©Copyright 2019, Associates of Cape Cod, Inc., All rights reserved.

This document has been prepared for use by the customers and authorized personnel of Associates of Cape Cod, Inc. The
information contained in this manual is proprietary. The manual may not be copied, reproduced, translated or transmitted in
any form without the express written permission of Associates of Cape Cod, Inc.
While Associates of Cape Cod, Inc. has made every effort to produce an accurate and useful manual, no representation or
warranties of any kind, expressed or implied, are made regarding the contents of this manual, including, but not limited to,
completeness or typographical errors.

G_1392 Rev 1

Microsoft®, Microsoft® .NET, Windows Vista®, Windows® XP, Windows Server®, Microsoft SQL Server®, SQL Server®, Windows Azure®, and
Excel® are registered trademarks of Microsoft Corporation in the United States and/or other countries.
Windows® and the Windows logo are trademarks of the Microsoft group of companies.
ELx808™, BioTek® and the BioTek logo are registered trademarks of BioTek Instruments, Inc.
Pyros® and Pyros Kinetix® are registered trademarks of Associates of Cape Cod, Inc.

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress

Contents
1 Using this Manual ................................................................................................................................. 1
1.1 Intended Use ................................................................................................................................. 1
1.2 Kinetic Assays ................................................................................................................................ 1
1.3 Compatibility with Tube Readers and Plate Readers .................................................................... 2
2 Installing Pyros® eXpress ...................................................................................................................... 3
2.1 Pre-Install Checklist ....................................................................................................................... 3
2.2 Required Equipment ..................................................................................................................... 5
2.3 Installation Procedure ................................................................................................................... 5
2.3.1 Standalone (Local) Installation .............................................................................................. 5
2.3.2 Network (Remote) Installation ............................................................................................. 6
2.4 First-time Login ............................................................................................................................. 7
2.5 Changing the Admin Password ..................................................................................................... 9
2.6 Navigating the Home Screen ...................................................................................................... 10
2.7 Anti-Virus Information ................................................................................................................ 11
2.8 Backup and Restore Procedures ................................................................................................. 11
3 Setting up The Work Environment ..................................................................................................... 13
3.1 Administering User Accounts and Permissions .......................................................................... 13
3.1.1 Editing the Name of a Workgroup ...................................................................................... 16
3.1.2 Adding a User to a Workgroup ........................................................................................... 16
3.1.3 Removing a User from a Workgroup .................................................................................. 17
3.1.4 Editing a User ...................................................................................................................... 17
3.1.5 Resetting a User Password .................................................................................................. 17
3.1.6 Unlocking a User ................................................................................................................. 18
3.1.7 Changing a User's Status ..................................................................................................... 18
3.2 Setting Up Instruments and Testing System Communication .................................................... 18
3.2.1 Editing or Deleting an Instrument ....................................................................................... 19
3.3 Setting Up Global Options........................................................................................................... 20
3.4 Setting Up Reports ...................................................................................................................... 21
3.5 Setting Up Notifications .............................................................................................................. 22
3.6 Using the Service Tab .................................................................................................................. 23
4 Setting up The Testing Environment ................................................................................................... 25
4.1 Adding Supplies to the Library .................................................................................................... 25

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 4.1.1 Retiring a Supply ................................................................................................................. 27
4.1.2 Viewing and Editing Supplies .............................................................................................. 27
4.1.3 Matching Supplies in the Library......................................................................................... 27
4.1.4 Editing or Removing a Matched Supply .............................................................................. 28
4.1.5 Adding a Standard to a Matched Supply ............................................................................ 29
4.1.6 Qualifying an Analyst on a Reagent Combination .............................................................. 29
4.1.7 Adding Products to the Library ........................................................................................... 31
4.1.8 Retiring a Product ............................................................................................................... 32
4.1.9 Editing a Product ................................................................................................................. 33
4.1.10 Adding Methods to the Library ........................................................................................... 33
4.1.11 Viewing and Editing Methods ............................................................................................. 35
4.1.12 Retiring a Method ............................................................................................................... 35
4.1.13 Reinstating a Supply ............................................................................................................ 36
4.1.14 Reinstating a Product .......................................................................................................... 36
4.1.15 Reinstating a Method .......................................................................................................... 36
4.1.16 Using the Toolbar Calculator............................................................................................... 36
4.1.17 Setting up Templates .......................................................................................................... 37
4.1.18 Setting Up a Reagent Verification Template ....................................................................... 38
4.1.19 Setting up an Inhibition/Enhancement (I/E) Template ....................................................... 44
4.1.20 Setting up a Product Validation Template .......................................................................... 50
4.1.21 Completing I/E and Product Validation............................................................................... 54
4.1.22 Setting up a Routine Template ........................................................................................... 55
4.1.23 Setting up a Potency Template ........................................................................................... 59
4.1.24 Running a Potency Test ....................................................................................................... 64
5 Qualifying Reagents ............................................................................................................................ 71
5.1 Reagent Verification Testing ....................................................................................................... 71
5.1.1 Running a Reagent Verification Test ................................................................................... 71
6 Testing Products.................................................................................................................................. 78
6.1 Running an I/E Test ..................................................................................................................... 78
6.2 Running a Product Validation Test .............................................................................................. 87
6.3 Running a Routine Test ............................................................................................................... 94
6.4 Running a FreeForm Test .......................................................................................................... 101
7 Data Collection .................................................................................................................................. 109

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 7.1 Data Collection on a Tube Reader ............................................................................................ 109
7.1.1 Editing Parameters During Data Collection ...................................................................... 111
7.1.2 Adding a Sample During Data Collection .......................................................................... 111
7.2 Data Collection on a Plate Reader ............................................................................................ 113
7.2.1 Editing Parameters During Data Collection ...................................................................... 114
7.2.2 Changing Settings During Data Collection ........................................................................ 115
7.3 Viewing Data Collection Graphs................................................................................................ 115
7.3.1 Individual Graphs and Single Graphs ................................................................................ 116
7.3.2 List View Mode and Reader Layout Mode ........................................................................ 117
7.3.3 Removing Data Points from a Graph ................................................................................ 118
8 Reports .............................................................................................................................................. 119
8.1 Viewing Reports ........................................................................................................................ 119
8.2 Editing an Assay ........................................................................................................................ 121
8.3 Reading a Report ....................................................................................................................... 123
8.3.1 Report Summary ............................................................................................................... 123
8.3.2 Standard Curve.................................................................................................................. 123
8.3.3 Standard Results ............................................................................................................... 124
8.3.4 Section 4: Standards Evaluation........................................................................................ 125
8.3.5 Graphical Analysis Parameters.......................................................................................... 126
8.3.6 Product Results and Product Sample Evaluation .............................................................. 126
8.3.7 Consumables and Equipment ........................................................................................... 127
8.3.8 Section 8: Log Summary .................................................................................................... 128
8.3.9 Section 9: Signatures ......................................................................................................... 128
8.4 Signing a Report ........................................................................................................................ 128
8.5 Specific Test Reports ................................................................................................................. 129
8.5.1 Potency Test Report .......................................................................................................... 129
8.5.2 Reagent Verification Test Report ...................................................................................... 130
8.5.3 I/E Test Report .................................................................................................................. 131
8.6 Unlocking an Assay.................................................................................................................... 133
9 Audit Trail .......................................................................................................................................... 134
9.1 Accessing an Audit Trail Report ................................................................................................ 134
9.2 Viewing a Pre-Filtered Audit Trail Report ................................................................................. 137
10 Service ........................................................................................................................................... 139

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 10.1 Setting Up the Calibration Equipment Library .......................................................................... 139
10.1.1 Adding a Universal Absorbance Plate ............................................................................... 140
10.1.2 Adding a 340 nm Absorbance Plate .................................................................................. 141
10.1.3 Adding a Stepped Neutral Density Plate ........................................................................... 142
10.1.4 Adding a Temperature Probe............................................................................................ 143
10.1.5 Adding a Hygrometer ........................................................................................................ 144
10.1.6 Retiring Equipment in the Equipment Calibration Library ................................................ 145
10.1.7 Reinstating Equipment in the Equipment Calibration Library .......................................... 145
10.1.8 Editing Equipment in the Equipment Calibration Library ................................................. 145
10.2 ELx808™ System Test ................................................................................................................ 145
10.3 ELx808™ Universal Absorbance Test ........................................................................................ 147
10.4 ELx808™ 340 nm Absorbance Test ........................................................................................... 148
10.5 ELx808™ Stepped Neutral Density Test .................................................................................... 149
10.6 ELx808™ Empty Carriage Test ................................................................................................... 150
10.7 ELx808™ Shaker Test ................................................................................................................. 151
10.8 PKFlex Baseline Test .................................................................................................................. 152
10.9 PKFlex A/D Test ......................................................................................................................... 153
10.10 PKFlex A/D Calibration .......................................................................................................... 155
10.11 PKFlex Manual Temperature Record .................................................................................... 155
10.12 PKFlex Manual Temperature Adjustment ............................................................................. 156
10.13 PKFlex Transmitted Temperature Test ................................................................................. 156
11 Trending ........................................................................................................................................ 158
11.1 Permissions Required to Run Trending Report ......................................................................... 158
11.2 Product Trending ...................................................................................................................... 158
11.2.1 Filtered Product Trending Results ..................................................................................... 163
11.3 Standard Trending..................................................................................................................... 164
11.3.1 Filtered Standard Trending Results ................................................................................... 166
12 LIMS............................................................................................................................................... 168
13 Troubleshooting ............................................................................................................................ 170
13.1 Tube Reader .............................................................................................................................. 170
13.1.1 No Power........................................................................................................................... 170
13.1.2 Tube Reader Not Detected ............................................................................................... 170
13.1.3 Tubes Not Detected in the Software During Data Collection ........................................... 170

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 13.1.4 Tube Detect issues ............................................................................................................ 170
13.1.5 Tubes Cannot be Inserted in Wells ................................................................................... 171
13.1.6 Inconsistent Results or Poor Replication .......................................................................... 171
13.1.7 A/D Values Out of Range .................................................................................................. 171
13.1.8 Temperature Out of Range ............................................................................................... 172
13.1.9 BioTek® ELx808™ Plate Reader ......................................................................................... 172
13.2 Pyros® eXpress .......................................................................................................................... 172
13.2.1 Software Not Accessing Database .................................................................................... 172
13.2.2 Login Failure ...................................................................................................................... 172
13.2.3 Password Not Working ..................................................................................................... 172
13.2.4 No Available Methods When Creating a Template........................................................... 172
13.2.5 No Available Products When Running an I/E or Product Validation Assay ...................... 173
13.2.6 No Available Products When Running a Routine Assay .................................................... 173
13.2.7 No Available Samples When Running an I/E Test ............................................................. 173
13.2.8 Library is Missing a Supply, Product or Method ............................................................... 173
13.2.9 You Cannot Perform Certain Actions ................................................................................ 173
14 Pyros® eXpress and 21 CFR Part 11 Compliance........................................................................... 174
14.1 Overview of 21 CFR Part 11 ...................................................................................................... 174
14.2 EU Annex 11 .............................................................................................................................. 174
14.2.1 Part 11 Functionality in Pyros® eXpress ............................................................................ 174
14.2.2 Security Settings ................................................................................................................ 175
14.3 Meeting the Requirements of Part 11 ...................................................................................... 175
Appendix A: Glossary of Terms ................................................................................................................. 178
Appendix B: Program Calculations ............................................................................................................ 180
1 Onset Time ........................................................................................................................................ 180
2 Standard Curve Calculations ............................................................................................................. 180
2.1 Polynomial Regression .............................................................................................................. 180
2.2 Linear Regression ...................................................................................................................... 180
Index.......................................................................................................................................................... 181

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress v

1 Using this Manual
Before setting up and using the Pyros® eXpress Endotoxin and Glucan Analysis Software (referred
to as Pyros® eXpress throughout this Manual), read the following sections of this Manual:

 Installing Pyros® eXpress

 Setting Up the Work Environment

This release of Pyros® eXpress is compatible with instruments commonly used for running kinetic
assays: the Pyros Kinetix® Flex (PKFlex) and BioTek® ELx808™ (ELx808™) Absorbance Microplate
Reader.

1.1 Intended Use

Pyros® eXpress is designed for use in Limulus Amebocyte Lysate kinetic turbidimetric or
chromogenic assays for the quantitation of bacterial endotoxin and 1-3 β-D Glucan. The
software collects and processes data from the Pyros Kinetix® Flex tube readers or BioTek®
ELx808™ absorbance reader, stores the information in a database, and produces reports on
test results and data trends. Pyros® eXpress is designed to be compliant with 21 CFR Part 11.
For more information on Pyros® eXpress and 21 CFR part 11 Compliance, see Pyros® eXpress
and 21 CFR Part 11 Compliance.
Pyros® eXpress is designed for use with Turbidimetric and Chromogenic reagents.
 The Turbidimetric Assay Measures the turbidity that precedes a clot. The test is
performed by adding LAL to the liquid sample or standard endotoxin dilution. The
turbidity of the reaction mixture is measured in a spectrophotometer. At higher
endotoxin concentrations, the clotting enzyme is activated more rapidly, so the sample
becomes turbid more quickly. The assay is read as a kinetic assay, where the time for
each sample to reach a particular optical density (OD) is measured.
 The Chromogenic Assay The clotting enzyme acts on a colorless synthetic substrate and
cleaves a terminal chromophore that, when separated from the rest of the molecule,
results in a strongly colored solution. At higher endotoxin concentrations, this
chromophore is cleaved more rapidly, so the reaction rate is faster. The test can either
be read as an endpoint, after a fixed incubation period, or as a kinetic test in which the
time taken to reach a particular OD is determined.

1.2 Kinetic Assays

In kinetic assays, the optical density of a LAL/sample mixture is recorded at regular intervals
at 37°C. Pyros® eXpress stores the data in a database residing on a local drive or designated
network server. The software tracks the data during collection and calculates the amount of
time taken for the OD to cross a fixed threshold level. The amount of time for a given
reaction to cross the threshold is referred to as its onset time. Higher endotoxin levels result
in faster onset times.
Endotoxin concentrations of samples are determined relative to a standard curve
constructed using onset times of known concentrations of standard endotoxin. Note the

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 1

 kinetic reactions and the threshold line in the optical density is plotted against time as shown
in Figure 1. For kinetic reactions, the log of endotoxin concentration is inversely proportional
to the log of onset time. Utilizing this, Pyros® eXpress performs a log-log regression of onset
times and known endotoxin concentrations (standards) to calculate endotoxin concentration
in unknown samples as shown in the Standard Curve Regression Plot in Figure 2.

Figure 1. Optical Density Plotted Against Time

Figure 2. Standard Curve Regression

1.3 Compatibility with Tube Readers and Plate Readers

Pyros® Kinetix Flex
The Pyros® Kinetix Flex tube readers are designed for use with 8x75 mm borosilicate tubes
(tubes). Each reaction is timed individually, starting when a tube is inserted into the tube
reader.
Biotek® ELx808™ Absorbance Microplate Reader
The Biotek® ELx808™ is an eight-channel reader-assay system. It can measure the optical
density of solutions in 96-well microplates.

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2 Installing Pyros® eXpress
2.1 Pre-Install Checklist
Database Configuration (select
one):
Microsoft SQL Express (limited to 10 GB) 

Connection String:

Microsoft SQL Standard 

Connection String:

Microsoft SQL Enterprise 

Connection String:

Microsoft Azure SQL 

Connection String:

LocalDB (default install option; limited to 10GB) 

Operating System:
Supported operating system 
Power saving (Hibernate, Standby, Disk spin-down, 
Screensaver)
Modes disabled

Hardware:
Supported processor architecture 
Meets or exceeds memory requirements 
Meets or exceeds disk space requirements 

For Remote Databases: 
Firewall/Antivirus appropriately configured 
Other: 
CPU, Memory, Disk I/O intensive applications 
evaluated, if present
Installation to be performed using an account with 
administrative privileges


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Application
Configuration
Operating System:
Supported operating system 
Power-saving (Hibernate, Standby, Disk spin-down, Screensaver) 
modes disabled)

Hardware:
Supported processor architecture 
Minimum processor: Intel 7th generation M3 

Recommended processor: Intel 7th generation I5 

Meets or exceeds memory requirements 

Minimum RAM: 4GB 
Recommended RAM: 8 GB 

Meets or exceeds disk space requirements: 15 GB 

For Remote Databases:
Connected to network 
Other:
Firewall / Antivirus appropriately configured 
1 or more Serial or USB ports available 
CPU, Memory, Disk I/O intensive applications evaluated, if present 
Installation to be performed using an account with Administrative 
privileges

Notes:

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 2.2 Required Equipment
Refer to the manual accompanying the Pyros Kinetix® Flex Tube Reader Models PKF32,
PKF64, PKF96 or Biotek® ELx808™ Absorbance Microplate Reader for information on each
instruments' requirements.
Note: We strongly recommend that a Microsoft® Windows update be performed to ensure
the latest security fixes and critical updates are installed prior to installation.
Pyros® eXpress Software

Requirement Value

Operating System Microsoft® Windows® 10 OS

Physical Memory 4 GB

Free Disk Space 10 GB

2.3 Installation Procedure

This installation procedure assumes familiarity with basic Windows operations. If additional
assistance is required, call your local distributor.
Pyros® eXpress can be installed as a standalone system with the database in the same
location as the software or on a network where it can interface a network based database
that is accessible from multiple PCs.
Pyros® eXpress will automatically install and configure a local embedded database for
demonstration purposes. This database is limited to 10 GB of data. If additional space or the
advanced management features included in the server versions of Microsoft SQL server are
required, we recommend Microsoft SQL server or SQL Azure.
 For a standalone (local) installation, go to 2.3.1.
 For a network (remote) installation, go to 2.3.2.

2.3.1 Standalone (Local) Installation

1. Insert the Pyros® eXpress drive into the USB port and double-click the application
installer.
2. The Pyros® eXpress Setup window appears as shown in Figure 3. Review and
accept the License Agreement.

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 Figure 3. Pyros® eXpress Setup Window
3. Click Install. The Options button is not necessary for local installations.
4. Once the setup has completed running, the installation is complete.
5. To launch the program, click Launch. To close, click Close (see Figure 4).

Figure 4. Installation Successfully Completed Popup

2.3.2 Network (Remote) Installation
Obtain the proper database connection string from your network IT Administrator.
1. Insert the Pyros® eXpress drive into the USB port and double-click the application
installer.
2. The Pyros® eXpress Setup window appears. Review and accept the License
Agreement shown in the Pyros® eXpress Setup window (see Figure 3).
3. Click Options.
4. The Setup Options window appears as shown in Figure 5. In the Database
Connection String field, copy the appropriate database connection string.

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 Note: Consult your Database Administrator for the appropriate connection string
to enter.

Figure 5. Setup Options Window

5. Review and accept the License Agreement. Click OK, then click Install.
6. Once the setup has completed running, the installation is complete.
7. To launch the program, click Launch. To close, click Close (see Figure 4).
2.4 First-time Login
Once the installation is complete, the Pyros® eXpress Shortcut icon will appear on the
computer desktop.

Pyros® eXpress Shortcut Icon

To log into the system:
1. Double-click the Pyros® eXpress icon. The Pyros® eXpress Login screen appears as
shown in Figure 6.

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 Figure 6. Pyros® eXpress Login Screen
2. Enter the following information:
User name: admin
Password: password
3. Click the Green Arrow or click Enter.
4. The Register License window appears as shown in Figure 7.

Figure 7. Register License Window

5. In the Serial Number field, enter the Serial Number that appears on the back of
the media or on Sales Order.
6. If the computer has internet access, click Activate license online to activate the
license automatically.
7. If internet access is unavailable, click Generate offline license request file to
generate an offline license request. Save and e-mail the file to
[email protected]. An email with the license information will be
sent. Click Import license file from the email.
8. The Pyros® eXpress Home screen appears in Figure 8.

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 Figure 8. Pyros® eXpress Home Screen

2.5 Changing the Admin Password

Pyros® eXpress ships with a default account with permissions set to get started. The user
name is admin and password is password. From this account, the user accounts required to
manage the system and perform testing can be setup.
To prevent unauthorized access to the system, the password for the default account for an
installation of Pyros® eXpress must be changed to be compliant with 21 CFR Part 11
guidelines. Changing this password is essential.
Note: It is strongly recommended that two Administrator level users be setup after
installation. It is important to record and retain these login credentials to prevent lock
outs. If locked out, your data will be lost. For example:
1. Super Administrator (based in your IT department)
 Must have Manage System and Manage Workgroups permissions
 Manages the system and all passwords
 Has administrative rights on PC
2. System Administrator (based in your laboratory)
 Must have Manage Workgroups permissions
 Adds and edits workgroups and users
To change the Administrator password:

1. From the toolbar on the Home screen, click the Global Settings icon.
2. The User Management tab opens as shown in Figure 9. This tab contains the settings
used to edit and manage workgroups, users, passwords and permissions.

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 Figure 9. User Management Tab
3. Enter the existing password, and then enter a new password twice and click Submit.
4. There are 3 other options on this screen:
 Require Reason for Change (available to Administrators only and disabled for users
without administrative rights). Check this box to require that a reason be entered
when performing various actions. These are captured in the Audit Trail.
 Re-authentication Timeout (available to Administrators only and disabled for users
without administrative rights). Check this box to enter the time of inactivity, in
seconds, before the user will be required to re-authenticate using their credentials.
This feature allows the Administrator to define a time period that allows a user to
authenticate once and then perform actions without having to re-authenticate for
each action performed. All actions during this time period are automatically
authenticated and tracked in the Audit Trails. After the defined time period has
ended, the next action that requires authentication will cause the User
Authentication window to reappear, forcing the user to re-authenticate.
 Password Expiration Period (days). Check this box to set the number of days before
the password expires. In the box that appears, enter a number between 10-172.
 When finished, click Save to return to the Home screen, click Close to close this tab
or click Next to go to the Instrument tab.
2.6 Navigating the Home Screen
The menu at the top of the Home screen displays the available functions in a toolbar format.
Clicking an icon turns it blue and additional options slide open to the right.
The Pyros® eXpress toolbar includes the following icons:

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 Icon Function
Show or hide icon names.

Returns to Home screen.

Add, edit or view information on supplies, products and methods.

Retire, import, export, edit and run test templates.

View and print test reports.

Calculate MVD/MVC, the maximum dilution or minimum concentration of product at which

the endotoxin limit can be detected.

Opens a PDF version of this User Manual for quick reference.

Open these tabs: User Management, Instrument, Options, Reports, Trending, Audit Trail,
Notifications and Service.

2.7 Anti-Virus Information

It is strongly recommended that your organization's anti-virus software be installed and run
with the latest update on your system.

2.8 Backup and Restore Procedures

All backup and restore instructions below should be reviewed and tested for compliance with
corporate policies.
Associates of Cape Cod, Inc. (ACC) highly recommends that all customers establish a backup
procedure before implementing Pyros® eXpress in their production environment. All testing
should be performed in a test environment.
For remote database installations, follow your company's backup procedures.
For SQL Server LocalDB installations:
1. Create a backup location in the root of C: (for example, C:\pyrosbackup).
2. Configure corporate backup services to backup the designated folder location on a
regular schedule.
3. Stop service Pyros eXpress.
4. Copy content of folder C:\Program Files\Pyros eXpress\Service\data.
5. Paste content from the program file location to the backup location. Two files should
now be in the backup folder data.mdf and data_log.ldf.
6. Start service Pyros eXpress.
Note: For remote database installations, follow your company's restore procedures.

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 For SQL Server LocalDB installations:
1. Create a restore location in the root of C: (example C:\pyrosRestore).
2. Restore file to the designated restore location.
3. Stop service Pyros eXpress.
4. Delete content of folder C:\Program Files\Pyros eXpress\Service\data.
5. Copy data.mdf and data_log.ldf from the backup restore location (example
c:\pyrosRestore) to C:\Program Files\Pyros eXpress\Service\data.
6. Start service Pyros eXpress.

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3 Setting up The Work Environment
This section is designed to help setup and optimize Pyros® eXpress before running any assays.

Note: It is important to perform all of the tasks in this section before running the first assay.

This section outlines how to:

 Administer workgroups and users

 Set permissions for workgroups and users
 Setup instruments and test system communication
 Setup global options within each user group including methods, supplies, reports and
notifications

3.1 Administering User Accounts and Permissions

Pyros® eXpress has a permissions based user setup. Each user can be setup with certain
permissions to either grant or restrict access to certain functionality of the software.
Table 1 describes the global and workgroup level permissions available for Pyros® eXpress
users.
Global Level Permission Description
Manage Workgroups Allows the user permission to set up new users, edit user
permissions, change user status, change and reset passwords and
add workgroups.
Workgroup Level Permissions Description
Manage Workgroups Allows the user to edit workgroup level settings and change
workgroup permissions of the workgroup they are currently logged
into. Provides access to the following tabs in the Settings window:
Options, Report, Trending and Notifications.
Manage Templates Allows the user to add and edit templates in the Library and
add/edit consumables and equipment to templates.
Manage Products Allows the user to add, retire, reinstate and edit products in the
Library.
Manage Methods Allows the user to add, view, edit, retire and reinstate methods in
the Library.
Manage Supplies Allows the user to add, retire, reinstate, view/edit, match and
edit/remove matched supplies in the Library.
Manage Instruments Allows the user to add and edit instruments.
Manage Calibrations Allows the user to access the Service tab. See Using the Service Tab.
Perform Test Allows the user to perform a test.
Approve reports with e-Signature Allows the user to approve reports with an e-Signature.
Edit/Sign in place of another user Allows the user to edit/sign a report in place of another user.
Export to LIMS Allows the user to export data in an XML file to LIMS.

