 83

External Analysis Program Settings.................................................................... 83

Arrange Main Navigation buttons........................................................................ 84

Maintenance Options .......................................................................................... 85

Data Conversion ................................................................................................. 85

Group Setup Tab...................................................................................................... 85

User Setup Tab ........................................................................................................ 88

Create User Account Screen .............................................................................. 89

Batch Options Tab.................................................................................................... 91

Alert Options Tab...................................................................................................... 93

CSV Options Tab...................................................................................................... 95

CSV and Batch Export Options........................................................................... 95

Archive Tab .............................................................................................................. 97

Licensing Tab ........................................................................................................... 98

Schedule Tab ........................................................................................................... 99

Report Options Tab ................................................................................................ 100

Using the Software ........................................................................................................... 101

Starting the Software ................................................................................................... 101

Using Online Help ........................................................................................................ 101

Contents

Setting Administrative Options .................................................................................... 102

System Setup ........................................................................................................ 102

Application Settings.......................................................................................... 102

Arrange Main Navigation Buttons..................................................................... 102

LIS Settings ...................................................................................................... 102

Maintenance Options ....................................................................................... 102

External Analysis Program Settings ................................................................. 102

Data Conversion............................................................................................... 103

Group Setup .......................................................................................................... 104

User Setup............................................................................................................. 104

Define Global User Settings ............................................................................. 104

Adding a User................................................................................................... 105

Editing User Permissions ................................................................................. 105

Restoring Account Status................................................................................. 105

Batch Options ........................................................................................................ 105

Alert Options .......................................................................................................... 105

CSV Options .......................................................................................................... 106

Archive................................................................................................................... 106

Licensing................................................................................................................ 107

Schedule................................................................................................................ 107

Report Options....................................................................................................... 107

Adjusting the Sample Probe........................................................................................ 108

System Initialization .................................................................................................... 108

Run System Initialization ....................................................................................... 109

Add CAL or VER Kits............................................................................................. 109

Import CAL or VER Kits ......................................................................................... 110

Export CAL or VER Kits......................................................................................... 110

Delete CAL and VER Kit Information..................................................................... 110

Create Calibration Reports .................................................................................... 110

Managing Sample Lists............................................................................................... 110

Create New Sample List ........................................................................................ 111

Edit Sample Lists ................................................................................................... 111

Setting Up Batches ..................................................................................................... 111

Create a New Batch from an Existing Protocol...................................................... 112

Create a New Batch from a New Protocol ............................................................. 112

Create a Multi-Batch .............................................................................................. 114

Import Batch .......................................................................................................... 114

Export Batch .......................................................................................................... 114

Delete Batch .......................................................................................................... 115

Edit Batch .............................................................................................................. 115

Run Batch .............................................................................................................. 115

Performing Analysis .................................................................................................... 115

Analyze Current Batch........................................................................................... 116

Manage Saved Batches......................................................................................... 116

Replay Batch .................................................................................................... 116

Analyze Saved Batch ....................................................................................... 117

View and Print Reports .......................................................................................... 119

iii

Luminex xPONENT 4.0 Software Manual

Transmit a Batch .................................................................................................... 119

Using Protocols, Lots, and Kits .................................................................................... 119

Protocols................................................................................................................. 119

Create Qualitative Assay Protocol .................................................................... 120

Edit Qualitative Analysis Settings...................................................................... 120

Create Quantitative Assay Protocol .................................................................. 121

Edit Quantitative Analysis Settings ................................................................... 122

Create an Allele Call Protocol ........................................................................... 123

Import Protocol.................................................................................................. 124

Add New Lot for Protocol .................................................................................. 124

Delete Protocol.................................................................................................. 124

Export Protocol.................................................................................................. 124

Edit Protocol...................................................................................................... 125

Lots and Kits........................................................................................................... 125

Create Kit .......................................................................................................... 125

Create Lot ......................................................................................................... 125

Import Lot.......................................................................................................... 126

Delete Lot.......................................................................................................... 126

Export Lot.......................................................................................................... 126

Edit Lot.............................................................................................................. 126

Performing System Maintenance................................................................................. 126

Performing Individual Maintenance Commands..................................................... 126

Perform System Calibration.................................................................................... 127

Manage Maintenance Routines.............................................................................. 127

Create New Routine.......................................................................................... 127

Edit Routine....................................................................................................... 127

Run Routine ...................................................................................................... 128

Delete Routine .................................................................................................. 128

Import Routine................................................................................................... 128

Export Routine .................................................................................................. 128

Support Utility ......................................................................................................... 128

Shutting Down the Analyzer......................................................................................... 129

Logging Out of the Software ........................................................................................ 129

Exiting the Software ..................................................................................................... 129

Technical Support ........................................................................................................ 129

Luminex Website ......................................................................................................... 129

Glossary............................................................................................................................ 131

Index ................................................................................................................................. 137

CHAPTER 1 Introduction

The Luminex system was developed to improve workflow and efficiency in the clinical laboratory and in research and development. End users in the laboratory must run microtiter plates using xMAP

Software Packages

based assay kits developed for use with xMAP technology.

xPONENT® software has different levels of functionality:

1. Basic - Basic package allows you to perform analysis, create protocols and batches

(both of which can be exported for use with an Instrument Control enabled software package), review and print reports, and perform Luminex system maintenance.

2. Instrument Control - This configuration allows the application to connect to and

communicate with an instrument identified by a specific serial number.

