SCIEX OS Software 3.4 Software Installation Guide

SCIEX OS Software 3.4

Software Installation Guide

RUO-IDV-02-7371-Z July 2024

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Contents

1 Introduction............................................................................................................................... 5

Important Information to Know Before Installation.................................................................... 5

Functionality Included............................................................................................................... 6

2 Requirements............................................................................................................................ 7

Computer Requirements...........................................................................................................7

Windows Requirements............................................................................................................ 8

Network Requirements..............................................................................................................9

Software Updates Feature................................................................................................... 9

CAC Software...................................................................................................................... 9

Software Requirements...........................................................................................................10

Licensing Requirements..........................................................................................................10

Compatible Systems............................................................................................................... 10

Compatible Software...............................................................................................................12

3 Installation Instructions......................................................................................................... 14

Back up the Data Folders to a Safe Location..........................................................................14

Install the SCIEX OS Software................................................................................................15

Install the CAC Software.........................................................................................................19

Upgrade the Software............................................................................................................. 21

Upgrade SCIEX OS Software to Version 3.4 from Versions 1.4 Through to 3.3.x............. 22

Upgrade from Earlier Versions of the SCIEX OS Software................................................24

Migrate from the Analyst Software..........................................................................................25

Install Optional Vertical Applications....................................................................................... 26

Downgrade to Earlier Versions of the SCIEX OS Software.................................................... 26

Remove the SCIEX OS Software............................................................................................27

4 MS FW Updater Utility............................................................................................................ 28

5 Electronic Licensing...............................................................................................................31

Activate a Server-Based License............................................................................................31

Activate a Node-Locked License.............................................................................................31

6 Troubleshooting......................................................................................................................34

SCIEX OS Installation Repair Tool..........................................................................................34

Installation Troubleshooting Tips.............................................................................................36

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Installation Cleanup.................................................................................................................38

A Mass Spectrometer Firmware Versions............................................................................... 41

B Devices and Firmware........................................................................................................... 44

C Windows Operating System Configuration......................................................................... 51

Windows Update.....................................................................................................................51

System Restore.......................................................................................................................51

Customer Security Guidance: Backups............................................................................. 52

User Account Control Settings................................................................................................52

Region Settings.......................................................................................................................53

Language Settings.................................................................................................................. 54

Local Settings..........................................................................................................................55

D Configure Windows Firewall................................................................................................. 58

Configure Incoming Connections............................................................................................58

Configure Outgoing Connections............................................................................................59

E Install the Software Using a Deployment Tool.....................................................................60

F Documentation for the SCIEX OS Software......................................................................... 63

Contact Us.................................................................................................................................. 65

Customer Training...................................................................................................................65

Online Learning Center...........................................................................................................65

SCIEX Support........................................................................................................................65

Cybersecurity.......................................................................................................................... 65

Documentation........................................................................................................................65

Contents

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Introduction

This guide supplies information about, and procedures for, the installation of the SCIEX OS

software 3.4, the integrated vertical applications, and the Central Administrator Console (CAC)

software. The guide also includes information about supported devices and firmware and tips for

troubleshooting the installation.

For information about new software features, enhancements, and known issues, refer to the

document: Release Notes, which is included with the software package.

Important Information to Know Before

Installation

Read this guide before installation or upgrade of the SCIEX OS software.

Note: Back up the data folders for the SCIEX OS software to a safe location before an upgrade.

For more information, refer to the section: Back up the Data Folders to a Safe Location. These

folders contain the device configurations, security data, methods, and batches.

To make sure that the software installation is successful, read the following points carefully

before the start of any of the procedures in this guide:

• The SCIEX OS software uses electronic licensing. For license activation, refer to the section:

Electronic Licensing.

• All versions of the SCIEX OS software require a valid software license. These licenses

are provided with new instrument purchases and can also be purchased separately from

SCIEX. For information about the validity of the current license or about purchasing additional

licenses, contact a SCIEX sales representative or Technical Support through sciex.com/

request-support.

Note: In addition to a license for the SCIEX OS software, licenses for optional modules and

features might be required.

• Data files acquired with the SCIEX OS software 3.4 cannot be opened in earlier versions of

the SCIEX OS software. However, data acquired in earlier versions of the SCIEX OS software

can be opened in the SCIEX OS software 3.4.

• Results Tables created in the SCIEX OS software 3.4 cannot be opened in earlier versions of

the SCIEX OS software. However, Results Tables created in earlier versions of the SCIEX OS

software can be opened in the SCIEX OS software 3.4.

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• All devices supported in earlier versions of the SCIEX OS software continue to be supported

in the SCIEX OS software 3.4. Some devices might require firmware upgrades. Refer to the

section: Devices and Firmware.