Table 1. Global and Workgroup Level Permissions

Upon new install of the Pyros® eXpress network or standalone versions, only the
Administrative user and default workgroup will be listed.

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 To add a new workgroup:
1. From the Home screen, click the Settings icon on the far right of the toolbar. The User
Management tab opens.
2. Click the Manage Groups button. The system will display a list of workgroups once they
are created (see Figure 10).
3. Click New at the bottom of the screen. The Edit New Workgroup window opens.
4. Enter a name for the workgroup, for example QC Lab or R&D.

Figure 10. Manage Groups: Edit New Workgroup Window

5. Click OK, then Close to return to the User Management tab. The workgroup is available
to new and existing users.
6. Next, add users to this workgroup. From the User Management tab, click the Manage
Users button. The system will display a list of users once they are created (see Figure
11).
7. Click New.
Note: Pyros® eXpress uses Windows Operating System authentication when Active
Directory is selected. When adding users, ensure they have legitimate accounts on the
Windows OS and that their credentials are properly supplied.
8. In the Manage Users: Add/Edit User window, fill in the following information for each
new user (required items have an asterisk):

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 Figure 11. Manage Users: Add/Edit User Window
 User Name: Enter the name that the user will use to log into the software. Assign
each user a unique username and password to allow the Audit Trail to be
generated for individual users and to limit the use of certain functions of the
software.
 Full Name: Enter the user's full name.
 Password: Provide a password for the user.
 Check the Active Directory box to use Windows authentication. Enter the Domain
Name of the computer being used to collect data. Uncheck this box if you want
the user to use a different password for Pyros® eXpress.
 Check the Manage System box to allow the user to have permission to setup new
users, edit user permissions, change user status, change and rest passwords and
add workgroups.

9. Click the Add Workgroups button. A list of workgroups appears in the Select
Workgroup popup as shown in Figure 12.

Figure 12. Select Workgroup Popup

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 10. Highlight the name of the workgroup that this user should be added to and click OK.
11. The Add/Edit User window opens (see Figure 13).
12. Check the permissions for this user and click OK. For a description of each permission,
see Table 1. The user will now appear in the list of users.

Figure 13. Add/Edit User Window

13. Repeat this procedure until all users have been added. Once finished, click Close to
return to the User Management tab.
Note: A workgroup cannot be removed once it has been created.
3.1.1 Editing the Name of a Workgroup
1. From the Home screen, click the Settings icon on the far right of the toolbar. The
User Management tab opens.
2. Click Manage Groups. A list of workgroups appears (see Figure 10).
3. Highlight the name of the workgroup to edit or double-click on the name of the
workgroup.
4. Click Edit at the bottom of the screen. A Confirmation window prompts to
confirm the name change.
5. Enter the new name in the Name field and click OK or click Cancel to return to the
list of workgroups.

3.1.2 Adding a User to a Workgroup

1. From the Home screen, click the Settings icon on the far right of the toolbar. The
User Management tab opens.
2. Click the Manage Groups button. A list of the workgroups appears (see Figure
10).
3. Highlight the group to add a user to and click Add Users at the bottom of the
screen.
4. A list of current users in this workgroup opens in a new window. Highlight the
user to add and click OK or click Cancel to return to the list of workgroups.

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 5. Click Close to return to the User Management tab. The user is now part of the
selected workgroup.
6. A user may also be added to a workgroup by:
 Selecting Manage Users from the User Management tab.
 From the list of users, highlight the user to be added and click Add from my
current workgroup at the bottom of the screen.
 Click Close when finished to return to the User Management tab.

3.1.3 Removing a User from a Workgroup

1. From the Home screen, click the Settings icon. The User Management tab opens.
2. Click the Manage Groups button. A list of workgroups appears (see Figure 10).
3. Highlight the group to remove a user from and click Remove Users at the bottom
of the screen.
4. A list of current users in this workgroup opens in a new window. Highlight the
user to remove and click OK or click Cancel to return to the list of workgroups.
5. Click Close to return to the User Management tab. The user is removed from the
workgroup.
6. A user may also be removed from a workgroup by:
 Selecting Manage Users from the User Management tab.
 From the list of users, highlight the user to be removed and click Remove from
my current workgroup at the bottom of the screen.
 Click Close when finished to return to the User Management tab.

3.1.4 Editing a User

1. From the Home screen, click the Settings icon on the far right of the toolbar. The
User Management tab opens.
2. Click Manage Users. A list of current users in the system appears (see Figure 11).
3. Highlight the name of the user to edit and click Edit at the bottom of the screen.
4. The Add/Edit User window appears as shown in Figure 13. Edit the appropriate
properties on this screen and click OK when finished or Cancel to return to the list
of users. For more information on these fields, see Adding a User to a Workgroup.

3.1.5 Resetting a User Password

A user’s Pyros® eXpress password is single use, which means it is valid for one login
session only. This password must be reset after the first login.
Note: Perform this procedure if Active Directory is not being used.
1. From the Home screen, click the Settings icon on the far right of the toolbar. The
User Management tab opens.
2. Click Manage Users. A list of current users in the system appears (see Figure 11).
3. Highlight the name of the user whose password is being reset. Click Reset
Password at the bottom of the screen.
4. The Reset Password window opens as shown in Figure 14. Enter the new
password according to the online instructions.

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 5. Click OK when finished or Cancel to return to the list of users.

Figure 14. Reset Password Window

3.1.6 Unlocking a User
The System Administrator can unlock a user who has been locked out of the system.
1. From the Home screen, click the Settings icon on the far right of the toolbar. The
User Management tab opens.
2. Click Manage Users. A list of current users in the system appears (see Figure 11).
3. Highlight the name of the user to unlock and click Unlock at the bottom of the
screen.

3.1.7 Changing a User's Status

Use this option to change the status of a user from active to inactive or vice versa.
1. From the Home screen, click the Settings icon on the far right of the toolbar. The
User Management tab opens.
2. Click Manage Users. A list of current users in the system appears (see Figure 11).
3. Highlight the name of the user whose status is changing and click Change Status
at the bottom of the screen.
4. Confirm the status change by clicking Yes to confirm or No to cancel and return to
the list of users.

3.2 Setting Up Instruments and Testing System Communication

Connect the Biotek® ELx808™ Absorbance Microplate Reader or Pyros Kinetix® Flex
according to their instruction manuals.
1. Click the Settings icon and then click Instrument. The Instrument tab opens as shown in
Figure 15.
The Instrument tab stores information on the readers being used in the analysis and includes
a function to test communication between the reader and Pyros® eXpress.

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 Figure 15. Instrument Tab
2. Click the plus sign. Provide the following information (required items have an asterisk):
 *Instrument: Select the instrument from the dropdown list (PKFlex or ELx808™).
 *Port: Select the serial port that was used to connect to the instrument.
 *Serial Number: Enter the instrument's serial number.
 Equipment ID: Enter an Equipment ID if an additional identifier is needed.
 Calibration Due: Use the calendar to select the date that the instrument is due to
be calibrated. Use this to track the calibration due date.
 A/D Min and A/D Max: (for tube reader only). These values should only be edited
by a qualified Associates of Cape Cod, Inc. Technician.
 Computer Name: This field auto-populates with the name of the computer being
used to collect data. Pyros® eXpress fills in this name by reading the computer
name from the Windows OS.

3. The Test Communication button will become active when all of the required fields are
complete. Click Test Communication.
Note: If an error message appears, verify that:
 The instrument is turned on and connected to the computer.
 The serial port specified is the correct port on which the instrument is physically
connected.

4. When finished, click Save to save the instrument, Back to return to the User
Management tab, Next to proceed to the Options tab or Close to exit the Settings menu
without saving the changes.

3.2.1 Editing or Deleting an Instrument

1. Click the Settings icon and then click Instrument.
2. From the Instrument tab, select the instrument to edit or delete. To delete, click
the minus sign. To edit, complete the fields with new information.

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 3. Click Save to save the changes.

3.3 Setting Up Global Options

Pyros® eXpress allows customization of various global system options.
1. From the Home screen, click Settings and then Options. The Options tab appears as
shown in Figure 16.
Note: You must be logged in as an Administrator to view the Instrument and Service tabs.
2. Complete the fields in each section of the tab as described below:

Figure 16. Options Tab

 Require User Qualification: Select Yes if the analyst is required to qualify on the
reagent combination within the laboratory. See Qualifying an Analyst for more
information.
 Negative Control Separation Check: This setting toggles the Negative Control
Separation On or Off. Select On to enable the test to report this value, which is
the time in seconds beyond the slowest onset of the lowest standard that it takes
for a negative control to reach onset. (Default is On).
 Release Limit Operator: When product information is entered, the endotoxin
release limit must be entered. Select < if products with “less than” the accepted
endotoxin limit should pass the test or <= if products that have “less than or equal
to” the accepted endotoxin limit should pass the test. (Default is <).
 PPC Recovery (Min)/(Max): Enter the acceptable range of PPC Recovery. (Default
is Minimum= 50%, Maximum = 200%; Range: Minimum = 10-100%, Maximum =
100-400%).
 Automatic Test Naming: Select Off to preserve the existing naming procedure.
Select On to allow the system to automatically name the test. (Default is Off).

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  Auto-End (Default): Select On to allow the assay to run until it auto-terminates.
Turn this option Off to end the assay when the maximum run time (user-defined)
is reached. (Default is On).
 Select Linear Regression (default) for linear regression analysis to be used to
calculate the standard curve.
 Select Polynomial Regression for polynomial regression to be used to calculate
the standard curve.
 ADC Range: These values are defaults and linked to the Service tab. Do not edit.
 Tubes Present (Min/Max): These values are defaults and linked to the Service
tab. Do not edit.
 Tubes Absent (Min/Max): These values are defaults and linked to the Service tab.
Do not edit.

3. When finished setting options, click Close to close without saving the changes, Save to
save the changes, Back to return to the previous screen or Next to go to the next
screen.

3.4 Setting Up Reports

Pyros® eXpress allows for customization of the contents and format of reports using the
Reports tab. This tab stores the formatting and calculation settings for reports.
1. From the Home screen, click Settings and then Reports.
2. The Reports tab opens, as shown in Figure 17. Complete the fields in each section of the
tab as described below.

Figure 17. Reports Tab

 Custom Title Line: To add a custom title to the reports, click the checkbox and
enter the report title in the text box.
 Custom Logo: To specify a .JPG or .PNG file to be displayed in the top right corner
of the report, click the checkbox and then click Browse to locate the file on the
computer.

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  Reporting Significant Digits: Enter the number of non-zero digits to report for
Endotoxin Concentration and Spike Concentration values. (Default is 3 digits;
maximum allowed is 6 digits).
 Display CV Based On: The Coefficient of Variation (CV) indicates how well
replicates correspond to each other. From the dropdown list, select:
o Predictor Value: (default) Displays CV as the predictor value (onset time,
Vmean, Vmax or OD at endpoint.
o Concentration: Displays CV as the calculated endotoxin concentration value.
 CV Limit Exceeded: Leave this option Off to turn off Pass/Fail criteria for CV limit.
Select Pass/Fail to flag the CV value if it exceeds the percentage set in the CV
Limit (%) field. (Default is 10%).
 Standard Curve min CC (R-Value): Defaults to 0.980 per U.S. Pharmacopeia.
 PC outside allowed Recovery Range: Select Pass/Fail to report a Pass/Fail result
for the positive control within the range defined.
 PC Recovery (Min): Define the range for Positive Control Spike Recovery. (Default
range 25%-100%, default = 75 - 125%).

3. When finished setting Options, select Close to close without saving the changes, Save to
save the changes, Back to return to the previous screen or Next to go to the next
screen.

3.5 Setting Up Notifications

Use this section to customize when users receive real time popup notification messages
about tests while they are running. Users can be required to add comments when they make
any changes to a test.
1. From the Home screen, click Settings and then Notifications.
The Notifications tab appears as shown in Figure 18. This tab allows test setup
parameters to be customized as well as various run time and end of test popup
notifications. All features default to On as described below.

Figure 18. Notifications Tab

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  Calibration Due: Select On to notify users if a calibration is due.
 Consumable Expired: Select On to notify users if a consumable has expired.
 Temperature Out of Specification: Select On to notify users if a temperature is
out of specification during the test.
 Coefficient of Variation (CV) Limit Exceeded: Select On to notify users when the
CV has exceeded the limit set on the Reports tab.
 Correlation Coefficient (CC) Limit Exceeded: Select On to notify users when the
CC has exceeded the limit set in the Reports tab.
 PPC Recovery Range Exceeded: Select On to notify users if PPC recovery is
outside the range.
 PC Recovery Range Exceeded: Select On to notify users if the PC recovery is
outside the range.
 Sample Release Limit Exceeded: Select On to notify users if the sample shows an
endotoxin concentration above the release limit.
 Sample Alert Limit Exceeded: Select On to notify users if the sample alert limit
has been exceeded. Enter an Alert Limit (%) in the field provided.
 Negative Control Validity: Select On to notify users if the negative control has no
detectable endotoxin or if the detected endotoxin is less than that of the lowest
standard.

2. When finished setting Options, click Close to close without saving the changes, Save to
save the changes, Back to return to the previous screen or Next to go to the next
screen.

3.6 Using the Service Tab

The Service tab shown in Figure 19 provides preventative maintenance and diagnostic tests
for the instrumentation. This screen is visible if the System Administrator has set the user
with permission to Manage Calibrations. For more information on how to edit this setting, go
to Adding a User to a Workgroup.
For specific information on the Service tab, see the Service section.
Note: Improper use of the functions on this screen could potentially damage the
instrument or harm its validation status.

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 Figure 19. Service Tab

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4 Setting up The Testing Environment
The Pyros® eXpress Library stores all of the Supplies, Products and Methods that are required to
run assays. It is strongly recommended that all of this information be added to the Library before
running the first assay.
This section discusses how to:

 Add, edit, retire, reinstate and match supplies

 Add, edit, retire and reinstate products
 Add, edit, retire and reinstate methods

4.1 Adding Supplies to the Library

Use the Supplies tab to enter the supplies needed for all assays including reagents,
standards, consumables, equipment and buffers.
To add a new supply to the Library:
1. From the Home screen, click Libraries on the left side of the toolbar. The toolbar
expands to the right and displays three additional options:
 Supplies
 Products
 Methods

2. Click Supplies.
3. The Supplies list opens as shown in Figure 20. Any previously added supplies are listed
here by Group, Type, Lot # and Description. Click New at the bottom of the screen.

Figure 20. Supplies List

4. A new window called Supply opens as shown in Figure 21. From here, select the Group
and Type of supply to be added from the dropdown lists, described Table 2.

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 Figure 21. Supply Window
Group Type
Reagents ChromoLAL®
Glucatell®
Pyrotell®-T
Pyrochrome®
Standards Glucan Standard
RSE
CSE
Consumables Combitip Sample Container
Pyroplate Reagent Water
Water Buffer
Syringe Reagent Reservoir
Dilution Tubes Serological Pipette
Pipette Tip Reaction Tubes
Equipment Vortex Mixer
Pipette
Buffer Pyrosol Buffer
Reconstitution Buffer
Glucashield Buffer

Table 2. Supply Group and Type Options

5. Enter other information on this screen as described below.
 Description: Provide an optional description for the supply.
 Lot/SN: Enter the Lot or Serial Number for the supply.
 Expiration Date: Use the calendar to enter the expiration date for the supply.
6. When finished, click Save to save the changes and return to the Supplies list, Close to
close the window without saving the changes or Save As Copy to give the item a specific
lot number. Enter a lot number in the popup window that appears when this option is
selected.
7. Repeat this procedure for all supplies. When finished adding all of the supplies,
standards and reagents must be matched in the Library. Go to Adding or Removing a
Matched Supply.

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 4.1.1 Retiring a Supply
Retiring a supply removes the item from the Library but does not delete it from the
database. A retired item will not populate in any dropdown lists.
1. From the Home screen, click Libraries on the left side of the toolbar.
2. Click Supplies. The Supplies list opens as shown in Figure 20.
3. Highlight the name of the supply to retire and click the Retire button at the
bottom of the screen. (The Retire button will become active when an item in the
list is highlighted.)
4. The supply will be removed from the active list and moved to retired status.

4.1.2 Viewing and Editing Supplies

The Search button can be used to find a particular supply to edit.
1. From the Home screen, click Libraries on the left side of the toolbar.
2. Click Supplies. The Supplies list opens as shown in Figure 20.
3. Select the Group or Type from the dropdown lists or enter the Lot Number of the
supply. Click Search or Clear to start again.
4. A list of supplies that fit in the criteria entered in Step 3 appears in the list.
Highlight the name of the supply to edit and click Edit at the bottom of the
screen.
5. The Supply window opens as shown in Figure 21. Edit the fields as described in
the Adding Supplies to the Library section.
6. When finished, click Save. Click Save As Copy to save this supply with a different
lot number.

4.1.3 Matching Supplies in the Library

To run a test using CSE, there must be a matched standard and reagent in the
Library. Matching can occur in either order: you can match any CSE with an
existing/new Lysate or existing/new Lysate to a CSE.
Note: When using RSE reagents do not need to be matched.
To match standards and reagents:
1. View the list of all supplies added by clicking Libraries and then Supplies. To view
the entire list of supplies, the Clear button may need to be clicked if any searches
were previously run in the Supply window.
2. Double-click the item to match. The Supply window opens as shown in Figure 21.
3. Click the Matching button. A Standards Matching window opens as shown in
Figure 22. Any previously matched items will be listed here.
4. Click the Add button at the bottom of the window.

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 Figure 22. Standards Matching Window
5. A popup window appears as shown in Figure 23. Select the Standard Type and
Buffer Type to be matched as described below.

Figure 23. Defining a Matched Item

 Standard Type: Glucan Standard, RSE or CSE.
 Standard Lot: Specify the lot information for the standard.
 Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer.
 Buffer Lot: Specify the lot information for the buffer.
6. Click Clear to start again. When finished, click Save. The matched items will now
appear in the list.
7. Click Close.
8. Repeat this procedure to match all supplies and reagents.

4.1.4 Editing or Removing a Matched Supply

1. From the Home screen, click Libraries and then Supplies. To view the entire list of
supplies, the Clear button may need to be clicked if any searches were previously
run in the Supply window.

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 2. Locate the supply to edit or remove from the list. The supply can be searched by
selecting its Group, Type or entering a lot number and clicking the Search button.
3. When the supply to edit or remove is located, double-click it to open the Supply
window (Figure 21).
4. Click the Matching button. The Standards Matching window opens as shown in
Figure 22.
5. Highlight the supply and click Remove to remove the matched item or Edit to edit
the matched item.
 The Reagent Type, Standard Type, Reagent Lot and Standard Lot can be edited
as described in the Matching Supplies in the Library section.
 Click Clear to start again.
6. When finished, click Close to return to the Supply window.

4.1.5 Adding a Standard to a Matched Supply

1. From the Home screen, click Libraries and then Supplies. To view the entire list of
supplies, the Clear button may need to be clicked if any searches were previously
run in the Supply window.
2. Locate the supply to add to the standard. The supply can be searched by selecting
its Group, Type or entering a Lot number and clicking the Search button.
3. Double-click the supply to open the Supply window as shown in Figure 21.
4. Click the Matching button. The Standards Matching window opens as shown in
Figure 22.
5. Highlight the item and click the Add button. The Defining a Matched Item popup
opens as shown in Figure 23.
6. Select the Standard Type and Buffer Type of the item to add and click Save. Click
Clear to start again.
7. When finished, click Close twice to return to the Supply window.

4.1.6 Qualifying an Analyst on a Reagent Combination

Prerequisite: On the Options tab (Figure 24) select Yes to Require User Qualification,
as shown below.

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 Figure 24. Options Tab
To indicate that an analyst fulfilled the required criteria to become qualified on a
specific reagent:
1. From the Home screen, click Libraries and then Supplies. To view the entire
supply list, the Clear button may need to be clicked if any searches were
previously run in the Supply window.
2. Locate the supply (reagent, standard or buffer) to qualify an analyst. The supply
can be searched by selecting its Group, Type or entering a lot number and clicking
the Search button.
3. Double-click the supply (reagent, standard or buffer) to open the Supply window.
4. Click the Matching button.
5. Click the Qualification button. A window with a list of analysts appears as shown
below.

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 6. Highlight the name(s) of the user that requires qualification for this supply and
check the Qualified box next to their name. To select all users, click the Select All
button. To save changes, click Save. To clear the selections and start again, click
Clear.
7. When finished, click Close twice to return to the Supply window.

4.1.7 Adding Products to the Library

Before running tests, use the Products screen to enter products to be used for
testing.
1. From the Home screen, click Library and then Products.
2. A list of products appears in the Products window. If entering products for the
first time, the list will be empty as shown in Figure 25.

Figure 25. Products Window

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 3. Click New. A new Products window opens as shown in Figure 26. Complete the
fields as described below.

Figure 26. Products Window (New)

 Product Name: Enter the name of the product as it should appear on the
screen.
 Description: Enter a description of the product.
 Release Limit: Enter the maximum concentration of endotoxin allowable for
the product to be released. The product can be set to be released when the
concentration is less than the release limit or less than or equal to the release
limit in the Options menu.
 Initial Concentration: Enter the initial concentration of the product.
 Unit: Select the unit of measure from the dropdown menu.
 I/E Completed: Check this box after the I/E Verification Test has been
completed. See Completing I/E and Product Validation.
 Product Validation Completed: Check this box after the Product Validation
Test has been completed. See Completing I/E and Product Validation.
 Method: Select the method used to complete the Product Validation. See
Setting Up a Product Validation Template.
4. When finished, click Save to save the changes, Close to exit without saving or
Save As Copy to give the product a new name. Enter a product name in the
popup window that appears when this option is selected.

4.1.8 Retiring a Product

Retiring a product removes the method from the Library, but does not delete it from
the database. A retired item will not populate in any dropdown lists.
1. From the Home screen, click Library and then Products.
2. The Products list appears.

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 3. Highlight the name of the product to retire and click the Retire button at the
bottom of the screen. The Retire button will become active when an item in the
list is highlighted.
4. The product will be removed from the active list and moved to retired status.

4.1.9 Editing a Product

1. From the Home screen, click Library and then Products.
2. The Products list appears. Highlight the name of the product to edit and click the
Edit button at the bottom of the screen.
3. The Products window opens as shown in Figure 26. Edit in the fields as described
in the Adding Products to the Library section.
4. When finished, click Save. Click Save As Copy to save this product with a different
name.

4.1.10 Adding Methods to the Library

A method contains specific parameters to perform a test. Pyros® eXpress provides a
set of default methods that are optimized per the reagents' Instructions for Use
(IFU). These methods cannot be edited. However, a new method can be created with
the same parameters using the Save As Copy option.
Before running any tests, add the necessary test methods to the Library:
1. From the Home screen, click Library, then Methods.
2. The Methods tab opens as shown in Figure 27.

Figure 27. Methods Tab

3. Click New. The Methods window opens as shown in Figure 28. Complete the
fields as described below.

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 Figure 28. Methods Window
 Name: Enter the method name as it should appear on the screen.
 Instrument: Select Plate Reader or Tube Reader from the dropdown menu.
 Read Interval (s): The system provides results on a 10 second read interval.
Enter a different value in seconds if desired. (Default is 10 seconds).
 Primary Wavelength (nm): Enter the primary wavelength of data collection.
Note: Review the IFU for the reagent to determine the suitable wavelength.
 Reference Wavelength (nm): Enter an optional secondary wavelength that
can be used for OD subtraction.
 Assay Type: Onset, Endpoint, Vmean or Vmax.
 Reagent: ChromoLAL®, Glucatell®, Pyrochrome® or Pyrotell®-T.
 Maximum Test Time (s): Enter the maximum amount of time, in seconds, for
the test to run. The test will never go longer than this set time.
 Incubation Time (s): For plate reader only, enter the pre-incubation time, in
seconds. This is a timed incubation step prior to adding the LAL reagent.
Consult the manufacturer's IFU for instructions.
 Default Standard Concentrations: Click the calculator icon to enter the values
described below:
o Concentrations: Specify the number of standard concentrations that will be
included in the curve. A minimum of three standards is required.
o Highest Concentration: Enter the highest concentration of the standards
being used. This value defines the starting point of the automatic
generation of the standard curve series.
o Dilution Factor: Enter the dilution that will be employed to create the
standard curve. The Highest Concentration value and the Concentrations
value will be used with this number to generate a serially diluted standard
curve series.