3. 500 Analyte Support - This configuration gives access to run or replay a batch that

contains up to 500 analytes.

4. Secure - Has all of the Basic functionality, plus allows the administrator to set up user

permission levels.

5. 21 CFR Part 11 - Has all of the Secure functionality, plus allows the requirement of

electronic signatures to perform certain tasks. Electronic signatures are listed in the system log. Electronic signatures for batch functions are also listed in the batch audit log.

6. Automation - Has the ability to communicate with external hardware.

7. Remote Web Monitoring - Allows you to view alerts and system status via a webpage.

8. LIS - Has the ability to communicate with an external Laboratory Information System

(LIS) database. The LIS edition allows the export of patient result data in ASTM file format and the import of patient sample information in ASTM format.

9. Allelic Ratios - A feature enabling allelic ratios to be utilized.

You will need an instrument control license to operate the instrument.

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

Luminex xPONENT 4.0 Software Manual

About This Guide

The conventions in this document assume a basic familiarity with computers and a knowledge of Microsoft

more than one method, such as from the toolbar and from menus that appear when rightclicking an area of the screen. However, for ease of use the individual procedures in this manual describe only one method for accessing commands.

This guide is formatted as a PDF, and can be printed. However, the guide is best viewed online due to the bookmarks and hypertext included in the text.

This guide may be updated periodically. To ensure that you have a current version, access www.luminexcorp.com/support/tech_manuals.html. The most recent version of this guide, as well as all translations of this guide, are available for download at that URL.

Warnings, Notes and Symbols

The following informational notes and warnings appear as necessary in this manual.

Windows® software. Commands are often available through

NOTE: This message is used to provide general helpful information. No

safety or performance issues are involved.

CAUTION: This message is used in cases where the hazard is minor or only

a potential hazard is present. Failure to comply with the caution may result in hazardous conditions.

WARNING: This message is used in cases where danger to the operator or to

the performance of the instrument is present. Failure to comply with the warning may result in incorrect performance, instrument failure, invalid results, or hazard to the operator.

You may encounter these symbols during the use of xPONENT software. They represent warnings, conditions, identifications, instructions, and regulatory agencies.

TABLE 1. Symbols

Warning, Biological Hazard

General Warning, Caution, Risk of Danger

Heat/Hot Surface Warning

European Representative

Manufacturer

Introduction

General Guidelines

Modifying or deleting xPONENT® system files may cause degradation to system performance. You can repair modified or deleted xPONENT system files by uninstalling

and re-installing the xPONENT software.

Use of unauthorized third party software with xPONENT software may result in corruption or failure of the xPONENT software. Use third party software at your own risk.

If using a screen saver on the xPONENT system, be aware that xPONENT will prevent it from activating. A dialog box will display each time xPONENT is launched, recommending that the screen saver and any power management settings are turned off.

This system contains electrical, mechanical, and laser components that, if handled improperly, are potentially harmful. In addition, biological hazards may be present during system operation. Therefore, we recommend that all system users adhere to standard laboratory safety practices. The protection provided by the equipment may be impaired or the warranty voided if Luminex FLEXMAP 3D™ is used in a manner not specified by the instructions or by Luminex Corporation.

Biological Samples

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 - 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.

Bead Handling

xMAP beads come in various configurations. Avoid excessive agitation of the product to reduce foaming and surface precipitation. The xMAP beads will settle if left undisturbed. Always ensure that the xMAP beads are homogeneously resuspended prior to dispensing. The uncoupled xMAP beads are not monodispersed and tend to aggregate until coated. Multiple pipetting from the original container may affect bead concentrations. Protect the xMAP beads from light at all times. Store xMAP beads at 2 to 8°C.

NOTE: Refer to the product information sheet that accompanies your

xMAP beads or assay for additional information.

Limitations

xMAP beads are susceptible to photobleaching; photobleaching effects are cumulative. Minimize exposure of xMAP beads to light during your development and manufacturing phases to maintain product integrity.

xMAP beads are hydrophobic in the aqueous medium provided and will settle if left undisturbed. Resuspend prior to dispensing.

Do not use this product with strong organic solvents. For information on specific compatibility, visit the Luminex Technical Support website at www.luminexcorp.com. From the main page, click Support, then FAQs.

Luminex xPONENT 4.0 Software Manual

Safety Precautions

All samples should be regarded as potentially contaminated and treated as infectious. These samples should be handled at the Biosafety Level 2 as recommended for any potentially infectious human serum or blood specimen in the Center for Disease Control/ National Institutes of Health Manual, “Biosafety in Microbiological and Biomedical Laboratories” 1984.

Although beads do not contain hazardous or carcinogenic components at toxic levels, they may be toxic if swallowed. Contact with acids liberates toxic gases. If product comes in contact with skin, wash immediately with copious amounts of water. In case of accident, seek medical advice immediately and show the product label or container to your medical provider. A Material Safety Data Sheet is available upon request.

WARNING: Reagents may contain sodium azide as a preservative. Sodium

azide may react with lead and copper plumbing to form highly explosive metal azides. It is also highly toxic and rates a material safety data sheet (MSDS) health hazard 4. On disposal, flush drains with a generous amount of cold water to prevent azide build-up. Consult the manual guideline “Safety Management No. CDC-22, Decontamination of Laboratory Sink Drains to remove Azide salts” (Centers for Disease Control, Atlanta, Georgia, April 30, 1976).