• The SCIEX OS software 3.4 is available as a web download package. If a DVD is required,

then contact a local sales representative.

• If the SCIEX OS software will be installed on a computer with the Analyst or Analyst TF

software, then deactivate the hardware profile and close the Analyst or Analyst TF software

before the start of the installation.

• For more information about the compatibility of the SCIEX OS software with other software

applications, refer to the section: Compatible Software.

Functionality Included

The SCIEX OS 3.4 software contains the functionality in the previous release of the software.

Introduction

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Requirements

Computer Requirements

Acquisition Computer with the SCIEX OS Software

• Recommended Computer:

• SCIEX Workstation or Workstation+, with:

• An Intel Xeon W-2245 processor (8 core, 16.5 MB cache, 3.9 GHz, 4.7 GHz Turbo HT

16.5 MB, 155W DDR4-2933, with NVIDIA P400 or T400)

• 32 GB (2 × 16 GB) DDR4 3200 MHz RDIMM ECC

• SCIEX Workstation: 2 × 1 TB SSD (RAID1)

• SCIEX Workstation+: 2 × 2 TB SSD (RAID1)

• Supported Computers:

• SCIEX Alpha Workstation 2020, with:

• An Intel Core I5-8500 processor (6 core, 9 MB cache, 3.0 GHz, 4.1 GHz Turbo, with HD

Graphics 630)

• 32 GB (2 × 16 GB) DDR4 2666 MHz UDIMM Non-ECC

• 2 × 2 TB HDD (RAID1)

• Dell OptiPlex XE2 computer, with:

• An Intel Core I5-4570S processor (Quad core, 2.90 GHz, 6 MB with HD Graphics 4600)

• 32 GB DDR3 1600 MHz SDRAM

• 2 × 2 TB HDD (RAID1)

• Operating System: Windows 10 (64-bit), version 1809 LTSC. English operating system only.

• Ethernet: At least two Ethernet port connections.

Note: Newer computer models might become available. Consult the local sales representative

for the latest information.

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Processing Computer with the SCIEX OS Software

For the processing computer, we recommend the use of the computers shown in the section:

Acquisition Computer with the SCIEX OS Software. However, a different computer can be used,

if it meets the requirements in the following table.

Table 2-1 Requirements for the Processing Computer

Specification Requirements

Operating system Windows 10 (64 bit), version 1809 LTSC, 20H2, 21H2, or 22H2. English,

French, German, and Italian operating systems are supported.

Processor Intel Xeon W3-2435, 22.5 MB, 8 cores, 3.1 GHz to 4.5 GHz

RAM 32 GB DDR5, 4800 MHz

Data storage Nominal mass systems: 2 × 1 TB Raid 1, NVMe SSD, Class 40

Accurate mass systems: 2 × 2 TB Raid 1, NVMe SSD, Class 40

CAC Software

Note: The Central Administrator Console (CAC) software cannot be installed on the same

computer as the SCIEX OS software.

For the server for the CAC software, we recommend the use of the computers shown in the

section: Acquisition Computer with the SCIEX OS Software. However, a different computer can

be used, if it meets the requirements in the following table.

Table 2-2 Requirements for the Server for the CAC Software

Specification Requirements

Operating system Windows 10 (64 bit), version 1809 LTSC, 20H2, or 21H2; Windows Server

2019 and later. English operating system only.

Processor Multicore processor (with 64-bit support), 3 GHz

RAM 8 GB, 32 GB recommended

Data storage 1 TB SSD minimum

Windows Requirements

• Language settings: English

• Region settings: English, French, or German

• (Recommended) System Restore: Disabled

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• Windows Updates: Notify only

Note: The SCIEX OS software cannot be installed or used on a computer with Federal

Information Processing Standards (FIPS) enabled (System cryptography: Use FIPS

compliant algorithms for encryption, hashing, and signing).

Note: Every SCIEX computer is configured with a local Administrator-level account, abservice.

This account is used by SCIEX service and technical support to install, service, and support

the system. Do not remove or deactivate this account. If the account must be removed or

deactivated, then prepare an alternate plan for SCIEX access, and communicate it to the local

FSE.

Note: If the computer is not supplied by SCIEX, then make sure that the .NET Framework 4.x is

installed on the computer. If the .NET Framework is not installed, then before installation of the

SCIEX OS software, open the Install/NDP472-KB4054530-x86-x64-AllOS-ENU.exe

file, found in the installation package.

Network Requirements

Note: For information about the network security requirements for network acquisition,

refer to the document: Laboratory Director Guide. This document is in the

Install\ProductSpecificDocumentation folder in the installation package for the

SCIEX OS software.