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  Default PPC Concentrations: Enter the default concentration for Positive
Product Control.
 Pre-Incubate Shake: For plate reader only, define the number of seconds to
shake the plate before pre-incubation. (Default is 10 seconds).
 Pre-Collect Shake: For plate reader only, define the number of seconds to
shake the plate before collection. (Default is 10 seconds).
 OD Threshold (mOD): Defines the OD value, from which the onset time of the
reaction is determined. Once a well's OD reaches this threshold, an onset time
is generated.
 OD LR Window (s): Defines a period of time around the well's raw onset time
where data points are monitored for correct kinetics. This period of time is
used to calculate an adjusted onset time which is a more precise value
computed from the OD trend near onset.
 OD Zero Start/End: Defines a period of time over which a tube's base value is
calculated. The base value is added to the OD threshold to adjust for products
with a non-zero initial absorbance. (Previously, this was known as the baseline
adjustment.)
 Unit: For the standard curve: EU/mL, IU/m Lor pg/mL.
 Log Concentrations: Log10 standard concentration.
 Log Predictor: Log10 Onset OD, Vmean or Vmax, depending on test.
 Negative Control Separation (%): Percentage of Onset time of lowest standard
that is added to show clear separation from the lowest standard.
 Pipetting Delay: This option is NOT recommended for ACC products. Turn this
option On to compensate for pipetting delay when loading a plate with an 8-
channel pipettor. Delay is column-wise when the fill direction is set to vertical.
Delay is row-wise when the fill direction is set to horizontal. (Default is Off).

4. When finished, click Save to save the changes, Close to exit without saving or
Save As Copy to save the method with a new name.

4.1.11 Viewing and Editing Methods

1. From the Home screen, click Libraries and then Methods.
2. Use the Search button to find the method. Enter all or part of the method name
in the Method Name field and click Search. Click Clear to start again.
3. Double-click the method to edit. The Methods window opens as shown in Figure
28.
4. Edit the information as described in the Adding Methods to the Library section.
5. Click Save to save the changes, Save As Copy to save it with a different name or
Close to exit without saving.

4.1.12 Retiring a Method

Retiring a method removes the method from the Library but does not delete it from
the database. A retired item will not populate in any dropdown lists.
1. From the Home screen, click Libraries and then Methods.

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 2. Use the Search button to find the method. Enter part, or all, of the method name
in the Method Name field and click Search. Click Clear to start again.
3. Highlight the method to retire and click Retire. The Retire button will become
active when an item in the list is highlighted.
4. Click Save to save the changes, Save As Copy to save it with a different name or
Cancel to exit without saving.
5. Clicking Save removes the method from the active list and moves it to retired
status.

4.1.13 Reinstating a Supply

1. From the Home screen, click Libraries and then Supplies.
2. Check the Retired box next to the Lot # field and click Search.
3. A list of retired supplies appears. Highlight the supply to reinstate and click the
Unretire button at the bottom of the screen. The supply will reappear in the list.
4. Uncheck the Retired button at the top of the screen and click Search to return to
the active list of supplies.

4.1.14 Reinstating a Product

1. From the Home screen, click Libraries and then Products.
2. Check the Retired box next to the Product Name field and click Search.
3. A list of retired products appears. Highlight the product to reinstate and click
Unretire at the bottom of the screen.
4. The product will reappear in the list.
5. Uncheck the Retired button at the top of the screen and click Search to return to
the active list of supplies.

4.1.15 Reinstating a Method

1. From the Home screen, click Libraries and then Methods.
2. Check the Retired box next to the Method Name field and click Search.
3. A list of retired methods appears. Highlight the method to reinstate and click
Unretire at the bottom of the screen.
4. The method will reappear in the list.
5. Uncheck the Retired button at the top of the screen and click Search to return to
the active list of methods.

4.1.16 Using the Toolbar Calculator

The calculator that appears on the toolbar can be used to calculate the Maximum
Valid Dilution (MVD) or Minimum Valid Concentration (MVC) for a product.
Note: The endotoxin limit of the product must be known in order to perform the
calculation.
1. From the toolbar on the Home page, click the calculator icon. The following
window opens:

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 Figure 29. Toolbar Calculator
2. The software will calculate the MVD or MVC value when these values are entered
and OK is selected:
 Endotoxin Limit: The endotoxin limit of a product in EU/mL. The unit can be
changed to EU/mg if measuring weight rather than volume.
 Potency of Product: Use this option only if measuring in weight rather than
volume. Change the Endotoxin Limit unit to EU/mg if using this value.
 Sensitivity of Assay: Enter the lowest possible standard (lambda) on the test.

4.1.17 Setting up Templates

Pyros® eXpress allows Test Templates to be setup and stored to run assays.
Templates contain all of the required assay information, including:
 Equipment
 Supplies
 Identification numbers (lot and serial numbers)
 Number of products and replicates
 Layout of standards and products on the plate or tube reader
Templates make test preparation easy by auto-populating these parameters when
beginning a test. For this to occur, a template must be setup for each type of test.
There are four templates, each designed to perform a different aspect of LAL testing.
Once a test has been developed, using a template ensures that the test is run with
the same parameters each time.
An example of a Reagent Verification Template is shown in Figure 30.

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 Zoom In/Out to expand views
Layout of
standards and
samples

Test details

Consumables
and
equipment

Figure 30. Reagent Verification Test Template (Example)

4.1.18 Setting Up a Reagent Verification Template
The first template that must be setup before running any tests is the Reagent
Verification Template. This Test Template will be used to assure that the criteria for
the standard curve are valid and that the product solution does not interfere with
the test.
1. Click Templates on the toolbar. The toolbar expands to display the six types of
templates that can be created:
 Routine
 Reagent Verification
 I/E
 Product Validation
 Potency
 FreeForm
2. Click Reagent Verification.
3. A Reagent Verification Template appears as shown in Figure 31. There are 3 tabs:
General, Standards and Layout. On the General tab, fill in the fields as described
below.

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 Figure 31. Reagent Verification Template, General Tab
 Template: Enter the template name as it should appear on the screen. Naming
conventions are important for procedural understanding and efficiency.
Specific SOP requirements should be taken into consideration when naming
templates.
 Version: (Not editable.) Each time a template is edited, it gets an updated
version number.
 Type: (Not editable.) Reagent Verification should appear prepopulated in the
dropdown list.
 Retired: Check this box to retire the template.
 Method: Choose the method being used from the dropdown menu. The menu
prepopulates with the available methods. If methods have not been created,
one can be created by clicking the plus sign icon next to Methods. Follow the
instructions in the Adding Methods section.
 Books and Plus sign icon: Check to create a new method in the Library.
 Paper and pen icon: Click to view or edit the selected method assigned to this
template. The Save to Library button activates once editing begins. Follow the
instructions in the Adding Methods to the Library section.
 Auto End: Check this box to enable the Auto End feature. With Auto End
enabled, the assay will run until all of the lowest standard replicates have
reacted. Leave this box unchecked to disable the Auto End feature. With Auto
End disabled, data collection will stop after a set period of time (set in the
Maximum Test time field in the Method).

Note: If a specification is set for Negative Control Separation, the assay will
continue to run until that specification is met. For example, if a test is set for 10%
separation and the lowest standard has an onset time of 4,000 seconds, the test
will stop at 4,400 seconds.
 Standard Type: RSE, CSE or Glucan Standard.

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  Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer.
Click the Clear button to clear the selections and start again.
 Reader Layout Well Restriction Mask: Click this button to open the Reader
Layout Well Restriction Mask. Check the boxes that correspond to the wells to
be excluded from use (see Figure 32). This layout may look different
depending on the type of reader being used.
Note: Use this option if the reader has fewer than 96 wells to prevent mapping
samples to wells that are not present. Well restrictions will be saved when the
template is saved.

Figure 32. Reader Layout Well Restriction Mask

 Default Replicates: Use the up/down arrows to increase or decrease the
number of replicates (tubes used for each standard concentration) for this
template. The default set by the FDA and U.S. Pharmacopeia for reagent
verification testing is 3.
 Apply to All Replicates: Click this button to enable the Default Replicates
setting.
 Consumables & Equipment: This is a list of all commonly used consumable
and equipment products, populated from the items added. Use the arrow box
to move up and down the list.

Note: After completing a Reagent Verification, the reagent must be manually

matched to the standard in order for the software to record that the reagent has
been verified. If this is not done, the reagent cannot be used for further testing.
See Matching Supplies in the Library.

4.1.18.1 Adding Consumables and Equipment to a Template

Commonly used items such as pipettes, buffers, Pyroplates® and water can be
added to a template. Consumables and equipment are not required for all

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 tests. However, they should be added if you want to trend certain
components. For more information, see Trending.
Note: It is important to name items consistently in the Description field.
Naming conventions are important for procedural understanding and
efficiency.
1. Click the plus sign icon next to the words Consumables & Equipment. A
popup window opens as shown below.

2. Complete the information as described below.

 Group: Select a group for the item from the dropdown menu
(Consumables is the default).
 Type: Select a type for the item from the dropdown menu. Options will
change depending on the Group chosen as listed below:
o Reagent types: ChromoLAL®, Glucatell®, Pyrotell®-T Pyrochrome®.
o Standards types: Glucan Standard, RSE CSE.
o Consumables types: Combitip, Pyroplate®, Water, Syringe, Dilution
Tubes, Pipette Tip, Sample Container, Reagent Water, Buffer,
Reagent Reservoir, Serological Pipette, Reaction Tubes.
o Equipment types: Vortex Mixer, Pipettor.
o Buffer types: Pyrosol® Buffer, Reconstitution Buffer, Glucashield®
Buffer. Click the Clear button to clear options and start again.
 Description: Add an optional description for the item. Use a consistent
naming scheme to avoid confusion when locating items for testing.
 Retired: Check this box if to retire the particular item from the
template.
 Lot/SN: Enter the Lot or Serial Number for the item.
 Expiration Date: Enter the expiration date for the item.

3. Click Save to Library to save the item to the Library. It will now appear the
next time a template is added or edited. Click Cancel to close the popup
window and return to the General tab of the template.
4. Add the item to the template by clicking the plus sign. An empty row
highlighted in blue appears as the next entry in the list of Consumables &
Equipment as shown below. Locate the item from the list of dropdown
menus.

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 5. When finished, click Save to save the changes to the template, Close to exit
without saving or Save As Copy to save the template with a different name.
Enter the new name in the popup window that appears when this option is
selected.
6. Click the Standards tab (Figure 33) and complete the fields as described
below.

Figure 33. Standards Tab

 Negative Control Replicates: Use the arrows to increase or decrease the
number of negative replicates to use in the template.
 Standard Replicates: Use the arrows to increase or decrease the
number of positive control replicates to use in the template.
 Concentrations: Click the calculator to edit the concentrations as setup
in the Methods section. To edit these values, enter new values in these
fields and click OK. To cancel the edit and close the calculator, click
Cancel.
o Concentrations: Specify the number of standard concentrations that
will be included in the curve. This populates when the number of
samples (products) and replicates are entered. Default is 3. 5
concentrations are recommended to enable a sufficient range.
o Highest Concentration: This is the highest concentration within the
standard curve range.

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 o Dilution Factor: Enter the dilution employed to create the standard
curve. The highest concentration will be used with this dilution factor
and the set number of Concentrations and Replicates to generate
the standard curve series. This defaults to 10.

Example Calculation
For a valid range of potency of 0.005 - 50 EU/mL, enter:
Concentrations: 5
Highest Concentration: 50
Dilution Factor: 10
 Positive Control: Check this box to run a positive control. Options are
replicates and concentration.

7. When finished, click Layout to go to the Layout tab (Figure 34) and
complete the following information:

Figure 34. Layout Tab

 Replicate Direction: Select Horizontal to read the wells horizontally or
Vertical to read the wells vertically.
 Fill Direction: Select Vertical or Horizontal. The wells on a plate can be
filled from left to right (horizontally) or from top to bottom (vertically).
Note: Pyros® eXpress compensates for potential drift caused by fill delay.
Therefore it is important to fill the plate in the direction specified.
 PPC Insert: Select Inline to place the PPCs underneath the replicates.
Choose Adjacent to place the PPCs beside the replicates.
 Concentration / Dilution: Select Ascend to place the standard
concentrations in ascending order. Select Descend to place the standard
concentrations in descending order.

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  Type / Starting Well: The placement of each tube on the plate can be
fine-tuned by various methods. In the Type column, highlight the item
to relocate:
o Select Auto Layout to return the item to its default location on the
tube/plate.
o Select a specific coordinate (A1, A2, etc.) to move the item to that
location.
o Drag and drop individual wells or groups of wells to an empty area.

Once the Reagent Verification Template is setup, it is recommended that the

I/E Template be setup next. Go to Setting up an I/E Template.

4.1.18.2 Removing Consumables and Equipment from a Template

1. Go to the General tab of the template that the equipment is to be removed
from. See Figure 30 for an example template.
2. Highlight the item and click the subtract button.

4.1.19 Setting up an Inhibition/Enhancement (I/E) Template

An Inhibition/Enhancement assay determines what preparation of product
overcomes the inhibition or enhancement characteristics of the product under test.
Each product under test must be accompanied by a Positive Product Control (PPC).
The PPC recovery is used to determine if significant inhibition or enhancement is
occurring.
There are prerequisites to running an I/E assay:
1. There must be a product (sample) in the Library that has not already had an I/E
completed. Products that have already had an I/E will not appear in the
dropdown menus in this template. To add another sample, go to Adding Samples
to the Library.
2. All methods must be defined in the Library. If not, go to Adding Methods to the
Library.
3. After each I/E Test, return to the Library and check the I/E Complete box for the
product tested. The product will not appear in the dropdown menus as an option
when you run a test if this is not done. Go to Completing I/E and Product
Validation.
4. To set up an I/E Template:
1. Click Templates on the toolbar and select I/E.
2. An I/E Template appears as shown in Figure 35. There are 4 tabs: General,
Standards, Samples and Layout. On the General tab, fill in the fields as
described below.

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 Figure 35. I/E Template, General Tab
 Template: Enter the template name as it should appear on the screen.
Naming conventions are important for procedural understanding and
efficiency. Specific SOP requirements should be taken into consideration
when naming templates.
 Version, Type: These fields are prepopulated and not editable.
 Retired: Check this box to retire an existing template from the list of
templates.
 Method: Choose the method from the dropdown menu. The menu
prepopulates with the available methods. If methods have not been
created, create one by clicking the plus sign icon next to Methods. Follow
the instructions in the Adding Methods section.
 Books and Plus sign icon: Check to create a new method in the Library.
 Paper and pen icon: Click to view or edit the method that this template will
use. The Save to Library button activates once editing begins. Follow the
instructions in the Adding Methods section.
 Auto End: Check this box to enable the Auto End feature. With Auto End
enabled, the assay will run until all of the lowest standard replicates have
reacted. Leave this box unchecked to disable the Auto End feature. With
Auto End disabled, data collection will stop after a set period of time (set in
the Maximum Test time field in the Method).
Note: If the specification is set for Negative Control Separation, the assay will
continue to run until that specification is met. For example, if a test is set for 10%
separation and the lowest standard has an onset time of 4,000 seconds, the test
will stop at 4,400 seconds.
 Standard Type: RSE, CSE or Glucan Standard. This is the standard and
buffer type that was previously matched to run this template.
 Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer.
Click the Clear button to clear options and start again.

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  Reader Layout Well Restriction Mask: Click this button to open the Reader
Layout Well Restriction Mask. Check the boxes that correspond to the wells
to be excluded from use (see Figure 36).
Note: Use this option if the reader has fewer than 96 wells to prevent mapping
samples to wells that are not present. Well restrictions will be saved when the
template is saved.

Figure 36. Reader Layout Well Restriction Mask

 Default Replicates: Use the up/down arrows to increase or decrease the
number of replicates (tubes used for each standard concentration) for the
template. U.S. Pharmacopeia requires a minimum of 2 replicates.
 Apply to All Replicates: Click this button to enable the Default Replicates
setting.
 Consumables & Equipment: This is a list of all commonly used consumable
and equipment products, populated from the items added. Use the arrow
box to move up and down the list. To add items to the template, go to
Adding Consumables and Equipment to a Template.
3. When finished, click Save to save the changes to this template, Close to exit
without saving or Save As Copy to save the template with a different name. Enter
the new name in the popup window that appears when this option is selected.
4. Click the Standards tab (see Figure 37). All of the information that was entered
when setting up the methods should appear here. To edit this information, select
new values for the following fields:
 Negative Control Replicates: Use the arrows to increase or decrease the
number of negative replicates to use in the template.
 Standard Replicates: Use the arrows to increase or decrease the number of
positive control replicates to use in the template.
 Click the calculator icon to enter these values:
o Concentrations: Specify the number of standard concentrations that will be
included in the curve. A minimum of three standards is required.

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 o Highest Concentration: Enter the highest concentration of the standards
being used. This value defines the starting point of the automatic
generation of the standard curve series.
o Dilution Factor: Enter the dilution that will be employed to create the
standard curve. The Highest Concentration value and the Concentrations
value will be used with this number to generate a serially diluted standard
curve series.
 Positive Control: Check this box to run a positive control. Options are
replicates and concentration.

Figure 37. Standards Tab

5. Click Samples to go to the Samples tab shown in Figure 38. This is where samples
are added and removed (also referred to as products) to the template from the
Library.
Note: It is not required to add a sample to this template at this point. If you have
not already done so, add products to the Library. See Adding Products to the
Library. .

Click to add a sample

Figure 38. Samples Tab

6. Click the plus sign. A new window opens as shown in Figure 39. Complete the
information as described below.

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 Note: Products will not appear in the dropdown menus unless they have had an I/E
performed and been updated in the Library.

Figure 39. Adding a Sample to a Template

 Product Name: Select the name for the product from the dropdown list. This
list is prepopulated with the names of products entered in the Library.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product (Default is 3).
 Plus sign icon: Click to add another product to the Library. Complete the fields
as described below and click Close when finished:
o Product Name: Enter the name of the product as it should appear on the
screen.
o Description: Enter a description of the product.
o Retired: Check this box to retire the product.
o Release Limit: Enter the maximum concentration of endotoxin allowable
for the product to be released. Set whether the product is released when
the concentration is less than the release limit or less than or equal to the
release limit.
o Initial Concentration: Enter the initial concentration of the product.
o Unit: Select the unit of measure from the dropdown menu.
o I/E Completed: Uncheck this box to use the product or to add a new
product. Check this box when I/E testing is complete. When this box is
checked, the Sample Defaults popup window appears.
o Product Validation Completed: Check this box once the Product Validation
Test has been completed. See Completing I/E and Product Validation.
o Method: Select the method used to complete the Product Validation.
 PPC: Check this box to have a PPC present for the product. Uncheck this box
to have 1 PPC for the entire dilution set.
 PPC/Dilution: Check this box to have the PPC by dilution rather than by
product being tested.
 PPC Concentration: Enter a concentration for PPC. To ensure accurate results,
enter 3 decimal places of precision.

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  PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for
the product (Default is 3).
 Click the calculator icon to set dilutions.
o Dilutions: The number of different product dilutions.
o Initial Dilution: This value is used to define the dilution of the original
concentration of a product in a series.
o Dilution Factor: The dilution factor employed to create the standard curve.

7. Set up product (samples) until the reader is full. The I/E Test can be run with as
many products as needed. Continue adding products, each with different
dilutions. Add products until the reader is full.
8. When finished with the Samples tab, click Save to save the changes, Close to exit
without saving or Save As Copy to save this product with a new name.
9. Click Layout to go to the Layout tab as shown in Figure 40 and complete the
following information:

Figure 40. Layout Tab

 Replicate Direction: Select Horizontal to read the wells horizontally or Vertical
to read the wells vertically.
 Fill Direction: Select Vertical or Horizontal. Wells can be filled from left to
right (horizontally) or from top to bottom (vertically).
 PPC Insert: Select Inline to place the PPCs underneath the replicates. Choose
Adjacent to place the PPCs beside the replicates.
 Concentration / Dilution: Select Ascend to place the standard concentrations
in ascending order. Select Descend to place the standard concentrations in
descending order.
 Type / Starting Well: It is possible to fine-tune the placement of each tube on
the plate by various methods. In the Type column, highlight the item to be
relocated:
o Select Auto Layout to return the item to its default location on the
tube/plate.
o Select a specific coordinate (A1, A2, etc.) to move the item to that location.
o Drag and drop individual wells or groups of wells to an empty area.

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 10. When finished with the Layout tab, click Save to save the changes, Close to exit
without saving or Save As Copy to save this product with a new name.
4.1.20 Setting up a Product Validation Template
The product validation is used to formally confirm that an assay is not influenced by
inhibition or enhancement, and that sample preparation used will consistently
produce results that are not compromised by assay interference. Upon completion
of the formal validation, this product preparation is then the method that will be
used consistently to test this product in the future.
1. Click Templates on the toolbar and select Product Validation.
2. A Product Validation Template appears as shown in Figure 41. This template has
4 tabs: General, Standards, Samples and Layout. On the General tab, fill in the
fields as described below.

Figure 41. Product Validation Template, General Tab

 Template: Enter the template name as it should appear on the screen. Naming
conventions are important for procedural understanding and efficiency.
Specific SOP requirements should be taken into consideration when naming
templates.
 Version: (Not editable.) Each time a template is edited, it gets an updated
version number.
 Type: (Not editable.) Product Validation should appear prepopulated in the
dropdown list.
 Retired: Check this box to retire an existing template from the list of
templates.
 Method: Choose the method from the dropdown menu. The menu
prepopulates with the available methods created in the Library. If methods
have not been created, create one by clicking the plus sign icon. Follow the
instructions in the Adding Methods section.

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  Books and Plus sign icon: Check to create a new method in the Library.
 Paper and pen icon: Click to view or edit the method that the template will
use. The Save to Library button activates once editing begins. Follow the
instructions in the Adding Methods to the Library section.
 Auto End: Check this box to enable the Auto End feature. With Auto End
enabled, the assay will run until all of the lowest standard replicates have
reacted. Leave this box unchecked to disable the Auto End feature. With Auto
End disabled, data collection will stop after a set period of time (set in the
Maximum Test time field in the Method).
Note: If a specification is set for Negative Control Separation, the assay will
continue to run until that specification is met. For example, if a test is set for 10%
separation and the lowest standard has an onset time of 4,000 seconds, the test
will stop at 4,400 seconds..
 Standard Type: RSE, CSE or Glucan Standard. This is the standard type
matched to run this template.
 Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer.
Click the Clear button to clear options and start again.
 Reader Layout Well Restriction Mask: Click this button to open the Reader
Layout Well Restriction Mask. Check the boxes that correspond to the wells to
be excluded from use (see Figure 42).
Note: Use this option if the reader has fewer than 96 wells to prevent mapping
samples to wells that are not present. Well restrictions will be saved when the
template is saved.

Figure 42. Reader Layout Well Restriction Mask

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  Default Replicates: Use the up/down arrows to increase or decrease the
number of replicates (wells used for each standard concentration) for the
template. U.S. Pharmacopeia requires a minimum of 2 replicates.
 Apply to All Replicates: Click this button to enable the Default Replicates
setting.
 Consumables & Equipment: Consumables and equipment are not required for
this test. Add them to trend these components.
3. When finished, click Save to save the changes to this template, Close to exit
without saving or Save As Copy to save this template with a different name. Enter
the new name in the popup window that appears when this option is selected.
4. Click the Samples tab, which will populate the items on the Standards tab from
the product settings in the Library. The Standards tab (Figure 43) will become
available to make any necessary or desired changes to the standards.

Figure 43. Standards Tab

5. On the Samples tab shown in Figure 44, complete the information as described
below.
Note: Products will not appear in the dropdown menus unless they have had an I/E
performed and been updated in the Library.

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 Figure 44. Adding a Product to a Template
 Product Name: Select the name for the product from the dropdown list. This
list is prepopulated with the names of products entered in the Library.
 Samples: Add the number of product samples in the template.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product in this template.
 PPC Replicates: Use the arrows to increase or decrease the number of PPC
replicates of this product in this template.
 Override Product Library Parameters: Check this box to change the product
dilution and PPC values entered when the products were originally setup.
6. Setup products until the reader is full. When finished with the Samples tab, click
Save to save the changes, Close to exit without saving or Save As Copy to save
this product with a new name.
7. Click Layout to go to the Layout tab shown in Figure 45 and complete the
following information:

Figure 45. Layout Tab

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  Replicate Direction: Select Horizontal to read the wells horizontally or Vertical
to read the wells vertically.
 Fill Direction: Select Vertical or Horizontal. The wells can be filled from left to
right (horizontally) or from top to bottom (vertically).
 PPC Insert: Select Inline to place the PPCs underneath the replicates. Choose
Adjacent to place the PPCs beside the replicates.
 Concentration / Dilution: Select Ascend to place the standard concentrations
in ascending order. Select Descend to place the standard concentrations in
descending order.
 Type / Starting Well: The placement of each tube on the plate can be fine-
tuned by various methods. In the Type column, highlight the item to be
relocated:
o Select Auto Layout to return the item to its default location on the
tube/plate.
o Select a specific coordinate (A1, A2, etc.) to move the item to that location.
o Drag and drop individual wells or groups of wells to an empty area.
8. When finished with the Layout tab, click Save to save the changes, Close to exit
without saving or Save As Copy to save this product with a new name.
4.1.21 Completing I/E and Product Validation
To complete the Product Validation Test on a product:
1. From the toolbar, click Libraries and then Products.
2. From the list of products, select the product name and double-click to open it.
3. Check the I/E Completed box and in the Method dropdown field, select the
method used for the I/E Test.
4. Check the Product Validation Completed box.
5. The Sample Defaults popup window opens. Click the Enable Edit button to
complete the information in the Sample Defaults window shown below.