CAUTION: The sheath fluid and the solution in which beads are stored

contain proclin, which may cause an allergic reaction. Use personal protective equipment, including gloves and safety glasses.

Bead Concentration

The concentration of beads in an assay is a factor in system speed. If running an xMAPbased kit, follow the instruction found on the kit’s product insert or use the provided software protocol. We generally recommend using 2000 to 5000 beads per target, depending on the assay.

Repetitive xMAP Bead Measurements

In an xMAP assay, the reporter signal is the result of the assay. Due to small bead size, xMAP bead suspension exhibits near solution phase reaction kinetics. This means that each set of xMAP beads used for a particular assay will show a statistically even distribution of reporter molecules bound to the surface of each bead. During data acquisition, numerous beads of each set are analyzed and the median statistic is computed for that set by the software. The more beads of a set measured, the more confidence that can be given for that particular measurement. If running an xMAP-based kit, follow the kit’s product insert or use the provided software protocol.

Classification and Reporter Fluorochromes

Each xMAP bead set is internally dyed with two classification dyes, or three dyes for beads above 100-plex. The fluorescence signal of these dyes allows for classification of each bead set. Since each bead is analyzed individually, even when the sets are mixed in a multiplex assay they can still be distinguished by their emission signals. The fluorescence signal of reporter molecules bound to the surface of each bead set is

Introduction

measured and used to determine the result of each assay in a multiplex. Again, since each bead is analyzed individually, reporter signals for each bead set can be accurately quantified.

The following table displays acceptable reporter fluorochromes and their excitation and emission wavelengths.

TABLE 2. Reporter Fluorochromes Wavelengths

R-Phycoerythrin Alexa 532

Formula weight (Daltons) 240,000 470

Absorbance max (nm) 480, 546, 565 531

Extinction max (M-1cm-1) 1,960,000 83,800

Emission max (nm) 578 554

Quantum yield 0.82 0.8

Sample Volume

Sample volumes or sample sizes range from 10 to 200 µL. Ensure that some 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 150 µL of sheath fluid back into the well for a 96-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) + 150 (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).

• 150 (µL) = Volume expelled back as stated in the above paragraph.

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

96-well microtiter plate.

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

information regarding 384-well plates, refer to the assay kit instructions or contact Luminex technical support.

Sample Dilution

Dilute concentrated biological samples, such as plasma or serum, at least 1:5 with reagents as part of assay setup or as a final dilution step. If running an xMAP-based kit, follow the dilution instructions found on the kit’s product insert.

Luminex xPONENT 4.0 Software Manual

Reagents

Formulated reagents must be free of particulates other than xMAP beads. Do not dilute xMAP calibrators or verifiers.

Gating

Gate positions are dependent upon buffer composition. Any changes made to the buffer composition in an assay may result in a different optimal gate location.

Determine the gating on the Doublet Discriminator channel for the assay during assay development. The numeric values appear on the left side of the histogram. Use the numerical gate position, as determined during assay development, to set the gate location in the protocol.

Gating information may change with a new lot of xMAP beads. Each time you receive a new lot of xMAP beads, evaluate them with the current protocols. If gating information changes, create a new protocol identical to the current protocol, but with a new version number and new gating information. If running an xMAP-based kit, follow the instructions found on the kit’s product insert or use the provided software protocol.

Plates

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

For heated assays, use CoStar plates; Eppendorf well heated assays, we also recommend the plate be covered with a pierceable foil plate

sealer.

For nonheated assays, select a 96-well plate or 384 well plate with an overall height no greater than one inch (25.4 mm). See “Bead Concentration” on page 4.

See the recommended consumables list on the Luminex website at http:// www.luminexcorp.com/support/recommendedmaterials/index.html for more information.

384-well plates, catalog number 951020737 or equivalent. For 384-

Thermowell® 96-well, thin-wall polycarbonate, model P

CHAPTER 2 Touring the Software

This chapter explores each section of the software and its functionality. For information about using the software, see “Using the Software” on page 101.

This chapter describes default views. Please note that views can be changed and functionality can be disabled by the xPONENT

system administrator.

Log In

To log in, type your user ID at the System Login tab. If you are using the secure version of the software, type your password. Once you have logged in, the Home page opens. The xPONENT system administrator must set up the User ID and initial logon passwords. Contact your xPONENT system administrator if you have not been assigned a user ID and password.

NOTE: If a user is locked out of the application, each time the Admin user

logs in, a dialog box opens to notify the Admin user that a user is locked out.

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

inaccurate data and test results. It is highly advised that users

read this manual thoroughly before operating the software.

Luminex xPONENT 4.0 Software Manual

Help

English-language help is available for each window in the software by clicking the blue “i” button in the upper right portion of the window in which you are working. You can also access the complete system-wide help by clicking Help at the very top of the screen, and then clicking Contents and Index.

FIGURE 1. Help Icons

1 System-wide Help 2 Help for current window

Log Off

Click Log Off to log out of the software, then click OK in the Confirm Logout dialog box.

Exit

After you log out, click Exit, then Yes to exit the software completely.

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Screen Elements

The following section details the screen elements and the common terms used in this manual to describe them.

FIGURE 2. Screen Elements

Page

3 Right-Click Menu

Page. The main elements at the top of the window are “Pages”. Click a page to go to that section of the software. All but the Home, and in some cases the Admin, page can be moved or deleted. For more information, see “System Setup Tab” on page 82.