Software Updates Feature

The Software Updates feature has the following additional requirements:

• Outbound connectivity that uses the HTTPS protocol on port 443 is enabled.

• The firewall lets outbound communications be sent from the SCIEX OS software to Amazon

Web Services (AWS), including: https://sciexos.com.

• Transport Layer Security (TLS) 1.2, or later, is installed.

Contact the local network administrator to make sure that these requirements are obeyed.

The Software Updates feature in this version of the SCIEX OS software does not support

communication to the Internet through a corporate proxy server. If a proxy server is used, then

an error is shown when the user clicks Check for updates on the Software Updates page.

CAC Software

• The Central Administrator Console (CAC) software uses TCP ports 63333 and 44144 for

communication with the SCIEX OS software.

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• The CAC server is open for inbound traffic on port 63333, and it is open for outbound

traffic on ports 44144 and 63333.

• The computer with the SCIEX OS software is open for inbound traffic on ports 63333 and

44144, and it is open for outbound traffic on port 63333.

• If the queue monitoring feature is in use, then ports 5000 and 5001 must also be open for

inbound traffic on the CAC server.

• If the queue monitoring feature is being used with multiple domains, then configure a trust

relationship between all of the domains.

To configure the Windows firewall for use with the CAC software, refer to the section: Configure

Windows Firewall.

Software Requirements

• Microsoft Office 2013, 2016, or 2021, 32 bit or 64 bit, is required to create, open, and edit the

report templates that are used in the Analytics workspace.

Note: These report template functions are not supported in Microsoft Office 365.

Note: The SCIEX OS software can be installed on a computer with Microsoft Office 365.

If the SCIEX OS software and Microsoft Office 365 are installed on the same computer,

then the user can use Microsoft Office 365 to generate and open reports in the SCIEX OS

software.

Note: Acquisition and processing computers, such as the Alpha and SCIEX workstations,

with the Windows 10 LTSB/LTSC operating systems are not compatible with Microsoft Office

365.

• The Chrome and Edge browsers are recommended for use with the central monitoring

feature.

Licensing Requirements

The SCIEX OS software 3.4 requires activation with a valid SCIEX OS software 3.4 license file.

The license file controls the features and applications that are available, such as acquisition or

processing. Additional license files might be required for optional features, such as CFR, Scout

triggered MRM (stMRM) acquisition, and the Molecule Profiler software.

For the SCIEX OS software, both node-locked and server-based licenses are available. For the

Central Administrator Console (CAC) software, only node-locked licenses are available.

Compatible Systems

The following sytems are compatible with the SCIEX OS software 3.4.

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Table 2-3 Supported Mass Spectrometers and Ion Sources

Mass Spectrometer Supported Ion Sources

X500R QTOF or X500B QTOF system Turbo V ion source

ZenoTOF 7600 system Turbo V ion source

OptiFlow Turbo V ion source

ZenoTOF 7600+ system Turbo V ion source

OptiFlow Turbo V ion source

Echo

MS+ system with ZenoTOF 7600

system

Turbo V ion source

OptiFlow Turbo V ion source

SCIEX 4500 system Turbo V ion source

SCIEX 5500 system Turbo V ion source

OptiFlow Turbo V ion source (Micro probe)

SCIEX 5500+ system Turbo V ion source

OptiFlow Turbo V ion source (Micro probe)

SCIEX 6500 system IonDrive Turbo V ion source

OptiFlow Turbo V ion source

Turbo V ion source

SCIEX 6500+ system

IonDrive Turbo V ion source

OptiFlow Turbo V ion source

Turbo V ion source

Echo

MS system with SCIEX Triple Quad

6500+ system

IonDrive Turbo V ion source

OptiFlow Turbo V ion source

Turbo V ion source

Echo

MS+ system with SCIEX Triple Quad

6500+ system

IonDrive Turbo V ion source

OptiFlow Turbo V ion source

Turbo V ion source

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Table 2-3 Supported Mass Spectrometers and Ion Sources (continued)

Mass Spectrometer Supported Ion Sources

SCIEX 7500 system OptiFlow Pro ion source

SCIEX 7500+ system OptiFlow Pro ion source

Compatible Software

The following applications are compatible with the SCIEX OS software 3.4 on Windows 10

operating systems.

Table 2-4 Compatible Software

Software Name Additional Information

Biologics Explorer software 1.0, 1.1, 2.0,

3.0, 3.1, and 4.0

Use the tile on the Home page in the SCIEX OS

software to get access to Biologics Explorer

software 3.0, 3.1, and 4.0.

CloudConnect 1.8 The PeakView software 2.2 or later is required.