 Sample Dilution: Enter the found optimal dilution for testing.

 PPC: Check this box to use the optimal PPC found.
 PPC/Sample: This box defaults to being checked. There must be a PPC per
sample dilution tested.
 PPC Concentration: Enter the PPC concentration.
 Standard Curve Defaults:
o Use the Concentration calculator to compute the range of the standard
curve using the number of concentrations, highest concentration, and
dilution factor. Click OK when finished.

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 o Product SC: Check this box to enter the Product Concentration and Product
Lot information.
6. Click Save when finished or click the Disable Edit button to turn off editing for the
product. Click Save As Copy to save the product with a different name.
4.1.22 Setting up a Routine Template
This template allows routinely tested products to be selected and run in compliance
with the validated method found in the Product Library.
Note: The Standards tab remains empty until a product from the Sample tab is
selected. Only products that have been validated will be available to use with a
Routine Template.
1. Click Templates on the toolbar and select Routine.
2. A Routine Template appears as shown in Figure 46. On the General tab, fill in the
fields as described below.

Figure 46. Routine Template, General Tab

 Template: Enter the template name as it should appear on the screen. Naming
conventions are important for procedural understanding and efficiency.
Specific SOP requirements should be taken into consideration when naming
templates.
 Version: (Not editable.) Each time a template is edited, it gets an updated
version number.
 Type: (Not editable.) Routine should appear prepopulated in the dropdown
list.
 Retired: Check this box to retire an existing template from the list of
templates.
 Method: Choose the method from the dropdown menu. The menu
prepopulates with the available methods. If methods have not been created,

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 create one by clicking the plus sign icon next to Methods. Follow the
instructions in the Adding Methods section.
 Paper and pen icon: Click to view the method that the template will use. Note
that a method may not be edited from here. To edit a method, go to Viewing
and Editing Methods.
 Auto End: Check this box to enable the Auto End feature. With Auto End
enabled, the assay will run until all of the lowest standard replicates have
reacted. Leave this box unchecked to disable the Auto End feature. With Auto
End disabled, data collection will stop after a set period of time (set in the
Maximum Test time field in the Method).
Note: If a specification is set for Negative Control Separation, the assay will
continue to run until that specification is met. For example, if a test is set for 10%
separation and the lowest standard has an onset time of 4,000 seconds, the test
will stop at 4,400 seconds.
 Standard Type: RSE, CSE or Glucan Standard. This is the standard and buffer
type matched to run this template.
 Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer.
Click the Clear button to clear options and start again.
 Reader Layout Well Restriction Mask: Click this button to open the Reader
Layout Well Restriction Mask. Check the boxes that correspond to the wells to
be excluded from use (see Figure 47).
Note: Use this option if the reader has fewer than 96 wells to prevent mapping
products to wells that are not present. Well restrictions will be saved when the
template is saved.

Figure 47. Reader Layout Well Restriction Mask

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  Default Replicates: Use the up/down arrows to increase or decrease the
number of replicates (tubes used for each standard concentration) for the
template. U.S. Pharmacopeia requires a minimum of 2 replicates.
 Apply to All Replicates: Click this button to enable the Default Replicates
setting.
 Consumables & Equipment: This is a list of all commonly used consumable
and equipment products, populated from the items added. Use the arrow box
to move up and down the list. To add items to this template, go to Adding
Consumables and Equipment to a Template.
3. When finished, click Save to save the changes to this template, Close to exit
without saving or Save As Copy to save this template with a different name. Enter
the new name in the popup window that appears when this option is selected.
4. Click the Samples tab, which will populate the items on the Standards tab from
the product settings in the Library. The Standards tab (Figure 48) will then
become editable to make any necessary or desired changes to the standards.

Figure 48. Standards Tab

5. From the Samples tab, click the plus sign. A new window opens as shown in
Figure 49. Complete the information as described below.
Note: Products will not appear in the dropdown menus unless they have gone
through product validation and I/E testing.

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 Figure 49. Adding a Product to a Template
 Product Name: Select the name for the product from the dropdown list. This
list is prepopulated with the names of products entered in the Library.
 Samples: Use the arrows to increase or decrease the number of products.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product and PPC in this template.
 PPC Replicates: Use the up/down arrows to enter a value.
 Plus sign icon: Click to add another product.
 Override Product Library Parameters: Check this box to change the product
dilution and PPC values entered when the products were originally setup.
6. Setup products until the reader is full. The I/E Test can be run on as many
products as required. Continue adding products, each with different dilutions.
7. When finished with the Samples tab, click Save to save the changes, Close to exit
without saving or Save As Copy to save this product with a new name.
8. Click Layout to go to the Layout tab as shown in Figure 50 and complete the
following information:

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 Figure 50. Layout Tab
 Replicate Direction: Select Horizontal to read the wells horizontally or Vertical
to read the wells vertically.
 Fill Direction: Select Vertical or Horizontal. The wells on a plate can be filled
from left to right (horizontally) or from top to bottom (vertically).
 PPC Insert: Select Inline to place the PPCs underneath the replicates. Choose
Adjacent to place the PPCs beside the replicates.
 Concentration / Dilution: Select Ascend to place the standard concentrations
in ascending order. Select Descend to place the standard concentrations in
descending order.
 Type / Starting Well: The placement of each tube on the plate can be fine-
tuned by various methods. In the Type column, highlight the item to be
relocated:
o Select Auto Layout to return the item to its default location on the
tube/plate.
o Select a specific coordinate (A1, A2, etc.) to move the item to that location.
o Drag and drop individual wells or groups of wells to an empty area.
9. When finished with the Layout tab, click Save to save the changes, Close to exit
without saving or Save As Copy to save this product with a new name.

4.1.23 Setting up a Potency Template

The potency assay allows the user to determine the endotoxin potency of a weight of
CSE (ng) when compared against the activity of the international standard RSE. This
potency is specific to the combination of the particular Reagent Lot, CSE Lot and RSE.
The assay requires a single series of RSE dilutions and one or more sets of dilutions of
CSE. Potency can only be determined for one lot of CSE at a time. To setup a Potency
Template:
1. Click Templates on the toolbar and select Potency.
2. A Potency Template appears as shown in Figure 51. There are 4 tabs. On the
General tab, complete the fields as described below.

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 Figure 51. Potency Template, General Tab
 Template: Name the Potency Template with a unique name, for example add
"pot" to the end of the name. Naming conventions are important for
procedural understanding and efficiency. Specific SOP requirements should be
taken into consideration when naming templates.
 Version: (Not editable.) Each time a template is edited, it gets an updated
version number.
 Type: (Not editable.) Potency should appear prepopulated in the dropdown
list.
 Retired: Check this box to retire an existing template from the list of
templates.
 Method: Choose the method from the dropdown menu. The menu
prepopulates with the available methods. If methods have not been created,
create one by clicking the plus sign icon next to Methods. Follow the
instructions in the Adding Methods section.
 Books and Plus sign icon: Check to create a new method in the Library.
 Paper and pen icon: Click to view or edit the method that the template will
use. The Save to Library button activates once editing begins. Follow the
instructions in the Adding Methods section.
 Auto End: Check this box to enable the Auto End feature. With Auto End
enabled, the assay will run until all of the lowest standard replicates have
reacted. Leave this box unchecked to disable the Auto End feature. With Auto
End disabled, data collection will stop after a set period of time (set in the
Maximum Test time field in the Method).
Note: If a specification is set for Negative Control Separation, the assay will
continue to run until that specification is met. For example, if a test is set for 10%
separation and the lowest standard has an onset time of 4,000 seconds, the test
will stop at 4,400 seconds.

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  Standard Type: RSE, CSE or Glucan Standard. This is the standard type
matched to run this template.
 Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer.
Click the Clear button to clear options and start again.
 Reader Layout Well Restriction Mask: Click this button to open the Reader
Layout Well Restriction Mask. Check the boxes that correspond to the wells to
be excluded from use (see Figure 52).
Note: Use this option if the reader has fewer than 96 wells to prevent mapping
products to wells that are not present. Well restrictions will be saved when the
template is saved.

Figure 52. Reader Layout Well Restriction Mask

 Defaults: Use the up/down arrows to increase or decrease the number of
replicates (wells) used for each standard concentration) for the template. U.S.
Pharmacopeia requires a minimum of 2 replicates.
 Apply to All Replicates: Click this button to enable the Default Replicates
setting.
 Consumables & Equipment: Consumables and equipment are not required for
all tests. Add them to trend certain components.
3. When finished, click Save to save the changes to this template, Close to exit
without saving or Save As Copy to save this template with a different name. Enter
the new name in the popup window that appears when this option is selected.
4. Click the Standards tab (Figure 53). All of the information entered when the
methods were setup will appear here.

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 Figure 53. Standards Tab
5. Click the CSEs tab (see Figure 54). Complete the information as described below.

Figure 54. CSE Tab

 Samples: Enter the number of CSE vials being tested. This defaults to 1 but a
user can run up to as many as the reader can accommodate.
 Replicates: Use the arrows to increase or decrease the number of replicates of
concentration of CSE replicates. This defaults to 2.
 Concentrations calculator: Click the calculator icon to enter the number of
concentrations, highest concentration and dilution factor. The number of
concentrations defaults to 3.
 Click the calculator icon to set dilutions.
o Concentrations: Specify the number of standard concentrations that will be
included in the curve. This populates when the number of products and
replicates are entered. Default is 3. 5 concentrations are recommended to
enable a sufficient range.

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 o Highest Concentration: This is the highest concentration on the standard
curve range.
o Dilution Factor: Enter the dilution employed to create the standard curve.
The highest concentration will be used with this dilution factor and the
previously set number of Concentrations and Replicates to generate the
standard curve series. This defaults to 10.
6. When finished with the CSE tab, click Save to save the changes, Close to exit
without saving or Save As Copy to save this product with a new name.
7. Click Layout to go to the Layout tab. See Figure 55 and complete the following
information:

Figure 55. Layout Tab

 Replicate Direction: Select Horizontal to read the wells horizontally or Vertical
to read the wells vertically.
 Fill Direction: Select Vertical or Horizontal. You can fill the wells from left to
right (horizontally) or from top to bottom (vertically).
 PPC Insert: Select Inline to place the PPCs underneath the replicates. Choose
Adjacent to place the PPCs beside the replicates.
 Concentration / Dilution: Select Ascend to place the standard concentrations
in ascending order. Select Descend to place the standard concentrations in
descending order.
 Type / Starting Well: The placement of each tube on the plate can be fine-
tuned by various methods. In the Type column, highlight the item to be
relocated:
o Select Auto Layout to return the item to its default location on the
tube/plate.
o Select a specific coordinate (A1, A2, etc.) to move the item to that location.
o Drag and drop individual wells or groups of wells to an empty area.
8. When finished, click Save to save the changes, Close to exit without saving or
Save As Copy to save this product with a new name.

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 4.1.24 Running a Potency Test
Potency relates mass units of endotoxin to actual endotoxin units for a given lot
combination of LAL and CSE. The potency assay requires a single series of RSE
dilutions and one or more sets of dilutions of CSE.

Example:
Potency = 10
Units = EU/ng would describe a relationship where 1ng of endotoxin has 10 units of
activity

Potencies are available on Certificates of Analysis from Associates of Cape Cod, Inc.
Certificates of Analysis are documents accepted by the FDA. They can be obtained
online at http://www.acciusa.com, under Certificates of Analysis or contact an ACC
Customer Service Representative to receive the certificate by email or fax.
If you have not already setup a Potency Template in the Library, go to Setting up a
Potency Template.
1. Click Templates on the toolbar. The list of templates setup in the Library appears
as shown in Figure 56.

Drug 1

Drug 2

Figure 56. List of Templates

2. From the list, begin running the test right away or edit the test parameters before
running.
3. To edit test parameters highlight the name of the template and click Edit. The
Potency Template opens as shown in Figure 57. For descriptions of each
parameter, see Setting up a Potency Template. Click Run when finished editing.
4. To run the test without editing any parameters highlight the name of the
template and click Run.

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 Figure 57. Potency Template Edit Screen
5. The Pre-Collection Test window appears as shown in Figure 58. To expand the
view of the right side of the screen, click Zoom In. Click Zoom Out to return to the
view as shown below.

Figure 58. Pre-Collection Test Window

6. There are four tabs on the Pre-Collection Test screen: General, Consumables &
Equipment, Comments and Standards. On the General tab:
 Provide a unique name in the Test Name field. If the test is not named, the
software will generate a name. The default name generated is the test ID
suffixed by the date and time of the test.
 Instrument, Template, Version, Type and Method, Reagent Type, Standard
Type and Buffer Type will populate from the template.
 Select the Reagent Lot, Standard Lot, Buffer Lot and Water Lot from the
dropdown menus.

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  To add a CSE, click the plus sign icon. A popup appears as shown below. Click
OK when finished adding the information to the window. Click Cancel to
return to the Pre-Collection Test screen.

7. On the Consumables & Equipment tab:

 Check to make sure all of the equipment is correct. Equipment can be added
by clicking the plus sign. See Adding Consumables and Equipment to a
Template.
8. On the Comments tab, a general comment about the test can be added. (see
Figure 59).

Figure 59. Comments Tab

9. On the Standards tab, check that the information that has populated from the
template is correct.
10. Click Collect. The test begins to run and the Run Collection window appears as
shown in Figure 60. While the test runs, the active well changes color as tubes are
added to the reader. There are several options for viewing the test and editing
test parameters (see Table 3).
Note: If using a plate reader, the message below will appear. Add plate and click
Done.

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 Edit calculation parameters View report

View Plot up to
real time 8 replicates
updates
Drag and
Drop tube(s)
or well(s)
onto graph
area

Figure 60. Run Collection Window

Icon Function
View report while test is running. The report cannot be electronically
signed until the test has completed running. See Reports for more
information.
Print the mask layout.

Edit calculation requirements.

View average temperature of the reader.

View how long the test has been running and its status.
Return to test setup.

View well graphs individually (see Figure 62).

View well graphs on a single graph (see Figure 63).

Switch between list view and reader layout view.

Toggle between select series and select single mode.

Remove Remove an individual well from the graph.

Remove All Remove all data points from the graph.
Table 3. Icons on the Run Collection Window
11. To change calculation parameters, click the Settings icon. The Calculations
Parameters window appears as shown in Figure 61. Enter changes in this window.
Click OK when finished or click Cancel to return to the Run Collection window.

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 Figure 61. Calculations Parameters Window

Figure 62. Graph of Wells on a Single Plot

Figure 63. Graph of Wells on Different Graphs

12. When the test has run for a sufficient amount of time, such that all products have
run at least as long as the lowest standard, data collection can be stopped by
clicking the End Collect button. This will close the assay. The assay can be
reopened by clicking Results in the toolbar.
Note: Prematurely ending an assay may render it invalid.
13. The End Collect popup appears. Click Yes to end the test. To return to the
Runtime screen, click No. If a maximum test time or Auto End option has been
applied, let the assay run until it auto-terminates.

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 14. Once the test ends, the Collection Complete window appears as shown in Figure
64.
15. Click Analyze to edit any of the assay's parameters (Figure 65) or Report to
generate a report.

Figure 64. Collection Complete Window

Figure 65. Post-Analysis Run Screen

From here, the following actions can be performed:
Icon Function
Print the reader layout.

Add products to the test.

Remove products from the test.

Mask a well (a masked well will not be used in any calculations).

Unmask a well.

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 Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Switch between select series and select single mode.

Edit assay settings, including renaming the test and re-graphing

products
Table 4. Icons on the Post-Analysis Window

4.1.24.1 Setting up a FreeForm Template

A FreeForm Template allows a test to run without any restrictions. All non-
retired products in the Library are available regardless of where they are in the
testing process, and all standards and negatives are available to be edited.
The FreeForm Template is similar to a Routine Template but without any
prepopulated values. To define the parameters to be used in the FreeForm
Template, refer to Setting up a Routine Template for screen and window
descriptions.

4.1.24.2 Creating a New Template from an Existing Template

An existing template can be modified and saved under a different name to
create a new template.
1. From the toolbar, click Templates.
2. From the list of templates that opens, highlight the template to be used as
the base and click Edit.
3. Make the changes and click Save As Copy. A popup window appears and
prompts for the template name.
4. Enter a name in the Template Name field and click OK. Click Cancel to close
the popup without saving. The new template is saved.

4.1.24.3 Editing a Template

1. From the toolbar, click Templates.
2. From the list of templates that opens, highlight the template to edit and
click Edit.
3. When completed:
 Click Save to save the edits to this template.
 Click Close to return to the main Templates page without saving.
 Click Save As Copy to save this template with a different name. Enter
the new name in the popup window that appears when this option is
selected.

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5 Qualifying Reagents
Prior to testing, it is recommended that:
 All equipment, materials and reagents are setup in the Library. Go to Setting up your Testing
Environment. Note that this Test Template cannot be run without reagents being loaded into
the Library.
 A method is chosen and established in the Library. Go to Adding Methods to the Library.
 A Reagent Verification Template be setup. Go to Setting up a Reagent Verification.

5.1 Reagent Verification Testing

Reagent Verification Testing is intended to show performance of the matched reagents
meets the required specifications. The assay can also be used to qualify Technicians.

5.1.1 Running a Reagent Verification Test

Use the Reagent Verification Template to run the Reagent Test. To run a Reagent
Verification Test:
1. Click Templates on the toolbar. Templates that have been setup in the Library
appear as shown in Figure 66.

Drug 1

Drug 2

Figure 66. List of Templates

2. From the list, begin running the test right away or edit test parameters before
running.
 To edit test parameters highlight the name of the template and click Edit. The
Reagent Verification Template opens as shown in Figure 67. For descriptions of
parameters, see Setting up a Reagent Verification Template. Click Run when
finished editing.

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 Figure 67. Reagent Verification Template
 To run the test without editing any parameters highlight the name of the
template and click Run.
3. The Pre-Collection Test screen appears as shown in Figure 68. To expand the view
of the right side of the screen, click Zoom In. Click Zoom Out to return to the view
as shown below.

Figure 68. Pre-Collection Test Screen

4. There are four tabs on the Pre-Collection Test screen: General, Consumables &
Equipment, Comments and Standards. On the General tab:
 If Auto Naming is not enabled on the Options tab, the test must be named in
the Test Name field. If Auto Naming is enabled, the software will generate a
name. The default name generated is the test ID suffixed by the date and time
of the test.
 Select the Instrument from the dropdown menu.

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  Select the Reagent Lot, Standard Lot, Buffer Lot and Water Lot from the
dropdown menus.
 The Template and Method fields will auto-populate from the template.
5. On the Consumables & Equipment tab, ensure that all the equipment is correct.
Equipment can be added by clicking the plus sign. See Adding Consumables and
Equipment to a Template.
6. On the Comments tab, a general comment about the test can be added (see
Figure 69).

Figure 69. Comments Tab

7. On the Standards tab, check that the information that has populated from the
template is correct.
8. Click Collect. The test begins to run and the Run Collection window appears as
shown in Figure 70.

Figure 70. Run Collection Window

9. As the test runs, the active well positions change color as tubes are added to the
reader as displayed in Figure 71. The icons at the top of the screen offer options
for viewing the test and editing test parameters while the test is running. Table 3
describes these icons and their functions.

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 Icon Function
View report while test is running. The report cannot be electronically
signed until the test has completed running. See Reports for more
information.
Print the mask layout.

Edit calculation requirements.

View average temperature of the reader.

View how long the test has been running and its status.

Return to test setup.

View well graphs individually (see Figure 73).

View well graphs on a single graph (see Figure 74).

Switch between list view and reader layout view.

Toggle between select series and select single mode.

Remove Remove an individual well from the graph.

Remove All Remove all data points from the graph.
Table 3. Icons on the Run Collection Window

Plot up
Real time to 8
updates replicates

Drag and
drop tube(s)
or well(s)
onto graph
area.

Figure 71. Run Collection Window as Test Progresses

10. To change calculation parameters, click the Settings icon. The Calculations
Parameters window appears as shown in Figure 72. Enter the changes in this
window.
Note: If the Administrator has checked the Require Reason for Change box in the
User Management tab, text must be entered in the Reason text box.

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 Figure 72. Calculations Parameters Window
11. To view test results graphically, hover over an individual tube. Drag and drop a
single tube or group of tubes to the right side of the screen to be plotted on a
graph (see Figures 73 and 74).

Figure 73. Graph of Wells on Single Plot

Figure 74. Graph of Wells on Different Graphs

12. When the test has run for a sufficient amount of time, such that all products have
run at least as long as the lowest standard, data collection may be stopped by
clicking the End Collect button. This will close the assay. The assay can be
reopened by clicking Results in the toolbar.

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 13. The End Collect popup appears. Click Yes to end the test. To return to the
Runtime screen, click No. If a maximum test time or Auto End option has been
applied, let the assay run until it auto-terminates.
14. Once the test ends, the Collection Complete window appears as shown in Figure
75. Click Analyze to edit any of the assay's parameters or click Report to generate
a report. See Reports for more information.

Figure 75. Collection Complete Window

15. Click Analyze to view the Post-Analysis Run screen shown in Figure 76.

Figure 76. Post-Analysis Run Screen

Using the icons at the top of the screen, the following actions may be performed:
Icon Function
Print the reader layout.

Add products to the test.

Remove products from the test.

Mask a well (a masked well will not be used in any calculations).

Unmask a well.

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 Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Switch between select series and select single mode.

Edit assay settings, including renaming the test and re-graphing

products.
Table 4. Icons on the Post-Analysis Window

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6 Testing Products
This section discusses how to run the following assays:
 I/E
 Product Validation
 Routine
 FreeForm
While a test is running, many operations may be performed in the software with the exception of
running a simultaneous test. If a user attempts to run two templates simultaneously, the following
error message appears:

To return to a test that is running, click the Collect icon in the toolbar.

6.1 Running an I/E Test

There are some prerequisites to running an I/E Test:
 There must be a product in the Library that has not already had an I/E completed. A
product will not appear when an I/E assay has previously been performed. To add a
product to the Library, go to Adding Samples to the Library.
 There must be defined methods in the Library. To define a method, go to Adding
Methods to the Library.
 An I/E Template is used to run an I/E Test. If an I/E Template has not been setup, see
Setting up an I/E Template.
Note: After each I/E Test, return to the Library and check the I/E Complete box for the
product tested. Go to Completing I/E and Product Validation.
1. Click Templates on the toolbar. The list of templates that have been setup in the Library
appears as shown in Figure 77.

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 Drug 1

Drug 2

Figure 77: List of Templates

2. From the list, begin running the test right away or edit parameters.
 To run the test without editing any parameters highlight the name of the
template and click Run.
 To edit parameters highlight the template and click Edit. The I/E Template opens
as shown in Figure 78. For descriptions of each parameter, see Setting up an I/E
template. Click Run when finished editing parameters.

Figure 78: I/E Template, General Tab

3. The Pre-Collection Test screen appears as shown in Figure 79. To expand the view of the
right side of the screen, click Zoom In. Click Zoom Out to return to the view as shown
below.

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 Move up
for more
space below

Edit selected
sample
Add/remove
selected sample

Figure 79. Pre-Collection Test Screen

4. There are four tabs on the Pre-Collection Test screen: General, Consumables &
Equipment, Comments and Standards. On the General tab:
 If Auto Naming is not enabled on the Options tab, the test must be named in the
Test Name field. If Auto Naming is enabled, the software will generate a name.
The default name generated is the test ID suffixed by the date and time of the
test.
 Select the Instrument from the dropdown menu.
 The Template and Method fields auto populate from the template.
 Select the Reagent Lot, Standard Lot, Buffer Lot and Water Lot from the
dropdown menus.
 To add products, click the plus sign icon. Choose a product that is eligible for an
I/E from the list. Once a product is selected, the Product Name popup appears as
shown in Figure 80. Click OK when finished adding the information to the
window. Click Cancel to return to the Pre-Collection Test screen.

Figure 80. Product Name Popup

 Product Name/Lot #: Enter a name and lot number for the product.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product (Default is 2).
 PPC: Check this box to have a PPC present for the product.

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  PPC/Dilution: This box defaults to being checked. An I/E assay requires a PPC for
all dilutions.
 PPC Concentration: Enter a concentration for PPC. To ensure accurate results,
enter 3 decimal places of precision. The value will default to that found in the
method selected. The value should be at or near the middle of the standard
curve.
 PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for the
product (Default is 2).
 Dilutions: Click the calculator icon to enter values for the following fields:

o Dilutions: The number of different product dilutions of the product being

tested.
o Initial Dilution: This value is used to define the dilution of the original
concentration of a product in a series.
o Dilution Factor: The dilution factor employed to create the range of product
concentrations, to be tested in the I/E Test.
5. On the Consumables & Equipment tab, ensure that all of the equipment is correct.
Equipment can be added by clicking the plus sign. See Adding Consumables and
Equipment to a Template.
6. On the Comments tab, a general comment about the test can be added.
7. On the Standards tab, check that the information that populated from the template is
correct.
8. Click Collect. The test begins to run and the Run Collection screen appears as shown in
Figure 81. While the test runs, the active well changes color as tubes are added to the
reader. There are several options for viewing the test and editing test parameters (see
Table 3).