Tab. The elements on the left side of the window are “Tabs”. Click a tab to go to that section. Some tabs require you to go in order, and will not let you click a tab further down without performing a task on the current tab.

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 rightclicked.

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

2 Tab

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

• Import - Imports a file.

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345

• Export - Opens a File Dialog dialog box. Use the Browse button to select a location,

file name, and file type (either a text.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.

The histogram, dot plot, and 3D View within the Results page have specialty right-click menus. See those sections for more information.

System Monitor

The System Monitor remains at the bottom of all xPONENT® windows. It displays the physical state of the Luminex analyzer. The values displayed are reported directly from the

Luminex system.

FIGURE 3. System Monitor

1 System Status button 2 Command display

3 Progress bar and buttons 4 Delta Cal Temp status button

5 Sheath Pressure status 6 XY status

7 Laser status 8 Region Events status

9 Total events status

System Status. This button has two functions: When clicked, it opens the system log (see “System Status Tab” on page 79). 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, error, or other important user-notification, the button turns yellow with an exclamation point.

Command. Displays the command currently running on the system.

NOTE: A yellow Check Calibration button is visible in the command

display if the calibration or verification command has failed, when any verification is not current, or when the calibration or verification was performed prior to the calibration expiration setting.

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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.

Stop. Stops the system, regardless of command status.

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

Temp. Displays the difference in temperature between the current reading and the reading

when it was calibrated, in degrees Celsius. If the temperature is out of tolerance, it 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 and 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 and Heater tab.

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

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

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

Luminex xPONENT 4.0 Software Manual

Home

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

CAUTION: The sheath fluid and the solution in which beads are stored

contain proclin, which may cause an allergic reaction. Use personal protective equipment, including gloves and safety glasses.

FIGURE 4. Home Page

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

Click to Create a new Batch from a new Protocol. Creates a new batch from a new protocol by opening the Settings tab of the Batches page. Users can create protocols on the fly as a batch is created, and will have the option to save the protocol before or after the batch is run. For more information, see “Create a New Batch From a New Protocol” on page 24.

Click to Create a new Batch using the highlighted Protocol below. Creates a new batch using a selected protocol from the Installed Protocols list. For more information about creating a batch from an existing protocol, see “Create a New Batch from an existing Protocol” on page 18.

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

• Name

• Version

• Manufacturer

• Date

Use the up and down 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 xPONENT software:

• System Initialization - Opens the System Initialization command in the Auto Maint

tab on the Maintenance page. For more information about this tab, see “Auto Maint Tab” on page 69.

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

Maintenance page. For more information about this tab, see “Auto Maint Tab” on

page 69.

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

more information about this tab, see “Probe and Heater Tab” on page 75.

Sys Info. Opens the System Info tab of the Maintenance page. For more information, see “System Info Tab” on page 77.

Reports. Opens the Reports tab of the Results page. For more information, see “Reports Tab” on page 52.

Samples

Use this page to create new samples, view the details of a sample list, or to create a new batch. Samples can also be added via a Lab Information System (LIS).

This page contains the following tabs:

• Create Sample - Displays when the Create New Samples button is clicked.

• Edit Samples - Displays when the Details button is clicked.

• Protocol - Displays when the Create Batch button is clicked.

• Stds & Ctrls - Displays when the Create Batch button is clicked.

• Plate Layout - Displays when the Create Batch button is clicked.

Luminex xPONENT 4.0 Software Manual

Samples Tab

FIGURE 5. Samples Tab

This tab contains the following:

Create New Samples. Opens the Create Sample tab.

Sample Lists. Contains a list of protocols, including the version number and the number

of samples associated with each protocol.

Details. Opens the Edit Samples tab to view or edit sample details for the selected protocol.

Create Batch. Opens the Protocol tab to create a batch.

Create Sample Tab

Use this tab to type and view sample information.

FIGURE 6. Create Sample Tab

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This tab contains the following:

Protocol. Displays the protocol selected in the Samples tab. If xPONENT has an LIS license enabled, any sample details provided by the LIS also appear in the Sample list.

Version. Displays the protocol version number. It is not editable.

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

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

Sample. If you have the LIS-enabled version of the software and are currently connected to the LIS, the sample list autopopulates when the LIS provides samples orders. You can only view or run a sample list created in the LIS; you cannot edit it. Otherwise, use Create New Samples to create a new sample. Once you have typed and saved the sample information, it appears in the list to the left. This list displays the samples you have already created. To reorder the sample’s acquisition location, use the move arrows.

The following Delete, New, Edit, and Undo buttons only display depending on actions taken in the Create Sample tab.

Delete. Deletes a highlighted sample.

New. Creates a new sample.

Luminex xPONENT 4.0 Software Manual

Edit. Edits a highlighted sample.

Undo. Reopens the Create Sample tab without saving any changes made using the Edit or New buttons.

Save. Saves changes made to the Sample list.

Close. Returns to the Samples tab.

Batches

Use the Batches page to create and run a new batch from an existing protocol, a new batch from a new protocol, or a new multi-batch. This page contains the following tabs:

• Protocol - Displays when the Create a New Batch from an existing Protocol button

is clicked.

• Stds & Ctrls - Displays when the Create a New Batch from an existing Protocol and

Create a New Batch from a new Protocol buttons are clicked.

• Analytes - Displays when the Create a New Batch from a new Protocol button is

clicked.

• Plate Layout - Displays when the Create a New Batch from an existing Protocol

and Create a New Batch from a new Protocol buttons are clicked.

• New MultiBatch - Displays when the Create a New Multi-Batch button is clicked.

Batches Tab

The Batches tab displays the following:

FIGURE 7. Batches Tab

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Create a New Batch from an existing Protocol. Opens the Protocol tab, where you can create a new batch from an existing protocol. For more information, see “Create a New Batch from an existing Protocol” on page 18.

Create a New Batch from a new Protocol. Opens the Settings tab, where you can create a new batch from a new protocol. For more information, see “Create a New Batch From a New Protocol” on page 24.

Create a New Multi-Batch. Simultaneously opens the New Multibatch tab and the Select Pending Batch dialog box, where you can create a multi-batch from pending

batches. For more information, see “Create a New MultiBatch” on page 33.

Pending Batches. Displays a list of pending batches. It includes the batch name, protocol, protocol version, date, and status for each pending batch. If there is no data in the list of pending batches, the following buttons do not appear on the screen.

Single Step. Instructs the system to acquire two wells and then pause. This ensures the system is working correctly before running an entire batch.

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

Plate Layout. Opens the Report dialog box, which includes the Batch Plate Layout Report. See Figure 8 on page 17.

FIGURE 8. Batch Plate Layout Report

Import. Imports a batch.

Export. Exports a batch.

Delete. Deletes a batch.

Edit. Edits a batch.

Run. Runs a batch.

Luminex xPONENT 4.0 Software Manual

Create a New Batch from an existing Protocol

Creates a new batch from an existing protocol. The Protocol tab opens.

Protocol Tab

Use this tab to name a batch, type a description, select a protocol, and view active reagents.

FIGURE 9. Protocol Tab

This tab contains the following:

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

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

for each protocol.

Active Reagents. 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.

Stds & Ctrls Tab

Use this tab to apply a kit or lot to the batch.

FIGURE 10. Stds & Ctrls Tab

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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.

Manually 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.

• 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.

NOTE: The Dilution list and Apply Dilution button only appear if a

quantitative analysis has been selected.

• Dilution - Contains the following dilution options:

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

Luminex xPONENT 4.0 Software Manual

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

iteration.

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

iteration.

• Alternatively, type a number for your own dilution factor.

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

NOTE: Click a column header to resort the display.

NOTE: Click the Reagent column header to resort 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.

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 Value - 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. Opens the Plate Layout tab.

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Plate Layout Tab

Use this tab to define commands that apply to one or more wells. You can define off-plate and maintenance commands.

FIGURE 11. Plate Layout Tab

This tab contains the following:

Plate Image. This is a representation of the plate. Each well appears as a circle on the grid. Well commands appear in the appropriate circles as you assign them to wells on the plate. If using a 384 well plate, the Plate Navigation section in the lower right part of the window is a bounding box that can be used to display all the wells in the main plate image at the upper left portion of the window. Click and drag the box to display different portions of 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.

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.

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

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

options are:

Luminex xPONENT 4.0 Software Manual

• 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 simply 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

• Wash (W): Blue

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: You should first delete all standards from the plate layout if any of

the standards need to be rearranged, and 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 vary. You can assign a specific number of unknown wells to the plate when setting up a batch.

Commands. Assigns maintenance commands that run before or after single wells, ranges of wells, and rows or columns of wells. Select a well, and then select one of the following commands:

• Alcohol Flush

• Prime

• Sanitize

• Soak

• Wash

After selecting a maintenance command, click one of the following buttons:

• Before Well - The system performs the command before acquiring the well. An open

dot appears in the upper left corner of the selected well on the plate image. The command appears in the command sequence list before the selected well.

• After Well - The system performs the command after acquiring the well. A closed dot

appears in the lower right corner of the selected well on the plate image. The command appears in the command sequence list after the selected well.

• Clear Command - Select a well and click Clear Commands to remove all

maintenance commands from the well.

NOTE: If the batch has Before Well or After Well commands samples

will be run as in a standard syringe system, which will lengthen the batch run time.

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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. If you have selected a 384-well plate, there is a blue bounding box that can be clicked and dragged to display the full range of wells in the larger plate image at the upper left.

Single Step. Instructs the system to acquire two wells and then stop. Use this to ensure the system is working correctly before you run the whole batch.

Off Plate Area. Designates an alternate location for maintenance commands in the Commands: list. Highlight a command, and then click either a reservoir or strip well in the Off Plate Area to select a location for the command.

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

FIGURE 12. Save Protocol Dialog Box

• 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#

Luminex xPONENT 4.0 Software Manual

• Expiration

• Manufacturer

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 Create a New Batch from a new Protocol to create a new batch without using a protocol. The Settings tab opens. Raw data results write to a.CSV file. You can define parameters for samples, gates, regions, events, and commands.

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 Tab

Use this tab to name your new batch and configure acquisition settings.

FIGURE 13. Settings Tab

This tab contains the following:

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Name and Description boxes. Type a name and a description in the appropriate boxes.

Acquisition Settings. Use this section to set the following:

• Bead Type - Select either MicroPlex (standard) or MagPlex (magnetic) beads.

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

Type the desired sample volume in microliters. Use values from 10 to 200 µl for both 96-well and 384-well plates. 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.

• Timeout - Select Enabled to enable a timeout. Acquisition stops once the timeout is

reached. Type a value from 1 to 250 seconds.

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

in degrees Celsius. The temperature range is 35 to 60°C in 0.5 increments.

WARNING: Acquiring data before the heater has reached the proper

temperature can compromise test results.