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 Edit calculation parameters View Report

Plot up to 8
Real time replicates
updates

Drag and drop

tubes or wells
into graph
area

Figure 81. Run Collection Screen

Icon Function
View report while test is running. Note the test cannot be electronically
signed until the test has completed running. See Reports for more
information.
Print the mask layout.

Edit calculation parameters.

View average temperature of the reader.

View how long the test has been running and its status.

Change Settings (go to Step 7 below).

View graph of wells on a single plot (see Figure 82).

View graph of wells on different graphs (see Figure 83).

Switch between list view and reader layout view.

Toggle between select series and select single mode.

Remove Remove an individual well from the graph.

Remove All Remove all data points from the graph.
Table 3. Icons on the Run Collection Window

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 Figure 82. Graph of Wells on Single Plot

Figure 83. Graph of Wells on Different Graphs

9. To edit calculation parameters, click the Settings icon. The Calculations Parameters
window appears as shown in Figure 84. Enter changes in this window. Click OK when
finished or Cancel to return to the Run Collection screen.
Note: If the Administrator has checked the Require Reason for Change box in the User
Management tab, text must be entered in the Reason text box.

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 Figure 84. Calculations Parameters Window
10. To change test parameters, click the Change Settings icon in the upper right of the
screen to:
 Add a product
 Edit the Reagent Lot, Standard Lot, Buffer Lot and Water Lot
 Add consumables and equipment
 Add comments
11. The Change Settings screen opens as shown in Figure 85. There are 3 tabs on this
screen: General, Consumables & Equipment and Comments.

Add a sample

Drug 5

Figure 85. Change Settings Screen

12. To add a product, click the plus button. The screen changes as shown in Figure 86.
Complete the fields as described below.
 Product Name/Lot #: Enter a name and lot number for the product.
 Dilutions: Click the calculator icon to enter values for the following fields:

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 o Dilutions: The number of different product dilutions of the product being
tested.
o Initial Dilution: This value is used to define the dilution of the original
concentration of a product in a series.
o Dilution Factor: The dilution factor employed to create the range of product
concentrations to be tested in the I/E Test.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product.
 PPC: Check this box to have a PPC present for the product.
 PPC/Dilution: Check this box to have the PPC by dilution rather than by product
being tested.
 PPC Concentration: Enter a concentration for PPC. To ensure accurate results,
enter 3 decimal places of precision. The value will default to that found in the
method selected. The value should be at or near the middle of the standard
curve.
 PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for the
product.
 Min. PPC Recovery (%) and Max PPC/Recovery (%): These values are
prepopulated with those entered in Options within Settings.
 Standard Curve Index: Enter the standard curve being used (there may only be
one).
 Preferred starting well number: (Default None.) Choose a well for this product
from the dropdown. If None is chosen, the next available well will be used.

Figure 86. Change Settings Screen, Adding a Product

13. To add a consumable, click the Consumables & Equipment tab.
14. To add a comment, click the Comments tab.
15. When the test has run for a sufficient amount of time, such that all products have run at
least as long as the lowest standard, data collection may be stopped by clicking the End
Collect button. This will close the assay. Clicking Results in the toolbar reopens the
assay.

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 Note: Prematurely ending an assay may render it invalid.
16. The End Collect popup appears. Clicking Yes ends the test. To return to the Runtime
screen, click No. If a maximum test time or Auto End option has been applied, let the
assay run until it auto-terminates.
17. Once the test ends, the Collection Complete window appears as shown in Figure 87.
Click Analyze to view the Post-Analysis Run screen (Figure 88), or click Report to
generate a report. See Reports for more information.

Figure 87. Collection Complete Window

Figure 88. Post-Analysis Run Screen

18. Using the icons at the top of the Post-Analysis Run screen, the following actions may be
performed:
Icon Function
Print the reader layout.

Add products to the test.

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 Remove products from the test.

Mask a well (a masked well will not be used in any calculations).

Unmask a well.

Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Switch between select series and select single mode.

Edit assay settings, including renaming the test and re-graphing products.

Table 4. Icons on the Post-Analysis Window

6.2 Running a Product Validation Test

There are some prerequisites to running a Product Validation Test:
 There must be a product in the Library that has not already had a validation completed
and has had an I/E completed. To add a product to the Library, go to Adding Samples to
the Library.
 There must be defined methods in the Library. To define a method, go to Adding
Methods to the Library.
 A Product Validation Template will be used to run a Product Validation Test. If you have
not set up a Product Validation Template, see Setting Up a Product Validation Template.
Note: After each Product Validation Test, return to the Library and check the Product
Validation box for the product tested. The product will not appear in the dropdown
menus as an option when a Routine assay is run if this is not done. Go to Completing I/E
and Product Validation.
1. Click Templates on the toolbar. The templates that have been setup in the Library
appear as shown in Figure 89.

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 Figure 89. List of Templates
2. From the list, begin running the test right away or edit parameters.
 To run the test without editing any parameters highlight the name of the
template and click Run.
 To edit parameters highlight the template and click Edit. The I/E Template opens
as shown in Figure 90. For descriptions of each parameter, see Setting Up a
Product Validation Template. Click Run when finished editing parameters.

Figure 90. Product Validation Template, General Tab

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 3. The Pre-Collection Test screen appears as shown in Figure 91. To expand the view of the
right side of the screen, click Zoom In. Click Zoom Out to return to the view as shown
below.
Note: Click Save As Copy to save any changes made to the template under a new name.

Move up for
more space
below

Edit selected
sample

Add/remove
selected
sample

You
Figure 91. Pre-Collection Test Screen
4. There are four tabs on the Pre-Collection Test screen: General, Consumables &
Equipment, Comments and Standards. On the General tab:
 If Auto Naming is not enabled on the Options tab, the test must be named in the
Test Name field. If Auto Naming is enabled, the software will generate a name.
The default name generated is the test ID suffixed by the date and time of the
test.
 Select the Instrument from the dropdown menu.
 The Template and Method fields auto-populate from the template.
 Select the Reagent Lot, Standard Lot, Buffer Lot and Water Lot from the
dropdown menus.
 To add products, click the plus sign icon. Choose a product that is eligible for a
validation from the list. Once a product is selected, the Product Name popup
appears as shown in Figure 92. Complete the information as shown below and
click OK when finished. Click Cancel to return to the Pre-Collection Test screen.

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 Figure 92. Product Name Popup
 Product Name/Lot #: Enter a name and lot number for the product.
 Samples: Use the arrows to increase or decrease the products. The value should
be 1 product, but three different batches of the sample.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product.
 PPC: Check this box to have a PPC present for the product.
 PPC/Sample: This box defaults to being checked. There must be a PPC per
product dilution tested.
 PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for
this product.
 Standard Curve Index: Enter the standard curve being used (there may only be
one).
 Preferred starting well number: (Default None.) Choose a well for this new
product from the dropdown. If None is chosen, the next available well will be
used.
On the Consumables & Equipment tab, ensure that all of the equipment is correct.
Equipment can be added by clicking the plus sign. See Adding Consumables and
Equipment to a Template.
On the Comments tab, a general comment about the test can be added.
On the Standards tab, check that the information that populated from the template
is correct.

5. Click Collect. The test begins to run and the Run Collection screen appears as shown in
Figure 93. While the test runs, the active well changes color as tubes are added to the
reader. There are several options for viewing the test and editing test parameters (see
Table 3).

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 Edit calculation parameters View Report
Change
settings

Real time Plot up to 8

updates replicates

Drag and
drop tubes
or wells into
graph area

Figure 93. Run Collection Screen

Icon Function
View report while test is running. Note that the report cannot be
electronically signed until the test has completed running. For more
information, see Reports.
Print the mask layout.

Edit calculation parameters.

View average temperature of the reader.

View how long the test has been running and its status.

Change Settings (see Step 7 below).

View graph of wells on a single plot (see Figure 94).

View graph of wells on different graphs (see Figure 95).

Switch between list view and reader layout view.

Toggle between select series and select single mode.

Remove Remove an individual well from the graph.

Remove All Remove all data points from the graph.
Table 3. Icons on the Run Collection Window

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 Graph of wells
on single plot

Figure 94. Graph of Wells on Single Plot

Figure 95. Graph of Wells on Different Graphs

6. To edit calculation parameters, click the Settings icon. The Calculations Parameters
window appears as shown in Figure 96. Enter changes in this window. Click OK when
finished or Cancel to return to the Run Collection screen.

Figure 96. Calculations Parameters Window

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 Note: If the Administrator has checked the Require Reason for Change box in the User
Management tab, text must be entered in the Reason text box.
7. To change test parameters, click the Change Settings icon in the upper right of the
screen to:
 Add a product
 Edit the Reagent Lot, Standard Lot, Buffer Lot and Water Lot
 Add consumables and equipment (click the Consumables & Equipment tab)
 Add comments (click the Comments tab)
8. When the test has run for a sufficient amount of time, such that all products have run at
least as long as the lowest standard, data collection may be stopped by clicking the End
Collect button. This will close the assay. Clicking Results in the toolbar reopens the
assay.
Note: Prematurely ending an assay may render it invalid.
9. The End Collect popup appears. Click Yes to end the test. To return to the Runtime
screen, click No. If a maximum test time or Auto End option has been applied, let the
assay run until it auto-terminates.
10. Once the test ends, the Collection Complete window appears. Click Analyze to view the
Post-Analysis Run screen (Figure 97) or click Report to generate a report. See Reports
for more information.

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 Figure 97. Post-Analysis Run Screen
Using the icons at the top of the screen, the following actions may be performed:
Icon Function
Print the reader layout.

Add products to the test.

Remove products from the test.

Mask a well (a masked well will not be used in any calculations).

Unmask a well.

Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Switch between select series and select single mode.

Edit assay settings, including renaming the test and re-graphing

products.
Table 4. Icons on the Post- Analysis Window

6.3 Running a Routine Test

The Routine Template is used to run a Routine Test. If a Routine Template has not been
setup, see Setting up a Routine Template.
1. Click Templates on the toolbar. The list of templates setup in the Library appear (see
Figure 98).

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 Drug 5

Drug 1

Figure 98. List of Templates

2. From the list, begin running the test right away or edit parameters,
 To run the test without editing any parameters highlight the name of the
template and click Run.
 To edit parameters highlight the template and click Edit. The Routine Template
opens as shown in Figure 99. For descriptions of each parameter, see Setting up
a Routine Template. Click Run when finished editing parameters.

Figure 99: Routine Template, General Tab

3. The Pre-Collection Test screen appears as shown in Figure 100. To expand the view of
the right side of the screen, click Zoom In. Click Zoom Out to return to the view as
shown below.

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 95

 Move up for
more space
below
Edit selected
sample
Add/remove
selected sample

Figure 100. Pre-Collection Test Screen

4. There are four tabs on the Pre-Collection Test screen: General, Consumables &
Equipment, Comments and Standards. On the General tab:
 If Auto Naming is not enabled on the Options tab the test must be named in the
Test Name field. If Auto Naming is enabled, the software will generate a name.
The default name generated is the test ID suffixed by the date and time of the
test.
 Select the Instrument from the dropdown menu.
 The Template and Method fields auto-populate from the template.
 Select the Reagent Lot, Standard Lot, Buffer Lot and Water Lot from the
dropdown menus.
 To add products, click the plus sign icon. Choose a product that is eligible for a
validation from the list. Once a product is selected, the Product Name popup
appears as shown in Figure 101. Complete the information as shown below and
click OK when finished. Click Cancel to return to the Pre-Collection Test screen.

Figure 101. Product Name Popup

 Product Name/Lot #: Enter a name and lot # for the product.
 Samples: Enter the number of products to test.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product.

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  PPC: Check this box to have a PPC present for the product.
 PPC/Sample: Check this box to run a PPC on every dilution of the product.
Uncheck the box to run the PPC on the last product of the set.
 PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for the
product.
 Standard Curve Index: Enter the standard curve being used.
On the Consumables & Equipment tab, ensure that all of the equipment is correct.
Equipment can be added by clicking the plus sign. See Adding Consumables and Equipment
to a Template.
On the Comments tab, a general comment about the test can be added.
On the Standards tab, check that the information that populated from the template is
correct.
5. Click Collect. The test begins to run and the Run Collection screen appears as shown in
Figure 102. While the test runs, the active well changes color tubes are added to the
reader. There are several options for viewing the test and editing test parameters (see
Table 3).

Edit calculation parameters View Report

Change
settings

Plot up to 8
Real time replicates
updates
Drag and
drop tubes
or wells into
graph area

Figure 102. Run Collection Screen

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 Icon Function
View report while test is running. Note that the test cannot be
electronically signed until the test has completed running. For more
information, see Reports.
Print the mask layout.

Edit calculation requirements.

View average temperature of the reader.

View how long the test has been running and its status.

Change Settings (see Step 6 below).

View graph of wells on a single plot (see Figure 104).

View graph of wells on different graphs (see Figure 105).

Switch between list view and reader layout view.

Toggle between select series and select single mode.

Remove Remove an individual well from the graph.

Remove All Remove all data points from the graph.
Table 3. Icons on the Run Collection Window
6. To edit calculation parameters, click the Settings icon. The Calculations Parameters
window appears as shown in Figure 103. Enter the changes in this window. Click OK
when finished or Cancel to return to the Run Collection screen.

Figure 103. Calculations Parameters Window

Note: If the Administrator has checked the Require Reason for Change box in the User
Management tab, text must be entered in the Reason text box.

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 7. To change test parameters, click the Change Settings icon in the upper right of the
screen to:
 Add a product
 Edit the Reagent Lot, Standard Lot, Buffer Lot and Water Lot
 Add consumables and equipment (click the Consumables & Equipment tab)
 Add comments (click the Comments tab)

Graph of
wells on
single plot

Figure 104. Graph of Wells on Single Plot

Figure 105. Graph of Wells on Different Graphs

8. When the test has run for a sufficient amount of time, such that all products have run at
least as long as the lowest standard, data collection may be stopped by clicking the End
Collect button. This will close the assay. Clicking Results in the toolbar reopens the
assay.
Note: Prematurely ending an assay may render it invalid.
9. The End Collect popup appears. Click Yes to end the test. To return to the Runtime
screen, click No. If a maximum test time or Auto End option has been applied, let the
assay run until it auto-terminates.

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 10. Once the test ends, the Collection Complete window appears. Click Analyze to view the
Post- Analysis Run screen (Figure 106) or click Report to generate a report. See Reports
for more information.

Figure 106. Post-Analysis Run Screen

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 Using the icons at the top of the screen, the following actions may be performed:
Icon Function
Print the reader layout.

Add products to the test.

Remove products from the test.

Mask a well (a masked well will not be used in any calculations).

Unmask a well.

Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Switch between select series and select single mode.

Edit assay settings, including renaming the test and re-graphing

products.
Table 4. Icons on the Post-Analysis Window

6.4 Running a FreeForm Test

1. Click Templates on the toolbar and then click FreeForm.
2. The FreeForm Template opens as shown in Figure 107. There are four tabs in this
template: General, Standards, Samples and Layout. On the General tab, complete the
fields as described below and click Save.

Figure 107. FreeForm Template, General Tab

 Template: Enter a name for the new FreeForm Test. It will be saved as a template
for future FreeForm Tests.

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  Version, Type: These fields are prepopulated and not editable.
 Retired: Check this box to retire this template.
 Method: Choose the Method from the dropdown menu. The menu prepopulates
with the available methods. If methods have not been created, create one by
clicking the plus sign icon next to Methods. Follow the instructions in the Adding
Methods section.
 Books with plus sign icon: Click to create a new method for this test to use.
 Paper and pen icon: Click to view or edit the method that this template will use.
The Save to Library button activates once editing begins. Follow the instructions
in the Adding Methods section.
 Auto End: Check this box to enable the Auto End feature. With Auto End enabled,
the assay will run until all of the Lowest Standard replicates have reacted. Leave
this box unchecked to disable the Auto End feature. With Auto End disabled, data
collection will stop after a set period of time (set in the Maximum Test time field
in the Method).
 Standard Type: RSE, CSE or Glucan Standard. This is the standard and buffer type
matched to run this template.
 Buffer Type: Pyrosol® Buffer, Reconstitution Buffer or Glucashield® Buffer. Click
the Clear button to clear options and start again.
 Reader Layout Well Restriction Mask: Click this button to open the Reader
Layout Well Restriction Mask. Check the boxes that correspond to the wells to be
excluded from use.
 Default Replicates: Use the up/down arrows to increase or decrease the number
of replicates (tubes used for each standard concentration) for this template. U.S.
Pharmacopeia requires a minimum of 2 replicates.
 Apply to All Replicates: Click this button to enable the Default Replicates setting.
 Consumables & Equipment: This is a list of all commonly used consumable and
equipment products, populated from the items added. Use the arrow box to
move up and down the list. To add items, lick the plus sign.
 On the Standards tab, click the plus sign to add a standard curve, shown in Figure
108. Complete the information as described below and click Save when finished.
 Negative Control: Check this box if using a negative control.
 Replicates: Use the arrows to enter the number of replicates for the negative
control.
 Positive Control: Check this box if using a positive control.
 Replicates: Use the arrows to enter the number of replicates for the standard
curve.

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  Concentrations: Click the calculator icon to enter values for Concentration,
Highest Concentrations and Dilution Factor.

Standard
Curve 1

Figure 108. FreeForm Template, Standard Tab

Note: To remove a standard curve, select it and click on the minus sign.
3. On the Samples tab, click the plus sign to add a product (see Figure 109). Note that all
products from the Library will appear in the Product Name dropdown list. There are no
restrictions on what products may be added to a FreeForm assay.

Figure 109. FreeForm Template, Samples Tab

4. Click the Layout tab to set up the following information:
 Replicate Direction: Select Horizontal to read the wells horizontally or Vertical to
read the wells vertically.
 Fill Direction: Select Vertical or Horizontal. The wells on a plate can be filled from
left to right (horizontally) or from top to bottom (vertically).

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  PPC Insert: Select Inline to place the PPCs underneath the replicates. Choose
Adjacent to place the PPCs beside the replicates.
 Concentration / Dilution: Select Ascend to place the standard concentrations in
ascending order. Select Descend to place the standard concentrations in
descending order.
 Type / Starting Well: The placement of each tube on the plate can be fine-tuned
by various methods. In the Type column, highlight the item to relocate:
o Select Auto Layout to return the item to its default location on the tube/plate.
o Select a specific coordinate (A1, A2, etc.) to move the item to that location.
o Drag and drop individual wells or groups of wells to an empty area.
5. When finished setting up the test parameters, click Run. The Pre-Collection Test screen
opens as shown in Figure 110. To expand the view of the right side of the screen, click
Zoom In. Click Zoom Out to return to the view as shown below.

Figure 110. Pre-Collection Screen

6. There are four tabs on the Pre-Collection Test screen: General, Consumables &
Equipment, Comments and Standards. On the General tab:
 If Auto Naming is not enabled on the Options tab, the test must be named in the
Test Name field. If Auto Naming is enabled, the software will generate a name.
The default name generated is the test ID suffixed by the date and time of the
test.
 Select the Instrument from the dropdown menu.
 The Template and Method fields auto-populate from the template.
 Select the Reagent Lot, Standard Lot, Buffer Lot and Water Lot from the
dropdown menus.

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  To add products, click the plus sign icon. Once a product is selected, the Product
Name popup appears as shown in Figure 111. Complete the information as shown
below and click OK when finished. Click Cancel to return to the Pre-Collection
Test screen.

Figure 111. Product Name Popup

 Product Name/Lot #: Enter a name and lot # for the product.
 Samples: Enter the number of products to test.
 Replicates: Use the arrows to increase or decrease the number of replicates of
the product.
 PPC: Check this box to have a PPC present for the product.
 PPC/Sample: Check this box to run a PPC on every dilution of the product.
Uncheck the box to run the PPC on the last product of the set.
 PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for
this product.
 Standard Curve Index: Enter the standard curve being used.
On the Consumables & Equipment tab, ensure that all of the equipment is correct.
Equipment can be added by clicking the plus sign. See Adding Consumables and
Equipment to a Template.
On the Comments tab, a general comment about the test can be added.
On the Standards tab, check that the information that populated from the template is
correct.
7. Click Collect. The test begins to run and the Run Collection screen appears as shown in
Figure 112. While the test runs, the active well changes color as tubes are added to the
reader. There are several options for viewing the test and editing test parameters (see
Table 3).

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 Figure 112. Run Collection Screen
Icon Function
View report while test is running. Note that the test cannot be electronically
signed until the test has completed running. For more information, see
Reports.
Print the mask layout.

Edit calculation requirements.

View average temperature of the reader.

View how long the test has been running and its status.

Change Settings (see Step 7 below).

View graph of wells on a single plot.

View graph of wells on different graphs.

Switch between list view and reader layout view.

Toggle between select series and select single mode.

Remove Remove an individual well from the graph.

Remove All Remove all data points from the graph.
Table 3. Icons on the Run Collection Window

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 8. To edit calculation parameters, click the Settings icon. The Calculations Parameters
window appears as shown in Figure 113. Enter changes in this window. Click OK when
finished or Cancel to return to the Run Collection screen.

Figure 113. Calculation Parameters Window

Note: If the Administrator has checked the Require Reason for Change box in the User
Management tab, text must be entered in the Reason text box.
9. When the test has run for a sufficient amount of time, such that all products have run at
least as long as the lowest standard, data collection may be stopped by clicking the End
Collect button. This will close the assay. Clicking Results in the toolbar reopens the
assay.
Note: Prematurely ending an assay may render it invalid.
10. The End Collect popup appears. Click Yes to end the test. To return to the Runtime
screen, click No. If a maximum test time or Auto End option has been applied, let the
assay run until it auto-terminates.
11. Once the test ends, the Collection Complete window appears. Click Analyze to view the
Post-Analysis Run screen (Figure 114) or click Report to generate a report. See Reports
for more information.

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 Figure 114. Post-Analysis Run Screen
Using the icons at the top of the screen, the following actions may be performed:
Icon Function
Print the reader layout.

Add products to the test.

Remove products from the test,

Mask a well (a masked well will not be used in any calculations).

Unmask a well.

Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Switch between select series and select single mode.

Edit assay settings, including renaming the test and re-graphing

products.
Table 4. Icons on the Post-Analysis Window

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7 Data Collection
This section reviews the data collection process in tube reader and plate reader environments. This
section explains how to:
 Edit assay parameters
 Add products to an assay
 View graphical data while an assay is running

7.1 Data Collection on a Tube Reader

1. In Pyros® eXpress, open the Test Template to be run.
2. Click Run at the bottom of the screen to open the Pre-Collection Test screen (Figure
115).
3. Click Collect. The Run Collection screen opens (Figure 116). Add tubes to the reader.
The tube layout map changes color as tubes are added. Insertion of the first tube or
plate or well triggers the start of data collection.
Note: Each well is individually timed, so tubes can be continually added to the reader until
all available wells are full.

Figure 115. Pre-Collection Test Screen

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 The assay run-time and instrument temperature are displayed and updated on this screen.

Instrument temperature
Assay run time
Current test
status

Figure 116. Run Collection Window Example, List View Mode

Figure 116 shows the Run Collection window in list view mode. It indicates that the first 4
tubes were inserted to begin the test, the software is collecting data and that 10 minutes has
elapsed in the test.
Figure 117 shows the Run Collection window in reader layout mode. It indicates that there
are 16 tubes and that the test has run for 14 minutes.

Edit calculations
Change
settings

Figure 117. Run Collection Window Example, Reader Layout Mode

A close up view of the tubes showing how each type of tube added are color coded for easy
recognition of controls, standards or products is shown below.

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 Negative control is light blue

Positive control is purple

Standard curve is dark blue

Sample without spike is

orange with solid border Sample with spike is
orange with broken
border

7.1.1 Editing Parameters During Data Collection

1. Click the Edit Calculations icon at the top of the window as shown in Figure 117.
2. The Edit Calculation window opens. Edit the parameters as shown in Figure 118
and click OK when finished.

Figure 118. Calculation Parameters Window

Note: The changes made here are applied to the entire data set, whether it has
been collected or not.

7.1.2 Adding a Sample During Data Collection

1. Click the Change Settings icon on the far right of the Data Collection screen as
shown in Figure 117.
2. The Test Template opens as shown in Figure 119. Click the plus sign on the
Samples section of the window.
3. Fill in the fields as described below and click OK when finished.

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 Drug 1

Figure 119. Test Template Window

 Product Name and Lot#: Enter a product name and lot number for the
product.
 Samples: Use the arrows to add or decrease the products.
 Replicates: Use the plus sign to increase the number of replicates. Default
value is 2.
 PPC: Check this box to have a PPC present for the product.
 PPC/Sample: This box is checked by default. This will add a PPC after each
sample per product.
 PPC Concentration: Enter the required concentration for the PPC.
 PPC Replicates: Use the up/down arrows to enter a value of PPC replicates for
this product. This is usually the same as the number of replicates product
dilution replicates.
 Standard Curve Index: If there is more than one SC, choose the one to be
used.
 Preferred starting well number: (Default None.) Choose a well for the new
product from the dropdown. If None is chosen, the next available well will be
used.
4. After clicking OK, the software adds the product graphically to the reader and will
start collecting data once the corresponding well on the reader has a tube added
to it.
Note: The tubes may be added physically before defining the new product,
however the wells will appear red until they are defined (see Figure 121).

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 Undefined wells are red

7.2 Data Collection on a Plate Reader

Data Collection on a plate reader looks different than on a tube reader. Data collection
graphs look the same, however.
Note: Products cannot be physically added to a plate reader once the test has started
running. However, parameters may be edited while a test runs. See Editing Parameters
During Collection.
1. In Pyros® eXpress, open the Test Template to be run.
2. Add all of the products to the plate. Click Collect.
3. A reminder to insert a plate appears as shown below. Insert the plate and click
Done.

4. The Run Collection window appears as in Figure 120. The plate reader shakes for
10 seconds (or the value entered in the Pre-Incubate Shake setting in the
Method). See Adding Methods to the Library to view or edit this setting.
5. When the pre-incubation is finished, the following window appears. Click OK to
begin the pre-collection process.

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 6. Figure 120 shows the Run Collection window in reader layout mode. The status in
the upper left corner will read Incubate Shaking while the shake step occurs. At
this point, data collection has not started.

Figure 120. Run Collection Window, Reader Layout Mode

7. Figure 121 shows the Run Collection window in list mode. It indicates that the
software is collecting data and that the test has been running for 10 minutes.

Edit calculations
Current
test status

Figure 121. Run Collection Window, List Mode

Note: In either of these modes, the user may drag and drop to the right side of the window
to plot the data points graphically. For more information on viewing graphical data, see
Viewing Data Collection Graphs.
7.2.1 Editing Parameters During Data Collection
1. Click the Edit Calculations icon at the top of the window as shown in Figure 121.
2. The Edit Calculation window opens. Edit the parameters as shown in Figure 122
and click OK when finished.

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 Figure 122. Calculations Parameters Window
Note: The changes made here are applied to the entire data set, whether it has
been collected or not.

7.2.2 Changing Settings During Data Collection

1. Click the Change Settings icon on the far right of the Data Collection screen as
shown in Figure 121.
2. The Test Template opens as shown in Figure 123. From here, a user can:
 Rename the test
 Change Reagent Lots
 Add consumables and equipment
 Add a comment
3. When finished, click OK to return to the Test Collection screen.

Figure 123. Test Template Window

7.3 Viewing Data Collection Graphs
The software displays data collection graphs on the right side of the Run Collection window
for both plate readers and tube readers. To view products graphically, drag and drop tubes
and plate wells from both the List View and Reader Layout views. The maximum number of
curves displayed on each graph is 8.

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 The number beside each
colored dot represents the
well or tube position.

Standard curve graph

Standard
curve
grouping

Graph of the sample

Figure 124. Graphing Products, Reader Layout View

Figure 124 shows the wells that comprise the standard curve selected as a group. The entire
group can be selected and dragged to the graph area.
7.3.1 Individual Graphs and Single Graphs
A user can view the data plots for each well on a single graph as shown in Figure 125,
or each well can be viewed on its own graph as shown in Figure 126.

Figure 125. Graph of Wells on Single Plot

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 Figure 126. Graph of Wells on Different Graphs
7.3.2 List View Mode and Reader Layout Mode
There are two modes to view the wells:
 List View (Figure 127) allows a user to monitor the onset time of each product in
a table format. In Figure 127, products with a greater than sign (>) in the Onset
column have not yet reached onset. Products without a greater than sign in the
Onset column have reached onset, and the value in the column represents the
amount of time, in seconds, that it took the product to onset.
 Reader Layout (Figure 128) allows a user to view the mapping of wells. Empty
wells appear gray.

Figure 127. Run Collection Window, List View Mode

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 Figure 128. Run Collection Window, Reader Layout Mode
7.3.3 Removing Data Points from a Graph
To remove an individual well from a graph, select the well and click Remove. To
remove all data points, select the wells to remove and click Remove All. The table
below shows the icons on the upper right of this window.
Icon Function
View graph of wells on one graph.

View graph of wells on different graphs.

Toggle between list view and reader layout view.

Toggle between select series and select single mode.

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8 Reports
Pyros® eXpress stores test results in the form of a report in the database. This section explains how
to:
 View a report while a test is running
 View a report after a test has completed running

8.1 Viewing Reports

After a test has run to completion, Pyros® eXpress displays a window indicating that
collection is complete. To view the report, click Report at the bottom of the window.
To view test results at any other time:
1. Click Results in the toolbar. All tests that ran to completion, or that have been started,
will have a report listed.
2. A list of all reports in the database opens as shown in Figure 129. The most recent
report appears at the top. From this window :
Click column head to
reorder items

Filter
Search for
results by
report
these
parameters

Edit test
Drug 1

Double click parameters

on row to Drug 1

Open the
view report
report
Drug 2

Drug 3

Open Locked
Test

Figure 129. List of Reports

 Reorder the list by clicking on the column header.
 Filter the list by selecting any of the criteria shown in the dropdown menus and
clicking Search (Name, Type, Method, Reviewer, etc.)
 Click Analyze to edit some of the test parameters in the Test Template. Go to
Editing an Assay.
 Click Report to open the report for the test.
 Click Force Unlock Tests to unlock a test that has been locked by another user. A
user must have Administrator permissions to use the Force Unlock button. See
Unlocking an Assay for more information.

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 3. Once the name of the report is located:
 Double-click on the name of the report or highlight the name of the report and
click Report.
 Highlight the name of the report and click the Analyze button. This allows some
of the parameters used to run the test to be reviewed and edited. When finished,
click Run Analysis to return to the report.
4. The report opens in a new window as shown in Figure 130. There are several options on
the left side of the window described below.

Drug 1

Figure 130. Sample Report

 Standards: If a test has more than one product, it will be listed in the Standards
section with the option to use linear regression or polynomial regression to
calculate the standard curve.
 Products: This section lists the products tested.
 Edit Assay: Select this option to reposition tubes or wells, or correct any errors in
the Reagent Lot numbering. Go to Editing an Assay.
 Sign: Select to apply an electronic signature. Go to Signing a Report.
 Export to LIMS: Select this option to export the test results to an XML file. A Save
As window opens when this option is selected. See LIMS for more information.
 Save As: Select to save the report as a PDF file.
 Print: Select to print the test results.
 View Reader Layout: Select to display the reader layout used for this test.
 Data Collection Graph: Select this option to view the graphing of raw data plots.
The Post Data Collection Graph window opens as shown in Figure 131.
 Close: Select to close the report.

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 Toggle between View data points on single
select series and plot or multiple plots

Toggle
between list
view and
reader view

Figure 131. Post Data Collection Graph

5. In this window, a user can:
 Hover over each well or group of tubes or wells to view graphical data. Use the
icons in the upper right to change the views of the tubes/wells on the graph.
 Drag and drop a single tube or group of tubes or wells to the right side of the
screen to be plotted on a graph as shown in Figure 131. Click the Remove button
to remove a well or Remove All to remove all data points from the graph.
 Click the Print button to print the layout.

8.2 Editing an Assay

An assay may be edited if it has not been electronically signed. Editing takes place in the Test
Template window. This window allows a user to review the parameters that were used to
run the test; however, since the test has already run, a user will only be able to:
 Reposition tubes or wells
 Add or remove tubes/wells
 Add or remove consumables/equipment
 Add a comment
 Correct any typographical errors
1. To edit an assay click Edit Assay from the Report window. The Test Template opens as
shown in Figure 132.

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 Figure 132. Edit an Assay in the Test Template
2. In this window, a user can hover over a well or group of wells to view graphical results,
drag and drop well(s) that have been positioned in the wrong place, as well as select any
of the icons described in Table 4 to perform the action described:
Icon Function
Print the layout.

Add products to the test.

Remove selected products from the test.

Mask a well (a masked well will not be used for any calculations).

Unmask a well.

Reverse the order of dilutions.

Change settings of a particular well or group of wells.

Toggle between select series and select single mode.

Edit calculation parameters (see Step 3 below).

Table 4. Icons on the Post-Analysis Window

3. To fix an error in the Reagent Lots, click the Settings icon. The Calculation Parameters
window appears as shown in Figure 133. Once finished editing, click OK or click Cancel
to return to the report.

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 Figure 133. Calculation Parameters
4. Click Run Analysis to make edits to the report and return to the report. Any changes
made here will be reflected in the report.

8.3 Reading a Report

Each report contains results specific to the type of assay that was run. Most of the sections in
each report are common among all types of tests. These sections are listed and explained
below.
8.3.1 Report Summary

The Report Summary lists general test information: Test Name, the name of the
Technician who performed the test, the template and method used to run the test,
the temperature of the reader incubation chamber during the assay, Reagent Lot,
Water Lot, Standard Lot, Buffer Lot, Instrument Type and Wavelength, Serial
Number, Read Interval Time, Threshold mOD, Test Start Date and Time and
Completion Date and Time.
8.3.2 Standard Curve
The Standard Curve section displays the Slope, Y-Intercept and Correlation
Coefficient for the standard curve regression analysis. The software will not calculate
a regression line if a standard is improperly configured or if each standard has not
reached onset.
Before a test is signed, a user can toggle between viewing the polynomial regression
and linear regression analysis types. Figure 134 shows that a linear regression
analysis was used to calculate the standard curve. Figure 135 shows that a
polynomial regression analysis was used to calculate the standard curve.

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 The
correlation
coefficient of
-0.999 is
greater than
or equal to
|r| of 0.980

Figure 134. Standard Curve, Linear Regression

Figure 135. Standard Curve, Polynomial Regression

8.3.3 Standard Results
The Standard Results section presents the raw test results as displayed in Figure 136.

Figure 136. Standard Results

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 A description of the columns in this section appears below:
Title Description
Identifier Identifies the type of product.
Well Identifies the location of the product in the reader.
Concentration Concentration of the standard or positive control before
dilution (user entered value).
Reaction Time Onset time of each product.
Average Reaction Time Average onset time of all products tested.
CV Coefficient of Variation of the replicates of the products or
positive control.
Back Prediction Calculation of EU/mL from the standard curve.

8.3.4 Section 4: Standards Evaluation

The Standards Evaluation section provides an evaluation of the results in the
Standard Results section as shown in Figure 137.

Figure 137. Standards Evaluation

In order for a product to pass, the test must have valid controls and meet the user
specified criteria for a valid standard curve. Once this is confirmed, the results for
individual products are evaluated against criteria specified for the products
themselves. If all criteria for a valid test have been satisfied and the measured
endotoxin concentrations of all of the replicates of a product are less than the
Endotoxin Limit, the product is marked as PASS in the status column.
A description of the columns in this section appears below:
Title Description
Identifier Identifies the type of product.
Concentration Concentration of the standard or positive control before
dilution (user entered value).
Parameter Lists the parameter used (CV, Endotoxin, PPC Recovery). This
parameter is CV%.

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 Value The CV of this particular standard.
Specification The CV% value set in global settings.
Status PASS: The CV % is less than or equal to the user defined limit
set in global settings.
FAIL: The CV % exceeds the user defined limit set in global
settings.
PASS: PPC Recovery or Endotoxin meets specification set in
global settings.
FAIL: PPC Recovery or Endotoxin does not meet specification
set in the template.
Note Any information the user wishes to enter.

8.3.5 Graphical Analysis Parameters

The Graphical Analysis Parameters section provides the absolute value for the
correlation coefficient. In order for a sample in a test to receive a PASS in the status
column, it must meet the criteria set by the FDA Guideline which states that the
absolute value of the correlation coefficient must be greater than or equal to 0.980
for the range of endotoxin concentrations. Otherwise, the status column will report
FAIL.

8.3.6 Product Results and Product Sample Evaluation

This section of the report varies depending on the type of test that was run. An
example from a Routine Test is shown below.

A description of the columns in this section appears below:

Title Description
Identifier Identifies the type of product.
Well Identifies the location of the product in the reader.
Dilution Dilution employed to create the standard curve.
Reaction Time Onset time of each product.
CV Coefficient of Variation of the replicates of the products or
positive control.
Average Reaction Time Average onset time of all products tested.
Concentration Concentration of the standard or positive control before

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 dilution (user entered value).
Final Concentration Concentration of endotoxin in the sample multiplied by the
dilution factor to give the final endotoxin concentration of the
product.
Release Limit User defined endotoxin limit.

A description of the columns in this section appears below:

Title Description
Identifier Identifies the type of product.
Dil./Conc. User entered dilution value.
Parameter Lists the parameter used (CV, Endotoxin, PPC Recovery). This
parameter is CV%.
Result Concentration of endotoxin (pre-dilution).
Specification Endotoxin limit.
Status PASS: The CV % is less than or equal to the user defined limit
set in global settings.
FAIL: The CV % exceeds the user defined limit set in global
settings.
PASS: PPC Recovery or Endotoxin meets specification set in
global settings.
FAIL: PPC Recovery or Endotoxin does not meet specification
set in the template.
Note Any information the user wishes to enter.

8.3.7 Consumables and Equipment

Figure 138. Consumables and Equipment

The Consumables and Equipment section lists all of the consumables and equipment
used in the assay as shown in Figure 138.

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 8.3.8 Section 8: Log Summary

Figure 139. Log Summary

The Log Summary shown in Figure 139 includes significant events that occurred while
the test was running, such as the time that the assay began and completed and
whether any wells were remapped.

8.3.9 Section 9: Signatures

Sam Smith

Sam Smith

Figure 140. Signatures Window

The Signatures section as shown in Figure 140 includes the name of the test
performer and test reviewer. For more information on signatures, see Signing a
Report.

8.4 Signing a Report

The Sign option in the Report window allows a user with Approve reports with e-Signature
permission to sign-off and lock test analyses. Users without this permission will not see the
Sign button as an option in the Report window.
A user with Edit/Sign in place of another user permission may edit and sign a report on an
assay that was run by a different user, as shown in Figure 141.

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 Sam Smith

Test
performer
Sam Smith

Test
reviewer

Figure 141. Sign in Place of Another User

A user with both Edit/Sign in place of another user and Approve reports with e-Signature
permissions is able to remove a signature by clicking the Amend button on the report.
Clicking this button removes the signature and allows the test to be edited.
To electronically sign a report:
1. Open the report as described in Viewing Reports and click Sign.
2. In the popup window that appears, enter the user password and click Sign.

Sam Smith

Sam Smith

3. The user’s signature will appear on the last page of the report as shown in Figure
140.
Once a test has been signed, it will open in read only mode. In this mode, several buttons will
be disabled and edits to test parameters will not be possible. A user can, however, view plots
and print reports.

8.5 Specific Test Reports

8.5.1 Potency Test Report
A Potency Report can only be generated if multiple standard curves are present in
the test. The report is relevant when calculating the potency for control standard
endotoxin, using a reference standard endotoxin curve. Pyros® eXpress allows a user
to specify a single reference standard curve and up to 4 control standard curves. See
Figure 142 for an example of a Potency Test Report.

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 Figure 142. Potency Test Results
A description of the columns in this report appears below:
Title Description
Identifier Identifies the type of product.
Well Identifies the location of the product.
Concentration Concentration of the standard or positive control before
dilution (user entered value).
Reaction Time Onset time of each product.
CV Coefficient of Variation of the replicates of the samples or
positive control.
Average Reaction Time Average onset time of all products tested.
Found Concentration Is the endotoxin concentration found in the product.
Final Concentration Concentration of endotoxin in the product multiplied by the
dilution factor to give the final endotoxin concentration of the
product.

8.5.2 Reagent Verification Test Report

For reagent verification, a linear regression analysis must be used to calculate the
standard curve as shown in Figure 143. There is no option to run a polynomial result.

Figure 143. Reagent Verification Test Result, Standard Curve

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 8.5.3 I/E Test Report
When viewing an I/E Test result:
 In the Standards section, choose to view the graph with linear regression or
polynomial regression. There should be consistency in the regression analysis
chosen for I/E, Validation and Routine testing of a product (see Figure 144).
 In the Products section, check the boxes next to the product(s) to include in the
report.
8.5.3.1 Standard Curve

Drug 1

Drug 2

Figure 144. I/E Test Result, Standard Curve

8.5.3.2 Product Results

Figure 145. I/E Test Result, Product Results

In the Product Results section of an I/E Test, the name and lot number of each
product appears along the left side of the report.

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 Note: There will be as many samples as dilutions ran in the test.
Descriptions of the other columns appear in the table below.
Title Description
Identifier Identifies the type of product.
Well Identifies the location of the product.
Dilution Dilution employed to create the standard curve.
Reaction Time Onset time of each product.
CV Coefficient of Variation of the replicates of the samples or
positive control.
Average Reaction Time Average onset time of all products tested.
Concentration Concentration of the standard or positive control before
dilution (user entered value).
Final Concentration Concentration of endotoxin in the sample multiplied by the
dilution factor to give the final endotoxin concentration of the
product.
Release Limit User defined endotoxin limit.
8.5.3.3 I/E Evaluation
The I/E Evaluation section of the report indicates whether the product passed
or failed. Descriptions of the other columns appear in the table below.

Figure 146. I/E Test Result, Evaluation

Title Description
Identifier Identifies the type of product.
Dil./Conc. User entered dilution value.
Parameter Lists the parameter used (CV, Endotoxin, PPC Recovery).
Result Concentration of endotoxin (pre-dilution).
Specification Endotoxin limit.

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 Status PASS: The CV % is less than or equal to the user defined limit
set in global settings.
FAIL: The CV % exceeds the user defined limit set in global
settings.
PASS: PPC Recovery or Endotoxin meets specification set in
global settings.
FAIL: PPC Recovery or Endotoxin does not meet specification
set in the template.

8.6 Unlocking an Assay

Once a test is opened on one computer system, no other user will be able to open the same
test; thereby preventing scenarios where multiple users are attempting to setup, edit or
analyze the same test. To ensure data integrity, the software only allows a single user to
access a test at any given time.
If the computer fails for any reason, the test will continue to remain locked and no other user
will be able to open it. In the event that the sign-off status needs to be removed, a user with
Administrator permissions may unlock the test.
Users can unlock any test that they have locked. In addition, a user with Manage Permissions
can unlock any test.
Note: The Force Unlock feature should only be used if a user is sure that the previous
session is no longer in use.
To unlock an assay:
1. A user with Administrator rights can click Results in the toolbar to open the list of all
reports in the database.
2. Locate the locked assay and highlight it.
3. Click Force Unlock. Another window will open with the selected test listed, as shown
below.

Pjones

4. Highlight the test and click Unlock, then click Close.

5. The test is now unlocked.

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 9 Audit Trail
The Pyros® eXpress Audit Trail tracks changes made throughout the course of setting up, running,
analyzing and reporting tests. You can filter the contents of an Audit Trail Report to a desired date
range, user(s), instrument(s) and system(s).
To be Part 11 compliant, particular actions and events require a reason for change that the Audit
Trail will capture. The user must enter a reason when performing the following tasks if the System
Administrator has checked the Require Reason for Change box in the User Management tab:
 Editing calculation parameters while a test is running
 Moving tubes/plates
 Changing a test record

9.1 Accessing an Audit Trail Report

1. In the toolbar, click Settings and then Audit Trail.

2. The Audit Trail window opens with filtering options on the left side of the screen (Figure
147).
Settings

Filtering
Options

Figure 147. Audit Trail Window

3. The Audit Trail result appears on the right side of the window when filters are selected
and Search clicked. To view all events, leave the dates blank before clicking Search.

4. To filter the Audit Trail Report, enter information in the following fields:

 From/To: Enter a date range for the system to pull results from a certain period of
time (in days). From indicates the beginning date that information will be retrieved

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 from in the database. To indicates the last date for information to be included. Select
the date for each field by clicking the desired date on the popup calendar. The
selected date will be displayed in the field.
 Type: Select from the following categories:
Field Description
Assay Captures particular access or change events to a particular test ID that has been
run.
User Actions performed by each active user including login events, permission change,
workgroup change, password reset.
Workgroup Changes made to any workgroup.
Security Login information including successful and failed logins.
Template Library Changes made to the any template in the Library.
Product Library Items added, removed, retired or reinstated from the product Library.
Method Library Items added, removed, retired or reinstated from the method Library.
Supply Library Items added, removed, retired or reinstated from the supply Library.
Supply Type Changes made to supplies in the Library.
Global Settings Changes made to notifications, items created, automatic test naming, instrument
addition.
System Error Records any system errors.
Calibration Instances of calibration testing.

Calibration Additions/removals of calibration equipment.

Equipment
Resources Indicates that a test has been unlocked ("Unlock").
 User: Enter the exact username.
 Details: Enter any other details such as an event explanation (unsuccessful login,
tubes removed from well).
5. Click Search when finished or click Clear to start again. The Audit Trail Report appears as
shown in Figure 148. The sections of the report are described below.

Ssmith

Ssmith

Pjones

Ssmith

Ssmith Audit Trail

Pjones Report
Ssmith

Ssmith

Pjones

Ssmith

Ssmith

Ssmith

Ssmith

Figure 148: Audit Trail Report

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 Field Description
When Date and time of the event or action.
Event Type Type of event or action.
Details System-generated details of the event or action.
Who Initiator of event or action.
Target Name Who/what was affected by event (test name, template name, etc.).
Reason User entered reason for making the edit. This information is required if the
Administrator has checked the Require Reason for Change box in the User
Management tab.

6. From the Audit Trail Report screen:

 Click Clear to clear the filters but not the report. To get different results, perform
another search using different parameters.
 Click Save As to save the Audit Trail Report as a PDF file.
 Click Print to print the Audit Trail Report.
 Click Close to return to the Home page.
 Click Back to go to the Trending tab.
 Click Next to go to the Notifications tab.
Figure 149 shows an Audit Trail Report filtered by assay type. Figure 150 shows an Audit Trail
Report filtered by calibration.

Ssmith

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Sam Tech

Figure 149. Audit Trail Report Filtered by Assay

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 Figure 150. Audit Trail Report Filtered by Calibration
9.2 Viewing a Pre-Filtered Audit Trail Report
The Supply, Product, Methods and Template screens contain an Audit Trail button that
allows the Audit Trail Report to be viewed pre-filtered.
To view an Audit Trail Report filtered by:
 Product: go to Library > Products. Highlight a product and click Audit Trail (Figure 151).
 Supply: go to Library > Supplies. Highlight a supply and click Audit Trail (Figure 152).
 Method: go to Library > Methods. Highlight a method and click Audit Trail (Figure 153).
 Template: Go to Templates. Highlight a template and click Audit Trail (Figure 154).

Ssmith

Ssmith

Figure 151. Audit Trail Report Filtered by Product

Ssmith

Ssmith

Ssmith

Figure 152. Audit Trail Report Filtered by Supply

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 Figure 153. Audit Trail Report Filtered by Method

Ssmith

Figure 154. Audit Trail Report Filtered by Template

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10 Service
The Service tab provides access to preventative maintenance and diagnostic tests for the
Customer’s instrument. This screen is visible if the System Administrator has set a user with
permission to Manage Calibrations.
To access the tests available on the Service tab, click Settings from the Home screen and then
Service (see Figure 155).
Warning: Using these functions could compromise the calibration of the instrument. Consult the
Associates of Cape Cod, Inc. Technical Services team before using the Service function of the
software.

Settings

Figure 155. Service Tab

Before running any tests, setup the Calibration Equipment Library. This Library is where the
equipment needed for calibration purposes is setup, viewed and edited.

10.1 Setting Up the Calibration Equipment Library

1. From the Service tab, click the Calibration Equipment button at the bottom of the
Service tab as shown in Figure 156.

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 Figure 156. Service Tab
The Calibration Equipment window opens as shown in Figure 157.

Search for
equipment
by Type

Figure 157. Calibration Equipment Window

2. From the Calibration Equipment window, begin to setup the equipment to be used for
the calibration tests. To search for equipment that has already been setup, use the Type
dropdown menu and click Search. Click Clear to begin again.
10.1.1 Adding a Universal Absorbance Plate
1. From the Calibration Equipment window, click the Universal Absorbance Plate
button. The Edit/New Universal Absorbance Plate window opens as shown in
Figure 158.
2. Enter the information as described in the section Absorbance OD Standards
section. When finished, click Save or click Close to return to the Calibration
Equipment window.

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 Figure 158. Edit/New Universal Absorbance Plate Window
 Serial Number: Enter the serial number of the plate.
 Last Calibration Date: Enter the date of the last calibration, found on the
Certificate of Calibration for the instrument.
 Calibration Due Date: Enter the due date for the next calibration, found on
the Certificate of Calibration for the instrument.
 Absorbance OD Standards: Enter the Absorbance OD Standards information
from the Certificate of Calibration that comes with the plate. An example
appears below.

10.1.2 Adding a 340 nm Absorbance Plate

1. From the Calibration Equipment window, click the 340nm Absorbance Plate
button. The Edit/New Universal Absorbance Plate window opens as shown in
Figure 159.

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 2. Enter the information as described below. When finished, click Save. Or click
Close to return to the Calibration Equipment window.