• Plate Name - Click the Plate Name list and select Current 96-well plate, Current

384-well plate, or a plate that you have previously saved.

• DD gating - Use this to set the minimum and maximum DD gating values. Use values

within the range of 0 to 32767. In the first box, type the minimum value. In the second box, type the maximum value. The default minimum and maximum values are 7500 and 13500 respectively.

• Reporter Gain - Select Standard PMT from this list to decrease the reporter gain

level. The default option is Enhanced PMT. Refer to assay application instructions for more detailed information.

Analysis Settings. Use this section to set the analysis type, set the number of standards and controls, select an external analysis program, and choose whether to analyze results while acquiring samples.

• 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.

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. For information about changing the analysis settings, see “Analysis Settings Dialog Box” on page 28 and “Analysis Settings Dialog Box” on page 29.

Luminex xPONENT 4.0 Software Manual

• Quantitative - Determines the sample concentrations from standard curves using

regression methods Cubic Spline, Linear, Logistic 4P, and 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 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.

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

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

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

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

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

individual standard replicates when calculating the standard curve. For example if one runs duplicates of a 7-point standard curve, the software will calculate the standard curve by using 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.

Logistic 5P. Type the

Cancel. Click to return to the main Batches tab.

Next. Click to advance to the Analytes tab.

Analytes Tab

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

FIGURE 14. Analytes Tab

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This tab contains the following:

Analyte grid. A grid representing each analyte from 1 to 500. Drag the slider box at the far left up or down, or click the blue up and down arrows to display the full range of analytes. Select All selects all analytes, and Deselect All deselects all analytes. Click a numbered analyte to select it; click the analyte again to deselect it. You can also click and drag to select groups of analytes. Selected analytes are red. Deselected analytes are gray. An analyte marked as an intra-well normalization bead is blue.

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 the button is enabled in this tab. This displays the Analysis Settings dialog box.

Luminex xPONENT 4.0 Software Manual

FIGURE 15. 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 select Logistic 4P or Logistic 5P, select a weight type of either None or 1/Y

If you selected Qualitative on the Settings tab, the default analysis is Luminex Qualitative. Change the default value by selecting either Lum Qual 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 “Analysis Settings” on page 25.

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

Count. Type the desired bead count for the analytes by clicking in the Count box. 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 Count boxes to all analytes.

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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. For

information about this feature, see “Batch Options Tab” on page 91.

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.

FIGURE 16. Analysis Settings Dialog Box

• Select a method from the Method list.

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

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

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

normalization bead.

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

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

• Click Add Range to add a range.

Luminex xPONENT 4.0 Software Manual

• 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.

• Count - The total desired bead count for an analyte. Click this box to type a value. The

system continues analyzing until each bead set has met the minimum events as determined in the Count box above. If you select the Stop after total bead count reaches: check box and type a total count in the corresponding box, this column does not appear.

• Region - Refers to the specific analyte selected. It is a number from 1 to 500.

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 made.

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.

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Stds & Ctrls Tab

If you have specified standards and controls, use this tab to apply a lot or a kit. For more information about the functionality of this tab, see “Stds & Ctrls Tab” on page 19.

FIGURE 17. Stds & Ctrls Tab

Luminex xPONENT 4.0 Software Manual

Plate Layout Tab

Use this tab to select wells to add samples and maintenance commands to the plate. For more information about the functionality of this tab, see “Plate Layout Tab” on page 21.

FIGURE 18. Plate Layout Tab

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Create a New MultiBatch

Use this button to add or remove pending batches to the multi-batch set up and to run a multi-batch. A multi-batch is composed of one or more pending batches which, together, will fit on one plate. Use the multi-batch feature to conserve plates.

NOTE: 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.

FIGURE 19. New Multibatch Tab

Luminex xPONENT 4.0 Software Manual

FIGURE 20.

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.

FIGURE 21. Select Pending Batch dialog box

Plate layout. Depicts where batches are located on the plate.

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FIGURE 22. New Multibatch tab with plate layout displayed

Multi-Batch. Lists pending batches selected for the multi-batch. The list includes name

and “Start at” well.

Plate Layout. Opens the Multibatch 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.

The Multibatch Plate Layout Report includes the multibatch plate layout, command number, plate location, command type, sample ID and dilution. The report is date and time stamped.

Luminex xPONENT 4.0 Software Manual

FIGURE 23. Multibatch Report dialog box

New Batch. Opens the Create New Batch tab. Create your new batch. Click Save to return to the New Multibatch 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 will still remain in the Pending Batches section (This button only appears 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.

Run. Runs the batch.

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Results

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

• Current Batch

• Saved Batches

• Results

• Settings

• Log

• Sample Details

• LIS Results

• Reports

Current Batch Tab

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

NOTE: The buttons on this tab may change based on settings chosen by

the user.

FIGURE 24. Current Batch Tab

Statistic. To view a particular statistic for analytes in a batch, select one of the following:

Luminex xPONENT 4.0 Software Manual

• Median - The point in a data set where there are as many values occurring above it as

there are below it.

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

derived from standards with known values.

• Range - A sem-quantitative result for a particular numerical result falling between a

predefined set of values such as “Normal” or “Negative”.

• Count - Gated events, if gates are set.

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

• Mean - Average of all values in a set of results.

• % 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 largest number of times in the distribution list.

• Trimmed Count*

• Trimmed Mean*

• Trimmed%CV of microspheres*

• Trimmed Standard Deviation*

• Trimmed Peak*

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

results for replicate samples. %CV = 100 X Std Dev / Mean

• % Recovery - A measure of how accurately your observed results match your

expected results following regression analysis. (Observed concentration) / (Expected concentration) x 100%

• 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 Net Median - For each analyte in a well the Normalized Net Median

(NNM) = (net median of analyte) / (net median of normalization bead)

• Units - The unit of measure for an analyte, for example, pg/mL.

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

The statistics displayed change according to the analysis type selected.

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

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. Allows analysis one well at a time. Click to turn function on or off.

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Results. 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. A list of the available plates (if more than one).

WARNING: If using multiple plates, be careful to ensure that plates are used

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

Histogram/Dot Plot. Displays real-time monitoring of batch sampling during acquisition.

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 the 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 beads shows Classification 1 and

Classification 2. When running more 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 axes. 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 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 dependent upon buffer composition. Any

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

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

• X Axis - Use this 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.

Luminex xPONENT 4.0 Software Manual

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 settings 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:

• Date

• Message

• Code

Log entries indicating warnings are highlighted 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.

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Details. Opens the Results tab, enabling more analysis and results. For more information, see “Results Tab” on page 48.

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 display 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 wells. 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. Displays the 3D view of the dot plot.

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 better display regions, specific events, and results outside expected parameters.

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.

Luminex xPONENT 4.0 Software Manual

FIGURE 25. 3D View

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:

• Display Mode - Select either Logarithmic or Linear. The default is logarithmic.

• Display Position - Select from 3D View, CL1/CL3 View, CL1/CL2 View, or CL2/CL3

View.

• Show Regions - Select from 3D View, CL1/CL3 Plane, Cl2/CL3 Plane, or CL1/CL2

Plane.

• Show Beads - Select from 3D View, CL1/CL3 Plane, CL2/Cl3 Plane, CL1/CL2

Plane.

• View - Select either All Events or Gated Events.

• Cursors - Turns cursors on or off. Cursors are shown as arrows on the display,

allowing you to narrow down the section you wish to view.

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 Region View Box by clicking Settings for an easier way to manipulate the viewing angles.

Region. A list that enables viewing of a 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.

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Sample Lists. Contains a list of protocols, including the version number and the number of samples associated with each protocol.

Settings. Opens the 3D Settings dialog box. This dialog box has the following options:

• Show Regions

• 3D

• CL1/CL3 Plane

• CL2/CL3 Plane

• CL1/CL2 Plane

• Show Beads

• 3D

• CL1/CL3 Plane

• CL2/CL3 Plane

• CL1/CL2 Plane

• Display Mode

• Logarithmic

• Linear

• Display Position

• 3D View

• CL1/CL3 View

• CL2/CL3 View

• CL1/CL2 View

• View

• All Events

• Gated Events

• Show Cursors

• Show Region Labels

• Show 3D Region View Box

These settings are also available by right-clicking in the applicable sections of the main 3D display.

All Regions. Displays all regions of the batch.

2D. Returns to the default display.

Default. Returns to the histogram and dot plot display.

Saved Batches Tab

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

Luminex xPONENT 4.0 Software Manual

Completed Batches. Displays a list of completed batches which includes the Name, Protocol, Protocol Version, Date, Status, and User information for each batch. This list

does not include batches which have not been run.

FIGURE 26. Saved Batches Tab

Filter. Opens the Filter Setup dialog box.

FIGURE 27. 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 the following check boxes:

• Batch Name

• Protocol

• Batch Status

• Lot ID

• Kit ID

• Analyte

• Sample ID

• First Name

• Last Name

• User ID

• Date

Reset - Clears all check boxes.

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

Cancel - Closes the dialog box and cancels any changes you made.

Save Prtcl. Saves the protocol and kit information for the selected batch. For more

information, see Figure 12 on page 23.

Plate Layout. Opens the Report dialog box, which includes the Batch Plate Layout Report. See Figure 28 on page 45.

FIGURE 28. 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. Once you have approved a batch, the status of the batch changes to Approved in the Completed

Batches list.

Exp Results. Opens the Save As dialog box to choose an export destination for the.CSV

file containing your results.

Luminex xPONENT 4.0 Software Manual

Import. Opens the Open dialog box to choose a batch file (.mdf) to import. Select Include Raw Files (LXB) to import the raw data file as well.

Export. Opens the Export Batch dialog box to choose a destination for the batch file (.mdf). Select Include Raw Files (LXB) to include the raw file in the export. Select Overwrite to overwrite pre-existing files.

Replay. Opens the Select Replay Mode dialog box.

FIGURE 29. Select Replay Mode Dialog Box

Replay batch - Uses 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.

NOTE: 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 a new batch, creating a separate batch entry and output file.

Replay a batch to replay the raw bead data files. The bead data files will be replayed using the gate, analyte, analysis settings, and plate layout selected in the new (or updated) protocol. Settings such as bead type, volume, timeout, XY heater, and report gain will have no effect.

Recalculate data - Reanalyzes the batch results using only the batch’s MFI values.

The batch MFI values will be 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, gate, report, and gain will have no effect. Because only the MFI values are reanalyzed, no data will be displayed in the dot plot or histogram.

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 will vary based on whether you created a new batch from a new protocol or a new batch from an existing protocol. The functionality of the tabs you see while configuring the replay batch is the same as described in “Batches Tab” on page 16.