Figure 159. Edit/New 340nm Absorbance Plate Window

 Serial Number: Enter the serial number of the plate.
 Last Calibration Date: Enter the date of the last calibration, found on the
Certificate of Calibration.
 Calibration Due Date: Enter the due date for the next calibration, found on
the Certificate of Calibration.
 Absorbance OD Standards: Enter the information from the Certificate of
Calibration that comes with the plate. An example appears below.

10.1.3 Adding a Stepped Neutral Density Plate

1. From the Calibration Equipment window, click the Stepped Neutral Density Plate
button. The Edit/New Stepped Neutral Density Plate window opens as shown in
Figure 160.
2. Enter the information as described below. When finished, click Save or click Close
to return to the Calibration Equipment window.

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 Figure 160. Edit/New Stepped Neutrality Density Plate Window
 Serial Number: Enter the serial number of the plate.
 Last Calibration Date: Enter the date of the last calibration, found on the
Certificate of Calibration.
 Calibration Due Date: Enter the due date for the next calibration, found on
the Certificate of Calibration.
 405nm Slope: Enter the 405 nm slope data as shown on the Stepped Neutral
Density Plate Factory Acceptance Certificate. An example appears below.
 340nm Slope: Enter the 340 nm slope data as shown on the Stepped Neutral
Density Plate Factory Acceptance Certificate. An example appears below.

10.1.4 Adding a Temperature Probe

1. From the Calibration Equipment window, click the Adding a Temperature Probe
button. The Edit/New Temperature Probe window opens as shown in Figure 161.
2. Enter the information as described below. When finished, click Save or click Close
to return to the Calibration Equipment window.

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 Figure 161. Edit/New Temperature Probe Window
 Serial Number: Enter the serial number of the plate.
 Last Calibration Date: Enter the date of the last calibration, found on the
Certificate of Calibration.
 Calibration Due Date: Enter the due date for the next calibration, found on
the Certificate of Calibration.

10.1.5 Adding a Hygrometer

1. From the Calibration Equipment window, click the Adding a Hygrometer button.
The Edit/New Hygrometer window opens as shown in Figure 162.
2. Enter the information as described below. When finished, click Save or click Close
to return to the Calibration Equipment window.

Figure 162. Edit/New Hygrometer Window

 Serial Number: Enter the serial number of the plate.
 Last Calibration Date: Enter the date of the last calibration, found on the
Certificate of Calibration.
 Calibration Due Date: Enter the due date for the next calibration, found on
the Certificate of Calibration.

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 10.1.6 Retiring Equipment in the Equipment Calibration Library
Retiring equipment removes the equipment from the Library, but does not delete it
from the database. A retired item will not populate in any dropdown lists.
1. From the Calibration Equipment window (Figure 157), highlight the equipment to
retire and click the Retire button at the bottom of the screen.
2. The equipment will be removed from the list.

10.1.7 Reinstating Equipment in the Equipment Calibration Library

1. From the Calibration Equipment window (Figure 157), select the equipment to
reinstate from the Type dropdown menu.
2. Check the Retired box.
3. Click Search.
4. A list of retired equipment appears. Select the equipment to reinstate and click
Unretire.
5. The equipment will be added back to the Library.

10.1.8 Editing Equipment in the Equipment Calibration Library

1. From the Calibration Equipment window (Figure 157), double-click on the
equipment to edit.
2. The equipment’s particular parameters will open in a new window. For details on
the parameters in these windows, refer to the sections mentioned below. Click
Save when finished editing.
 To edit a Universal Absorbance Plate, see Adding a Universal Absorbance
Plate.
 To edit a 340 nm Absorbance Plate, see Adding a 340 nm Absorbance Plate.
 To edit a Stepped Neutral Density Plate, see Adding a Stepped Neutral Density
Plate.
 To edit a Temperature Probe, see Adding a Temperature Probe.
 To edit a Hygrometer, see Adding a Hygrometer.

10.2 ELx808™ System Test

The ELx808™ System Test conducts a series of tests at each wavelength defined in the filter
table to confirm adequate light levels, low electronic noise, adequate photodiode sensitivity,
overall system cleanliness and (if equipped), proper function of the incubator. The testing is
designed to verify that the ELx808™ will give in-specification performance for each set
wavelength over the specified OD range.
Prerequisite: The instrument must be set up in the Library.
1. On the Service tab, click the ELx808™ System Test icon. The System Test Run
screen opens as shown in Figure 164. A description of the options available on
this screen appears below.

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 Figure 164. System Test Run Screen
 Instrument: Select the instrument to test from the dropdown menu.
 Back: Click to return to the Service tab.
 Calibration History: Click to view all of the system tests that have been run in
this workgroup.
 Start: Click to start the test.
 Calibration Equipment: Click to view all of the calibration equipment required
by the Service tab. To setup equipment, go to Setting Up the Calibration
Equipment Library.
2. Select the instrument from the dropdown menu. All available ELx808™ readers
will appear. Select the instrument to run the test on and click Start.

3. The reader begins the test. The system generates a report when the test has
completed running. The report appears automatically when the test has finished
running (see Figure 165).

4. Select Save As to save the report as a PDF file, Print to print the report, Export to
export the report as an XML file or Close to close the report and return to the
Service tab.

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 Figure 165. ELx808™ System Test Report
10.3 ELx808™ Universal Absorbance Test
This test uses the BioTek™ Absorbance Test Plate to confirm the mechanical alignment,
accuracy and linearity, repeatability and channel-to-channel uniformity of the ELx808™. The
Absorbance Plate Test compares the reader's optical density measurements and mechanical
alignment to NIST-traceable values.
Prerequisite: The test plate must be setup in the equipment Library.
1. From the Service tab, click the ELx808 Universal Absorbance Test icon. The System Test
Run screen opens as shown in Figure 166. A description of the options available on this
screen appears below.

Figure 166. ELx808™ Universal Absorbance Test Screen

 Instrument: Select the serial number of the instrument.
 Equipment: Select the serial number of the Universal Test Plate.
 Wavelengths: Select the appropriate wavelengths. Note that the wavelength has to
be on the Certificate of Analysis as well as the reader.
Note: A 340 nm cannot be run on the Universal Test Plate. If not using 340 nm as part of
routine testing, consider using a separate test plate specifically for use at 340 nm.

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 2. Add the plate to the reader and click Start.
3. When prompted, rotate the plate 180 degrees and click OK.
4. The report appears when the test has finished running (see Figure 167). A record of this
test and report will be added to the Calibration History.
5. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

Figure 167. Universal Absorbance Test Report

10.4 ELx808™ 340 nm Absorbance Test

Prerequisite: The test plate must be setup in the equipment Library.
1. From the Service tab, click the ELx808 340 nm Absorbance Test icon. The 340 nm
Absorbance Test screen opens as shown in Figure 168. A description of the options
available on this screen appears below.
2. Add the plate to the reader and click Start.

Figure 168. ELx808™ 340nm Absorbance Test Screen

 Instrument: Select the serial number of the instrument.

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  Equipment: Select the serial number of the Universal Test Plate.
3. When prompted, rotate the plate 180 degrees and click OK.
4. The report appears when the test has finished running (see Figure 169). A record of this
test and report will be added to the Calibration History.
5. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

Figure 169. ELx808™ 340nm Absorbance Test Report

10.5 ELx808™ Stepped Neutral Density Test

Prerequisite: The test plate must be setup in the equipment Library. The reader must have a
405 nm or a 340 nm filter.
1. From the Service tab, click the ELx808 Stepped Neutral Density Test icon. The Stepped
Neutral Density Test screen opens as shown in Figure 170. A description of the options
available on this screen appears below.

Figure 170. ELx808™ Stepped Neutrality Density Test Screen

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  Instrument: Select the serial number of the instrument.
 Equipment: Select the serial number of the Universal Test Plate.
 Select Wavelengths: Select the wavelengths to be tested.
2. Add the plate to the reader with the serial number facing up and the least dense filter to
the left.
3. Click Start.
4. The report appears when the test has finished running (see Figure 171). A record of this
test and report will be added to the Calibration History.
5. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

Figure 171. ELx808™ Stepped Neutrality Density Test Report

10.6 ELx808™ Empty Carriage Test

Prerequisite: The reader carriage must be empty. Remove any plates before running this
test.
1. From the Service tab, click the ELx808 Empty Carriage Test icon. The ELx808™ Empty
Carriage Test screen opens as shown in Figure 172. A description of the options
available on this screen appears below.

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 Figure 172. ELx808™ Empty Carriage Test Screen
 Instrument: Select the instrument.
 Wavelengths: Once the instrument is selected, the wavelength dropdown will
populate with available options.
2. Click Start.
3. The report appears when the test has finished running (see Figure 173). A record of this
test and report will be added to the Calibration History.
4. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

Figure 173. ELx808™ Empty Carriage Test Report

10.7 ELx808™ Shaker Test
1. From the Service tab, click the ELx808 Shaker Test icon. The ELx808™ Shaker Test screen
opens as shown in Figure 174.

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 Figure 174. ELx808™ Shaker Test Screen
2. Select the instrument and click Start.
3. Ensure that three distinct shake speeds can be heard: slow, medium, and fast. The
software will show the progression of the test with messages such as the one in Figure
175:

Figure 175. Test in Progress Message

10.8 PKFlex Baseline Test

This test provides the baseline readings at 405 nm and 660 nm wavelengths.
1. From the Service tab, click the PKFlex Baseline Test icon. The PKFlex Baseline Test
window opens as shown in Figure 176. A description of the options available on this
screen appears below.

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 Figure 176. PKFlex Baseline Test Window

 Instrument: Select the instrument.

 Test time: Defaults to 1800 seconds.
 Select Wavelength: This will populate once an instrument has been selected.
2. Click Start. A report will be generated when the test is complete (see Figure 177). A
record of this test and report will be added to the Calibration History.
3. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

Figure 177. PKFlex Baseline Test Report

10.9 PKFlex A/D Test

Prerequisite: Add at least 200µL of water to every tube in the reader.
1. From the Service tab, click the PKFlex A/D Test icon. The PKFlex A/D Test screen opens
as shown in Figure 178. A description of the options on this screen appears below.

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 Figure 178. PKFlex A/D Test Screen
 Instrument: Select the instrument.
 Select Wavelengths: Once the instrument is selected, the wavelength dropdown will
populate with available options.
 Test Variant: Select test option: Tubes Present, Tubes Absent or Both.
 Test Type: Select the test type: As Found, As Left.
2. Click Start.
3. At the prompt, fill the instrument with the tubes and click OK. (Depending on the test
choices, a prompt may appear to empty the instrument. If so, click OK to continue.)
4. The following information appears when the test has finished running the initial phase
(see Figure 179).

Figure 179. PKFlex A/D As Found Report

5. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.
6. Click Finish to terminate the test or click Next Step to continue to the next part of the
test, As Left.

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 7. Follow the prompts to add or remove instruments and click OK if continuing the test.
The test will generate a final As Found Report shown in Figure 180.

Figure 180. PKFlex A/D As Found Report

10.10 PKFlex A/D Calibration
This test should only be accessed by Associates of Cape Cod Inc. Technicians.

10.11 PKFlex Manual Temperature Record

1. From the Service tab, click the PKFlex Manual Temperature Record icon. The PKFlex
Manual Temperature Record screen opens. From here, select the reader and click Start.
The Temperature Record window appears as shown in Figure 181.

Figure 181. Temperature Record Window

2. Record the As Found temperature readings and the As Left temperatures on their
respective tabs. Click Done.
3. The report appears when the test has finished running (see Figure 182). A record of this
test and report will be added to the Calibration History.
4. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

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 Figure 182. PKFlex Manual Temperature Record Test Report
10.12 PKFlex Manual Temperature Adjustment
This test should only be accessed by Associates of Cape Cod, Inc. Technicians.

10.13 PKFlex Transmitted Temperature Test

This test captures the transmitted temperature from the reader.
From the Service tab, click the PKFlex Transmitted Temperature Test icon and click Start.
The PKFlex Transmitted Temperature Test in Progress screen appears briefly as the system
takes the measurement (see Figure 183).

Figure 183. PKFlex Transmitted Temperature Test

1. The report appears when the test has finished running (see Figure 184). A record of this
test and report will be added to the Calibration History.
2. Select Save As to save the report as a PDF file, Print to print the report, Export to export
the report as an XML file or Close to close the report and return to the Service tab.

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 Figure 184. PKFlex Transmitted Temperature Test Report

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11 Trending
Trending allows data such as product types, LAL lots, temperature and analyst performance over a
span of time to be analyzed. Trending data can be filtered over the multiple tests that are stored in
the Pyros® eXpress database. Filters can be applied to view valid test results or results that did not
meet designated acceptance criteria or required test specifications.
Trending provides a tool to identify and analyze out of specification results. For example, a trend
can indicate a problem such as interference in an assay or that a product is failing to meet a
required specification.

11.1 Permissions Required to Run Trending Report

Trending is accessible to any user who has permissions to run assays. Any test that has been
run will appear in the Trending Report.
Note: For trending data to pull results from the database, it is important to name products
and supplies in their respective Libraries consistently.
Attempting to trend over a long period of time or an extensive data set may result in a
time delay for the data to be retrieved.

11.2 Product Trending

Use the Product Trending option to analyze trends in replicates of a product. When searching
for product trends, the following three data sets can be viewed:
 Product Result
 PPC Recovery
 Product CV
To view product trending data:
1. From the Home screen, click the Settings icon and then Trending.
2. An empty Trending window opens as shown in Figure 185.

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 Select
Product Export
Trending or trending
Standard data to CSV
Trending

Rearrange
Add filters column
headers

Click and drag a

corner of
the graphing
pane to resize

View graph
results in a new
window
Select Product Trending
or Standard Trending Figure 185. Trending Window (empty)
3. Select the Product Trending radio button.
4. Choose the data set to view. One data set can be viewed at a time. Select:
 Product Result to view the amount of endotoxin in all products.
 PPC Recovery to view all PPCs that have been run.
 Product CV to view all product CVs that have been calculated.
5. For additional filters select:
 Global Filters to view results that meet the global requirements set for R-value, Max
CV and Negative Control separation. Uncheck the box to show every test result,
including results that failed to meet the global requirements.
 Use workgroup settings to view results based on the settings in a specific
workgroup, found on the Options tab (%CV and NC Separation) and Reports tab (R-
value). Uncheck this box to edit these values before searching.
 Export to CSV file to export and save the results to a CSV file.
6. To add a filter group, click the folder plus sign icon. A filter group allows filtering by a
combination of filters. For example filter by 2 analysts as shown in Figure 189.
7. To add a filter, click the plus sign. A series of dropdown menus appears. Select options
as shown below:

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 8. Continue to add or remove filters by clicking the plus or minus sign. When finished
making selections, click Submit to update the list of filters. Click Clear to empty the
database and remove all filters and start again.
Note: For multiple filter groups, the software will apply the first one listed once Submit is
clicked. Use the up arrow to move an individual filter to a filter group above it in the list.
9. After clicking Submit, a graph of the search results appears on the right side of the
window, and a Trending Report will appear on the bottom of the window.
 To view a different data set, select the appropriate options as described in Steps 4-6
and click Submit (see Figures 186-188).
 To view a results graph in its own window, click the graph icon. The graph will open
in a new window as shown in Figure 190.
 To rearrange the order of the default column headers of the Trending Report, select
and drag a header to a new location. The preferences will reset when the software is
closed and the user logs back in.
 For information about the contents of the Trending Report, see Table 5.

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 Each data
point
represents a
product
endotoxin
result

View graph
results in a
new window
Rearrange
Drug 1
column
headers

Click and
drag pane to
resize

Figure 186. Product Trending Displaying Product Result

Each data point
represents a
product PPC

Each date
represents a
test

Drug 1

Figure 187. Product Trending Displaying PPC Recovery

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 Each data point
represents a
sample CV

Figure 188. Product Trending Displaying Product CV

Drug 1

Drug 2

Figure 189. Results of Using a Filter Group (2 Analysts)

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 Figure 190. Product Trending Graph
10. From the graph window, select:
 Close to close the graph to return to the Trending window.
 Show Grid Line to show the graph with grid lines.
 Print icon to print the graph.
 Go to refresh the graph data.
11.2.1 Filtered Product Trending Results
Table 5 explains the contents of a Product Trending Report.
Field Description
Run Date The date the test was executed.
Analyst ID The name of the analyst who ran the test.
Test Name The name of the test.
Test Type The type of test.
Reagent Lot The Reagent Lot that was used for the test.
Standard Lot The Standard Lot that was used for the test.
Buffer Lot The Buffer Lot that was used for the test.
Water Lot The Water Lot that was used for the test.
Reader Serial Number The serial number of the reader that was used for the test.
Product Name The name of the product.
Product Lot The lot number of the product.
Dilution The dilution of the product.
Product Result The amount of endotoxin measured.
Units The units of measurement.
Product Status Indicates whether the product passed, failed or was invalid.
PPC Recovery The percent PPC Recovery of the product.
PPC Value The PPC value of the product.
CV The CV of the product.

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 Correlation Coefficient The correlation coefficient of the standard curve.
Negative Control The Percentage of Onset time of lowest standard that is added to show clear
Separation (%) separation from the lowest standard.
Min. Temperature The lowest temperature of the reader incubation chamber during the assay.
Max. Temperature The highest temperature of the reader incubation chamber during the assay.
Identifier Identifies the type of product.

Table 5. Product Trending Report Results

11.3 Standard Trending

Use the Standard Trending option to analyze the replicates of the standard curve. When
searching for standard trends, one of the following data sets can be viewed:
 Correlation Coefficient
 Standard CV
To view standard trending data:
1. From the Home screen, click the Settings icon and then Trending.
2. An empty Trending window opens as shown in Figure 185.
3. Select the Standard Trending radio button.
4. Choose the data set to view. One data set can be viewed at a time. Select:
 Correlation Coefficient to view the correlation coefficient of the curve.
 Standard CV to view the Standard CV included in the curve.
5. For additional filters, select:
 Global Filters to view results that meet the global requirements set for R-value, Max
CV and Negative Control separation. Uncheck the box to show every test result,
including results that failed to meet the global requirements.
 Use workgroup settings to view results based on the settings in a specific
workgroup, found on the Options tab (%CV and NC Separation) and Reports tab (R-
value). Uncheck this box to edit these values before searching.
 Export to CSV file to export and save the results to a CSV file.
6. To add a filter group, click the folder plus sign icon. A filter group allows filtering by a
combination of filters. For example, filter by 2 analysts as shown in Figure 189.
7. To add a filter, click the plus sign. A series of dropdown menus appears. Select options
as shown below.

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 8. Continue to add or remove filters by clicking the plus or minus sign. When finished
making selections, click Submit to update the list of filters. Click Clear to empty the
database and remove all filters and start again.
Note: For multiple filter groups, the software will apply the first one listed once Submit is
clicked. Use the up arrow to move an individual filter to a filter group above it in the list.
 Click Clear to empty the database and remove all filters.
9. After clicking Submit, a graph of the search results appears on the right side of the
window, and a Trending Report will appear on the bottom of the window.
 To view a different data set, select the appropriate options as described in Steps 4-6
and click Submit (see Figures 191 and 192).
 To view a results graph in its own window, click the graph icon. The graph will open
in a new window as shown in Figure 190.
 To rearrange the order of the default column headers of the Trending Report, select
and drag a header to a new location. The preferences will reset when the software is
closed and the user logs back in.
 For information about the contents of the Trending Report, see Table 6.
10. From the Graph window, select:
 Close to close the graph to return to the Trending window.
 Show Grid Line to show the graph with grid lines.
 Print icon to print the graph.
 Go to refresh the graph data.

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 Each data
point
represents a
correlation
coefficient

Each date
represents a
test

Click to
view the
graph in a
new
window

Figure 191. Standard Trending Showing Correlation Coefficient

Each data
point
represents
the CV of a
standard

Figure 192. Standard Trending Showing Standard CV

11.3.1 Filtered Standard Trending Results

Table 6 explains the content of a Standard Trending Report.
Field Description
Run Date The date the test was executed.
Analyst ID The name of the analyst who ran the test.
Test Name The name of the test.
Test Type The type of test.
Reagent Lot The Reagent Lot that was used for the test.
Standard Lot The Standard Lot that was used for the test.
Buffer Lot The Buffer Lot that was used for the test.
Water Lot The Water Lot that was used for the test.
Reader Serial Number The serial number of the reader that was used for the test.

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 166
 Correlation Coefficient The correlation coefficient of the product.
Concentration Concentration of the standard or positive control before dilution (user entered
value).
Standard CV Coefficient of Variation of the replicates of the standard concentration.
Average Reaction Time Average onset time of all products tested.
Negative Control The Percentage of Onset time of lowest standard that is added to show clear
Separation (%) separation from the lowest standard.
Slope The Slope for the standard curve regression analysis.
Y-Intercept The Y-Intercept for the standard curve regression analysis.
Identifier Identifies the type of product.

Table 6. Standard Trending Report Results

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12 LIMS
Assay results can be exported to a LIMS (Laboratory Information Management System) as an XML
file.
Note: To export assay results to a LIMS, Pyros® eXpress users must be assigned the Export to
LIMS permission by the System Administrator. To assign this permission, or to view permissions,
see Administering User Accounts and Permissions.
1. Click Results in the toolbar.
2. A list of all reports in the database opens with the most recent report at the top. Locate
the name of the report to export results. The list can be filtered by selecting criteria
shown in the dropdown menus and clicking Search:
 Name
 Type
 Method
 Product
 From/To Date
 Technician
 Signature
3. To open the report, double-click or highlight it and click the Report button. The report
opens in a new window as shown in Figure 193.

Drug 1

Figure 193. Sample Report

4. Click the Export to LIMS button highlighted in Figure 193.
5. A Windows Save As window opens as shown in Figure 194. Navigate to the appropriate
folder, name the file and click Save.

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 Figure 194. Save As Window
For more information on the contents of the LIMS XML file, contact the Technical Services
department of Associates of Cape Cod, Inc. via telephone or email at
[email protected].

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 169
13 Troubleshooting
Note: For technical assistance, contact the Technical Services department of Associates of Cape
Cod, Inc. via telephone at (800) 848-3248 / (508) 540-3444 or email at
[email protected].

13.1 Tube Reader

Warning: Canned air should NEVER be used to remove debris from a tube well in a Pyros
Kinetix Flex tube reader, as it will likely cause debris to become lodged within the light
path. The well(s) may be vacuumed out using a micro-vacuum, available at computer or
electronics stores.
13.1.1 No Power
No power to LCD screen or LEDs adjacent to the wells.
 Check that the power cord is plugged into the power outlet.
 Confirm that the power switch is in the ON position.

13.1.2 Tube Reader Not Detected

Pyros® eXpress software fails to detect the tube reader.
 Confirm that the tube reader power switch is turned on with LCD screen and LEDs
lit.
 Check that the serial cable is plugged into the reader and serial connection on the
computer or if using a Serial to USB adapter, ensure that the USB is plugged in to
a USB port.
 Verify that the instrument is turned on and equilibrated at 37ᵒC (the LEDs next to
each well are red, not orange).
 Within the software, verify that the selected comport number matches the
comport number assigned in Device Manager. Reset the instrument. Turn off the
instrument, wait for 1 minute and turn it back on. After the instrument exits the
warming cycle, attempt to reconnect to the software. If an USB adapter is used,
verify that the drivers are installed on the computer.

13.1.3 Tubes Not Detected in the Software During Data Collection

Well LEDs turn green after reaction tubes are inserted in them but the software does
not recognize them.
 Wait for up to 10 seconds (one data cycle) to let the software refresh the data on
the screen.
 Check that the cable connections between the instrument and the computer are
secure.

13.1.4 Tube Detect issues

Well LEDs Green with No Tubes Inserted.
 A well switch may be stuck: using a fresh reaction tube, insert the tube in and out
a few times to release it.

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  A well switch may not be operating correctly. Contact Associates of Cape Cod, Inc.
to arrange for repair of the instrument.

Tubes inserted; LEDs Not Green.

 A well switch may be stuck: using a fresh reaction tube, insert the tube in and out
a few times to release it.
 A well switch may not be operating correctly. Contact Associates of Cape Cod, Inc.
to arrange for repair of the instrument.

13.1.5 Tubes Cannot be Inserted in Wells

 Inspect the well in question for debris or broken glass.
 The wells of Pyros® Kinetix Flex instruments are designed for 8x75 mm round-
bottom borosilicate tubes (TK100 in the ACC catalog). If the tube fits part way into
the well, but will not go all the way down, the tube may be deformed or
incorrectly sized. Attempt to insert a new tube gently.
 Contact Associates of Cape Cod, Inc. to arrange for repair of the instrument.

13.1.6 Inconsistent Results or Poor Replication

 Check that the outside surfaces of the reaction tubes and the vortex mixer used
to mix the products are clean and dry.
 Ensure tubes are pushed to the bottom of the well.
 Avoid excessive vortexing of the reaction tube prior to insert, as foaming may
cause inconsistent results.
 Avoid touching or bumping a previously inserted tube, as tube movement
subsequent to insertion may contribute to poor replication.

13.1.7 A/D Values Out of Range

A/D Values are out of range and either A/D High or A/D Low scenarios are observed.
 To view the system values set for A/D Min and A/D Max, check the global
settings: Click the Settings icon and select the Instrument tab.