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Open. Opens the Results tab. Use this tab to view the saved batch results for the selected batch.

Luminex xPONENT 4.0 Software Manual

Results Tab

FIGURE 30. Results Tab

The Results tab has the same Save Image, Progress, Well Report, and 3-D buttons as the Current Batch tab. For more information about these buttons, see “Current Batch Tab” on page 37. The following buttons are added to the Results tab:

• 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. For more information, see “Analysis Settings Dialog Box” on page 28.

• 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.

• 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.

• 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 removed.

• Close - Closes the batch and reopens the Saved Batches tab.

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Settings Tab

Use this tab to view the acquisition parameters of the selected saved batch and print the batch settings report.

FIGURE 31. Settings Tab

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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Log Tab

This tab displays a log of the activity which occurred during the acquisition of the selected batch.

FIGURE 32. Log Tab

This tab displays the following information about each activity:

• Date

• Message

• Code

Log entries display yellow if a well was acquired but there was a possible problem. They display red if a problem occurred during the acquisition.

Print. Prints the log.

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.

Sample Details Tab

Use this tab to view sample results.

FIGURE 33. Sample Details Tab

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Arrows. Scrolls through the sample details.

Tra nsmit. 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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LIS Results Tab

This tab displays saved batches containing LIS samples.

FIGURE 34. LIS Results Tab

Filter. Opens the Filter Setup dialog box. For more information, see Figure 27 on

page 44.

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.

Tra nsmit. Transmits a batch to an LIS if xPONENT is connected to one.

Details. Opens the Sample Details tab to view sample results.

Reports Tab

Use this tab to view, generate, and print reports.

FIGURE 35. Reports Tab

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Report and Type lists. Choose a report from one of the following categories:

• Batch Reports - A list of batches appears below the Type list. The list includes Name,

Protocol, Protocol Version, Date, Status, and User information. Choose from the

following reports:

• Data Interpretation

• Batch Settings

• Plate Layout

• Batch Audit

• Patient Report

If you choose Data Interpretation, a Select Analytes 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 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 being viewed.

Luminex xPONENT 4.0 Software Manual

• 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 interpretation of an allele call batch report, be

aware that when choosing analytes from the Select Analytes list, selecting one analyte will select all analytes in that group.

• Protocol Reports - A list of protocols displays. Choose from the following reports:

• Protocol Settings

• Plate Layout

• Protocol Audit

Select a protocol and then click Generate to generate the report.

• 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 component, a date from the Date list, and click Generate to generate the report.

• Performance 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 click Generate to generate the report.

• System Log Reports - Displays a list of system log reports. Choose from the following

selections:

• All

• Maintenance

• Security

• Warning and Errors

Select a system log report, a date from the Date list, and click Generate to generate the report.

• Advanced Reports - Enables a single option, User Report, in the list.

Click Generate to generate the report.

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Protocols

The Protocols page enables you to create and edit the settings for protocols, in addition to adding standards and verifiers. This page contains the following tabs:

• Protocols

• Settings

• Analytes

• Plate Layout

• Stds & Ctrls

Protocols Tab

Use this tab to create, import, export, edit, or delete a protocol. You can also add new assay standard and or control information using one of the installed protocols.

FIGURE 36. Protocols Tab

This tab contains the following:

Create New Protocol. Opens the Settings tab to create a new protocol. For more information, see “Settings Tab” on page 56.

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. For more information, see “Std/Ctrl Details

Tab” on page 67.

Luminex xPONENT 4.0 Software Manual

Plate Layout. Opens the Report dialog box, which includes the Plate Layout Report. See Figure 37 on page 56.

FIGURE 37. Protocols 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 click Save.

Edit. Opens the Settings tab to edit a selected protocol. For more information, see

“Settings Tab” on page 56.

View. Opens the Settings tab to view the protocol. Click Next to advance to the Analytes tab, and Next again to advance to the Plate Layout tab. Click Close at any 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 Tab

Use this tab to name your new protocol and configure acquisition settings.

FIGURE 38. Settings Tab

Touring the Software

This tab contains the following:

Name and Description boxes. Type a name and a description in the appropriate boxes.

Acquisition Settings. Use this section to set the following:

• Bead Type - Select either MicroPlex (standard) or MagPlex (magnetic) beads.

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

• Timeout - Select Enabled to enable a timeout. Acquisition stops once the timeout is

reached. Type a value from 1 to 250 seconds.

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

in degrees Celsius. The temperature range is 35 to 60°C in 0.5 increments.

WARNING: Acquiring data before the heater has reached the proper

temperature can compromise test results.

• Plate Name - Click the Plate Name list and select Current 96-well plate, Current

384-well plate, or a plate that you have previously saved.

• DD gating - Use this to set the minimum and maximum DD gating values. Use values

within the range of 0 to 32767. In the first box, type the minimum value. In the second box, type the maximum value. The default minimum and maximum values are 7500 and 13500 respectively.

• Reporter Gain - Select Standard PMT from this list to decrease the reporter gain

level. The default option is Enhanced PMT. Refer to assay application instructions for more detailed information.

Luminex xPONENT 4.0 Software Manual

• 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,

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

• Quantitative - Determines the sample concentrations from standard curves using

regression methods Cubic Spline, Linear, Logistic 4P, 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.

and Logistic 5P. Type the

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

calculation of the curve fit.

• Allele Call - Sets analysis for an allele call. Analytes must put in groups of 2, 3, or 4

analytes