If an A/D out of range error occurs, the time, in seconds and whether the value is too
low (L) or high (H) is recorded. When a problem occurs with the A/D values, it is
normally specific to one or several wells. This is not fatal to the entire run, but may
be fatal to data collection for the offending well(s). During the zeroing period (70 to
120 seconds for each well), if the mean A/D value is outside the acceptable range, a
Low or High A/D message will be received. Possible causes of low A/D value include:
1. Product too turbid: repeat the testing at a higher dilution (not exceeding the
MVD).
2. The reaction tube does not contain the required minimal volume of 200uL
(meniscus blocking light path). Repeat the testing of the well in question.
3. Reaction tube is scratched or dirty: repeat testing of the well in question.

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 4. LED intensity is low: Contact Associates of Cape Cod, Inc. to arrange for repair of
the instrument.

13.1.8 Temperature Out of Range

The temperature of the reader incubation chamber during the assay can be found in
the Report Summary section of a Results Report.
The Temperature Out of Range error is displayed.
For Pyros® Kinetix Flex instruments with more than one heating unit, each heating
unit will be listed on the report. Those in specification will exhibit an N for normal
temperature.
If a temperature out of range error is noted, a complete temperature calibration
should be performed. Contact Associates of Cape Cod, Inc. to arrange for calibration
of the instrument.
13.1.9 BioTek® ELx808™ Plate Reader
For BioTek® ELx808™ issues and error codes, refer to the Biotek® ELx808™ manual.

13.2 Pyros® eXpress

13.2.1 Software Not Accessing Database
Pyros® eXpress is not communicating with the SQL database during a remote
installation.
Ensure that the correct database connection string has been entered. Contact the IT
department to verify that the connection string being used is correct.

13.2.2 Login Failure

If Active Directory has been selected for a particular user, Pyros® eXpress will use
Windows to authenticate their username and password. If the Invalid User
Name/Password message displays when trying to log in, the user may become locked
out of the Windows account. The System Administrator may have a security policy in
place to lock accounts after a certain number of unsuccessful attempts.
If Active Directory authentication is not being used, the account will lock after 3
attempts. Wait 15 minutes before trying to log in again.

13.2.3 Password Not Working

If logging into Pyros eXpress using a Windows password, ensure that the
Administrator has checked the Active Directory box on the User Management tab.
To view specific settings on the User Management tab, go to Administering User
Accounts and Permissions and see Figure 10, the Add/Edit User window.

13.2.4 No Available Methods When Creating a Template

In order for a method to appear in the dropdown menu, at least one method must
be in the Library.

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 Follow the instructions in Adding Methods to the Library.

13.2.5 No Available Products When Running an I/E or Product Validation Assay

Products will not appear in any dropdown menus unless an I/E assay has been
performed and updated in the Library.
Follow the instructions in Completing I/E and Product Validation.

13.2.6 No Available Products When Running a Routine Assay

When running a routine assay, products will not appear in the dropdown menus
unless they have gone through Product Validation and I/E Testing.
To notify the software that a product has gone through Product Validation and I/E
Testing, follow the instructions in Completing I/E and Product Validation.

13.2.7 No Available Samples When Running an I/E Test

There must be a product in the Library that has not undergone an I/E assay. Products
that have already had an I/E will not appear in the dropdown menus in this template.
To add a product, follow the instructions in Adding Samples to the Library.

13.2.8 Library is Missing a Supply, Product or Method

If a supply, product or method cannot be located in the Library, it is possible that
another user has retired it and it is still in the database. This allows it to be
reinstated. To reinstate a missing supply, product or method, go to:
 Reinstating a Supply
 Reinstating a Product
 Reinstating a Method

13.2.9 You Cannot Perform Certain Actions

If a user is unable to perform tasks such as running assays, approving reports with an
e-signature, editing templates, products, methods, supplies or instruments, the
System Administrator may not have granted them permission to do so.
Check their permissions on the User tab:
 From the Home screen, click Settings to open the User Management tab.
 Click Manage Users.
 Find the username in the list and double-click it. A window will open that displays
their permissions. For a description of these, see Table 1, Global and Workgroup
Level Permissions.

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14 Pyros® eXpress and 21 CFR Part 11 Compliance
14.1 Overview of 21 CFR Part 11
The Food and Drug Administration’s (FDA) Part 11 (21 CFR Part 11) Electronic Records and
Signatures became effective in 1997. The regulation describes the steps that must be
followed to ensure electronic records, electronic signatures and handwritten signatures
executed to electronic records, are trustworthy, reliable and generally equivalent to paper
records and handwritten signatures executed on paper.
The scope of Part 11 includes all records in electronic form that are created, modified,
maintained, archived, retrieved or transmitted, under any record-related requirement
expressed in FDA regulations.
Software associated with computerized systems used in GxP, (cGMP, GLP, and GCP),
processes must be Part 11 compliant. However, no software by itself is capable of being
compliant; software can only be developed with the technical controls necessary for
compliance with Part 11. Pyros® eXpress was developed with these required technical
controls.
To ensure that software is compliant with Part 11, procedures and systems must be in place
to establish the required environment. In fact, approximately 50% of the elements of the
Part 11 regulation deal with procedures and systems an organization must have in place for
software to meet the requirements of Part 11.
One of the major requirements of Part 11 is that software must be validated to ensure
accuracy, reliability and consistent intended performance.
Another aspect of the software validation process is that endusers must validate the
software system in their operating environment. ACC has created a User Validation Protocol
specific to the Pyros® Kinetix Flex and the Biotek® Elx808™ readers to assist with this
requirement. To order a Pyros® eXpress User Validation Protocol, contact a local sales
representative or call the Customer Service department.

14.2 EU Annex 11
The European Union’s (EU) Annex 11 Rules Governing Medicinal Products in the European
Union, Volume 4, Good Manufacturing Practice (GMP), Medicinal Products for Human and
Veterinary Use) and 21 CFR Part 11 share the same intent. Namely, all computerized systems
used in GxP-regulated environments require compliance for ensuring integrity of records and
data.
In 2010, the Annex was revised in response to the increased use of computerized systems
and the increased complexity of these systems. Pyros® eXpress is capable of fully complying
with EU Annex 11.

14.2.1 Part 11 Functionality in Pyros® eXpress

Pyros® eXpress is capable of fully complying with 21 CFR Part 11. To ensure
compliance, customers should follow best practices to ensure that passwords are

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 174
 periodically revised and that particular actions made (listed below) are accounted
for:
To be Part 11 compliant, certain actions require a reason for change that the Audit
Trail will capture. Users must enter a reason when performing the following tasks if
the System Administrator has checked the Require Reason for Change box in the
User Management tab:
 Editing calculation parameters while a test is running
 Moving tubes/plates
 Changing a test record

14.2.2 Security Settings

When Pyros® eXpress has been installed, an Administrator will have access and rights
to enable 21 CFR Part 11 features. An Administrator can activate or modify 21 CFR
Part 11 features in the User Management settings. The event will be captured in the
Pyros® eXpress Audit Trail.

14.3 Meeting the Requirements of Part 11

The table below contains a listing of the elements of 21 CFR Part 11 and the method of
obtaining compliance: either through Pyros® eXpress, an enduser procedure or both.

21 CFR Part 11 Sub-part Part B Electronic Records

11.10 Controls for Closed Systems Methods of Compliance
a. Validation of systems to ensure accuracy, reliability, consistent The enduser must validate the
intended performance, and the ability to discern invalid or altered Pyros® eXpress software. For
records. assistance, a User Validation
Protocol is available from ACC.
b. The ability to generate accurate and complete copies of records in Feature of Pyros® eXpress
both human readable and electronic form suitable for inspection,
review, and copying by the agency.
c. Protection of records to enable their accurate and ready retrieval Feature of Pyros® eXpress
throughout the records retention period.
d. Limiting system access to authorized individuals. Feature of Pyros® eXpress
e. Use of secure, computer-generated, time-stamped audit trails to Feature of Pyros® eXpress and
independently record the date and time of operator entries and enduser procedure. Please see Audit
actions that create, modify, or delete electronic records. Record Trail for more information.
changes will not obscure previously recorded information. Such
audit trail documentation will be retained for a period at least as
long as that required for the subject electronic records and will be
available for agency review and copying.
f. Use of operational system checks to enforce permitted sequencing Feature of Pyros® eXpress
of steps and events, as appropriate.
g. Use of authority checks to ensure that only authorized individuals Feature of Pyros® eXpress and
can use the system, electronically sign a record, access the operation enduser procedure
or computer system input or output device, alter a record, or
perform the operation at hand.
h. Use of device (e.g., terminal) checks to determine, as appropriate, Feature of Pyros® eXpress
the validity of the source of data input or operational instruction.

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 175
i. Determination that persons who develop, maintain, or use Enduser procedure
electronic record/electronic signature systems have the education,
training, and experience to perform their assigned tasks.
j. The establishment of, and adherence to, written policies that hold Enduser procedure
individuals accountable and responsible for actions initiated under
their electronic signatures, in order to deter record and signature
falsification.
k. Use of appropriate controls over systems documentation, including: See below:
(1) Adequate controls over the distribution of, access to, and use of Enduser procedure
documentation for system operation and maintenance.

(2) Revision and change control procedures to maintain an audit Enduser procedure
trail that documents time-sequenced development and modification
of systems documentation

(3) Persons who use open systems to create, modify, maintain, or Not applicable. Pyros® eXpress
transmit electronic records will employ procedures and controls operates under a closed system.
designed to ensure the authenticity, integrity, and, as appropriate,
the confidentiality of electronic records from the point of their
creation to the point of their receipt. Such procedures and controls
will include those identified in Section 11.10, as appropriate and
additional measures such as document encryption and use of
appropriate digital signature standards to ensure, as necessary
under the circumstances, record authenticity, integrity, and
confidentiality.
11.50 Signatures and Manifestations Methods of Compliance
a. Signed electronic records will contain information associated with Feature of Pyros® eXpress
the signing that clearly indicates all of the following:
(1) The printed name of the signer;
(2) The date and time when the signature was executed; and
(3) The meaning (such as review, approval, responsibility, or
authorship) associated with the signature.
b. The items identified in paragraphs (a) (1), (a) (2), and (a) (3) of this Feature of Pyros® eXpress
section (11.50) will be subject to the same controls as for electronic
records and will be included as part of any human readable form of
the electronic record (such as electronic display or printout).
11.70 Signatures Linking Methods of Compliance
Electronic signatures and handwritten signatures executed to Feature of Pyros® eXpress and
electronic records will be linked to their respective electronic enduser procedure
records to ensure that the signatures cannot be excised, copied or
otherwise transferred to falsify an electronic record by ordinary
means.
21 CFR Part 11 Sub-part C Electronic Signatures
11.100 General Requirements Methods of Compliance
a. Each electronic signature will be unique to one individual and will Feature of Pyros® eXpress and
not be reused by, or reassigned to, anyone else. enduser procedure
b. Before an organization establishes, assigns, certifies, or otherwise Enduser procedure
sanctions an individual's electronic signature, the organization will
verify the identity of the individual.

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c. Persons using electronic signatures will, prior to or at the time of Enduser procedure
such use, certify to the agency that the electronic signatures in their
system, used on or after August 20, 1997, are intended to be the
legally binding equivalent of traditional handwritten signatures.

11.200 General Requirements Methods of Compliance

a. Electronic signatures that are not based on biometrics will: See below:
(1) Employ at least two distinct identification components such as an Feature of Pyros® eXpress
identification code and password.
(i) When an individual executes a series of signings during a single, Feature of Pyros® eXpress
continuous period of controlled system access, the first signing will
be executed using all electronic signature components; subsequent
signings will be executed using at least one electronic signature
component that is only executable by, and designed to be used only
by, the individual.
(ii) When an individual executes one or more signings not performed Feature of Pyros® eXpress
during a single, continuous period of controlled system access, each
signing will be executed using all of the electronic signature
components.
(2) Be used only by their genuine owners. Enduser procedure
(3) Be administered and executed to ensure that attempted use of Feature of Pyros® eXpress and
an individual's electronic signature by anyone other than its genuine enduser procedure
owner requires collaboration of two or more individuals.
b. Electronic signatures based upon biometrics will be designed to Not applicable. Pyros® eXpress does
ensure that they cannot be used by anyone other than their genuine not use electronic signatures based
owners. on biometrics.
11.300 Controls for identification codes / passwords Methods of Compliance

a. Maintaining the uniqueness of each combined identification code Feature of Pyros® eXpress and
and password, such that no two individuals have the same enduser procedure
combination of identification code and password.
b. Ensuring that identification code and password issuances are Feature of Pyros® eXpress and
periodically checked, recalled, or revised (e.g., to cover such events enduser procedure
as password aging).
c. Following loss management procedures to electronically de- Feature of Pyros® eXpress and
authorize lost, stolen, missing, or otherwise potentially enduser procedure
compromised tokens, cards, and other devices that bear or generate
identification code or password information, and to issue temporary
or permanent replacements using suitable, rigorous controls.
d. Use of transaction safeguards to prevent unauthorized use of Feature of Pyros® eXpress and
passwords and/or identification codes, and to detect and report in enduser procedure
an immediate and urgent manner any attempts at their
unauthorized use to the system security unit, and, as appropriate, to
organizational management.
e. Initial and periodic testing of devices, such as tokens or cards, that Not applicable. Pyros® eXpress does
bear or generate identification code or password information to not use devices to bear or generate
ensure that they function properly and have not been altered in an identification code or password
unauthorized manner. information.

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Appendix A: Glossary of Terms
Below is a list of the terms and acronyms used in this document and the meaning of each.
Term Meaning
BET Bacterial Endotoxin Test
CSE (Control Standard Endotoxin) Endotoxin preparations other than the Reference
Standard Endotoxin that have been standardized
against RSE and are accepted endotoxin standards.
Certificates of Analysis document the
standardization of a CSE against the RSE and
provide a potency of the CSE to use in calculations
of standard concentrations.
Correlation Coefficient (r) Indicates the strength and direction of a linear
relationship between two variables, in this case
endotoxin concentration and onset time. The FDA
Guideline states that "the absolute value of the
correlation coefficient, |r|, must be greater than
or equal to 0.980 for the range of endotoxin
concentrations."
Coefficient of Variation (CV) The standard deviation expressed as a percentage
of the mean. If the data points are all close to the
mean, then the standard deviation, and hence the
CV, is low (closer to zero). If many data points are
very different from the mean, then the standard
deviation is high. If all the data values are equal,
then the standard deviation is zero.
C of A (Certificate of Analysis) The C of A states the potency (in EU/ng) of a CSE
determined with a particular LAL lot. This enables
you to convert the units of the CSE (ng) to
endotoxin units (EU).
Endotoxin Endotoxin is found in the outer membrane of the
cell wall of Gram-negative bacteria.
Endotoxin testing (LAL test) Endotoxin test (LAL Test) provides an analytical
technique that is accepted for the determination
of endotoxin in the release for use of therapeutic
products.
EU/IU Endotoxin is expressed in International Units (IU)
of endotoxin or Endotoxin Units (EU). One
International Unit (IU) of endotoxin is equal to one
Endotoxin Unit (EU).
Glucan A class of polysaccharides with repeating units of
glucose. They are part of the cell wall in fungi,
algae, some bacteria and plants, where they
contribute mechanical strength and integrity to
the cell wall.
I/E Test (Inhibition/Enhancement Test) The I/E Test provides the user with a way to
determine a method to overcome interference of

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 the sample and allow the validation of a non-
interfering assay. This validated assay is required
for routine testing of therapeutic products.
LAL (Limulus Amebocyte Lysate) An extract made from the blood cells of the
horseshow crab. It becomes turbid and clots in the
presence of bacterial endotoxin 1-3 D Beta Glucan.
LRW LAL Reagent Water
MVD (Maximum Valid Dilution) The maximum dilution at which the endotoxin
limit can be detected.
MVC (Minimum Valid Concentration) The product concentration at the Maximum Valid
Dilution.
OD (Optical Density) The ability of a laboratory specimen to absorb or
block the passage of light.
Onset Time The amount of time it takes for a given reaction to
cross a set threshold. Onset time is characterized
as the time needed to reach a preset Optical
Density threshold value and is usually expressed in
seconds.
PPC (Positive Product Control) Contains control standard endotoxin to give a
concentration at double the labeled sensitivity (2λ)
of the accompanying LAL reagent.
RSE (Reference Standard Endotoxin) Primary reference Standard for endotoxin testing.
USP BET chapter, European Pharmacopoeia and
Japanese Pharmacopoeia all require that
standards be calibrated against WHO International
Standard.
USP (U.S. Pharmacopeia) Primary reference for endotoxin testing. USP BET
chapter, European Pharmacopoeia and Japanese
Pharmacopoeia all require that standards be
calibrated against WHO International Standard.

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Appendix B: Program Calculations
1 Onset Time
The onset time is the time at which the OD value reaches the preset OD threshold.
The onset time is estimated using the OD readings taken before and the readings taken after the
threshold is reached. The slope and y intercept for the points are calculated by regression analysis.
The adjusted onset time (estimate of X) is then determined by substituting the threshold OD for Y in
the equation for a straight line.

2 Standard Curve Calculations

The standard curve is a series of known standard concentrations whose reactions are used to
create a model to estimate product concentrations.
When calculating the final concentration of a product, the software does not extrapolate the found
concentration beyond the bounds of the standard curve.
The software offers linear and polynomial regressions of the predictor value vs. concentration on
configurable axes. Replicates of standards concentrations are not averaged for Reagent Verification
Tests. Other tests average the predictor value post transformation.

2.1 Polynomial Regression

The software computes a Least-Squares fit of the points (x, y) to a 2nd order polynomial y:x -
> ax2+bx+c.

2.2 Linear Regression

The software computes a Least-Squares fit of the points (x, y) to a line y:x ->bx+a, where a is
the y-intercept and b is the slope.

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 180
Index
A Editing a User, 18
Editing a Workgroup, 17
Adding a New Workgroup, 15 Editing or Deleting an instrument, 21
Adding a user to a Workgroup, 17 EU Annex 11, 184
Administering User Accounts and Permissions, 14
Anti-virus information, 12 F
Assays
Editing, 125 Force Unlock Tests, 124
FreeForm, 74 FreeForm Assay
I/E and Product Validation, 57 How to Run, 105
Potency, 62 Setting up, 74
Reagent Verification, 75
Routine, 98 G
Unlocking, 138
Audit Trail, 140 Global Options
Accessing a Report, 140 Setting up, 21
Sample report, 143
Viewing a Pre-Filtered Report, 143 H
Highest concentration, 45
B Home screen, 9
Backup procedure, 12 Home Screen
Navigating, 11

C
I
Calibration Equipment Library, 145
Certificates of Analysis, 67 I/E and Product Validation
Changing a User's Status, 19 Completing, 57
Changing the Admin Password, 10 I/E Assay, 46
Chromogenic Assay, 1 How to Run, 82
Concentration calculator, 57 Prerequisites, 46
Concentrations, 44 I/E Template
Consumables and equipment, 42 Setting up, 46
Consumables and Equipment I/E Test
Removing from template, 46 Prerequisites, 82
Incubation Time, 35
Instruments
D Editing and deleting, 21
Data Collection, 113 Setting up and testing, 20
Adding a Sample during, 115
Changing Settings during, 119 K
Editing Parameters during, 115
On a Plate Reader, 117 Kinetic assay, 1
On a Tube Reader, 113
Data Collection Graphs, 120 L
Default Replicates, 42
Default Standard Concentrations, 35 Library
Dilution Factor, 45 Adding Products, 32
Adding Supplies to, 26
Matching Supplies, 29
E Librarys
Editing a Template, 74 Adding Methods, 34
LIMS, 176

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 Exporting Assay Results to, 176 Intended Use, 1
For More Information, 177 Local Installation, 6
Login Failure, 181 Pre-Install Checklist, 4
Login screen, 9 Remote Installation, 7
Reports, 123
M System Requirements, 6
Toolbar, 12, 26
Maximum Test Time, 35 User permissions, 14
Methods Pyros® eXpress Library, 26
Adding to Library, 34 Pyros® Kinetix Flex, 3
Reinstating, 37
Retiring, 37 Q
Viewing and Editing, 36
Qualifying an Analyst on a reagent combination, 31
N Qualifying Reagents, 75

Negative Control Separation, 36 R

Negative Control Validity, 25
Notifications Reader well restriction mask, 42
Pop-up Notifications tab, 24 Reagent Verification
Setting up, 24 Setting up template for, 40
Reagent Verification Test
O How to Run, 75
Reagents
Onset Qualifying, 75
OD LR Window, 36 Reauthentication Timeout, 11
OD Zero Start/End, 36 Register License window, 9
Onset Time, 1 Reinstating a Method, 37
Optical Density, 1 Reinstating a Product, 37
Reinstating a Supply, 37
P Release limit, 33
Removing a user from a Workgroup, 18
Passwords Removing Data Points from a Graph, 122
Resetting, 19 Reports
Potency Assay Consumables and Equipment, 132
How to Run, 67 Editing an Assay, 125
Product Trending, 165 Graphical Analysis Parameters, 131
Product Validation, 52 I/E Test, 136
Product Validation Test Log Summary, 132
How to Run, 91 Post Data Collection Graph, 125
Prerequisites, 91 Potency Test, 135
Products Product Results and Product Sample Evaluation, 131
Adding to Library, 32 Reading, 128
Editing, 34 Reagent Verification, 135
Reinstating, 37 Report Summary, 128
Retiring, 33 Setting Up, 22
Program Calculations, 191 Signing, 134
Pyros® eXpress Standard Curve, 128
21 CFR Part 11, 184 Standard Results, 129
Audit Trail, 140 Standards Evaluation, 129
Compatibility with tube and plate readers, 3 Viewing, 123
Compatiblity, 1 Require Reason for Change, 11
First-Time Login, 8 Resetting a User Password, 19
Installation, 6 Retiring a Method, 37

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 182
Retiring a Supply, 28 Trending, 165
Routine Template, 57 Filtered Product Trending Results, 171
Routine Test Filtered Standard Trending Results, 175
How to Run, 98 Permissions Required, 165
Product, 165
S Standard, 172
Troubleshooting, 178
Samples A/D Values Out of Range, 180
Completing I/E and Product Validation on, 57 Inconsistent Results, 179
Service tab Library, 182
Tests available on, 145 Login Failure, 181
Service Tab, 25 Methods, 181
Setting up Instruments and Testing Communication, 20 No Available Products, 182
Setting Up Options, 21 No Available Samples, 182
Setting up Testing Environment, 26 No Power, 178
Setting up your Work Environment, 14 Password Not Working, 181
Setup window, 7 Plate Reader, 180
Signing a Report, 134 Software Database Access, 181
Standard Trending, 172 Temperature Out of Range, 180
Supplies Tube Detect Issues, 179
Adding a Standard to a Matched, 30 Tube Reader, 178
Adding to Library, 26 Tube Reader Not Detected, 178
Editing and Removing a Matched, 30 Tubes Cannot be Inserted, 179
Matching, 29 Tubes Not Detected, 178
Reinstating, 37 Turbidimetric Assay, 1
Retiring, 28
Viewing and Editing, 28 U
T Unlocking a User, 19
Unlocking an Assay, 138
Template User Management tab, 10
Setting up Product Validation, 52 Users
Templates, 39 Changing status, 19
Adding consumables and equipment to, 42 Editing, 18
Creating new from existing, 74 Unlocking, 19
Editing, 74
Potency, 62 W
Removing consumables and equipment from, 46
Routine, 57 Workgroups
Setting up, 38 Adding New, 15
Setting up a Reagent Verification Template, 40 Adding users to, 17
Testing Products, 82 Editing, 17
Toolbar Calculator Removing users from, 18
How to use, 38

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress Page 183
Thank you for choosing Associates of Cape Cod, Inc. for your LAL testing needs. We pride ourselves on providing
the best quality reagents and the highest level of support for all of our products. If you have any questions,
comments or would like to participate in a customer survey, please contact our Customer Service department at
(800) LAL-TEST (525-8378) or (508) 540-3444.
We regularly publish LAL Updates, newsletters designed to address current questions and concerns confronting
members of the LAL community. You can subscribe, free of charge, to future editions of the newsletter online at
http://www.acciusa.com/lal/newsletter.html, where an archive of past articles is also available.

Contact Information
North America
Associates of Cape Cod, Inc.
124 Bernard E. Saint Jean Drive
East Falmouth, MA 02536-4445 USA
Tel: (888) 395-2221 or (508) 540-3444
Fax: (508) 540-8680
E-mail: [email protected]
http://www.acciusa.com/

United Kingdom
United Kingdom Associates of Cape Cod Int’l., Inc.
Deacon Park, Moorgate Road
Knowsley, Liverpool L33 7RX
United Kingdom
Tel: (44) 151–547–7444
Fax: (44) 151–547–7400
E-mail: [email protected]
http:// www.acciuk.co.uk

Germany
Associates of Cape Cod Europe GmbH
Opelstrasse 14
D-64546 Mörfelden-Walldorf
Germany
Tel: (49) 61 05–96 10 0
Fax: (49) 61 05–96 10 15
E-mail: [email protected]
http://www.acciusa.de

© Copyright 2019, Associates of Cape Cod, Inc. Pyros® eXpress