LibraryView software 1.6 The SCIEX OS software cannot be installed on the

same computer as the LibraryView software 1.0.x or

1.1 to 1.4.

Molecule Profiler software 1.3.1. The Molecule Profiler software is a part of the

installation package. For installation instructions,

refer to the section: Install the SCIEX OS Software.

MarkerView software 1.4 The MarkerView software is a part of the installation

package. For installation instructions, refer to the

section: Install the SCIEX OS Software.

OneOmics suite 3.4 The PeakView software 2.2 or later is required.

ProMassProcessor 1.0 —

StatusScope remote monitoring service

2.2, 2.2.1, 2.2.2, and 2.3

—

Note: The SCIEX OS software can also be installed for data processing on the same computer

as the Analyst software 1.6.3 or later and the Analyst TF software 1.7.1 or later.

Note: The SCIEX OS software is compatible with the data files that are acquired with the

Analyst software 1.6.2, 1.6.3, and 1.7 or later, and the Analyst TF software 1.7.1 or later.

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Note: The SCIEX OS software cannot be installed on the same computer as the Analyst Device

Driver (ADD), Cliquid, MasterView, or MPX software.

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Installation Instructions

Note: Internet access is required to download the software. We recommend that all of the

required software and materials be downloaded before the scheduled installation to decrease

the time required for the installation.

Back up the Data Folders to a Safe Location

Before upgrading the SCIEX OS software, back up these folders to a safe location, such as a

network drive or DVD:

• SCIEX OS Data: This folder contains all methods, batches, and data. By default, this folder

is installed in D:\SCIEX OS Data.

• ProgramData\SCIEX: This folder contains all security and device configuration data.

Note: This is a hidden folder. If it is not visible, then configure File Explorer to show hidden

items.

If the backup software encounters locked files, then skip them.

Note: The backups are required to go back to the previous version of the SCIEX OS software. If

the backups are not available, and the previous version of the SCIEX OS software is reinstalled,

then it will be necessary to recreate all methods and reconfigure security.

Do not rename the existing ProgramData\SCIEX folder. We recommend that the same SCIEX

OS Data folder be used for the new version of the SCIEX OS software, to provide access to

existing data, such as methods, batches, data, and Results Tables.

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Install the SCIEX OS Software

Prerequisites

• Echo

MS and Echo

MS+ systems: Make sure that the correct firmware version is installed

on the Echo

MS or Echo

MS+ system. Refer to the section, Devices and Firmware. To

upgrade the firmware version, contact SCIEX support.

• Make sure that a SCIEX OS software 3.4 license key is available. The license key might be

distributed on a printed activation certificate, or in an e-mail from SCIEX Now. If the license

key is missing, then contact a SCIEX sales representative.

• If a Windows Update is in operation, then wait until the update is completed.

• If a restart is required after a Windows Update, then restart the computer before the start of

the installation.

• ExionLC 2.0 systems: If the SCIEX OS software will be used for acquisition on a computer

that will also have the Analyst software 1.7.3, or the Analyst software 1.7.3 with HotFix

1 or 2 installed, then install the Analyst software and HotFixes, if applicable, before the

SCIEX OS software. Analyst 1.7.3 HotFix 3 can be installed before or after the SCIEX OS

software.

Note: The VC++2008 SP1 MFC Security Redistributable package is also required. If this

package is not installed, then the installation program will install it. Do not remove the package.

If the package is removed, then the SCIEX OS software will not operate correctly when an

ExionLC 2.0 system is used.

Use this procedure to install the SCIEX OS software and the optional integrated applications, the

MarkerView and Molecule Profiler software.

During the installation, the user selects the type of installation and the applications and features

to be installed.

To install the CAC software, refer to the section: Install the CAC Software.

Note: The CAC software is a part of the SCIEX OS installation package. However, the CAC

software and the SCIEX OS software cannot be installed on the same computer.

Note: The installation program disables the System Restore task.

Note: To make changes to the installation after the installation completes, deactivate the devices

in the SCIEX OS software before the use of the Modify option. Refer to the section: Installation

Troubleshooting Tips.

1. Log on to the computer as a Windows user with Administrator privileges.

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2. Make sure that all applications are closed.

3. To install the software from a DVD, put the DVD in the DVD drive.

4. To install the software from a downloaded file, do these steps:

a. Download the required zip file from sciex.com/software-downloads.

Tip! To prevent installation issues, save the file to the local computer, in a location other

than the computer desktop. Then, before the start of the installation, disconnect any

external USB storage devices.

b. After the download is complete, right-click the downloaded file and then click Extract

All to extract the installation package.

5. Acquisition computers for X500 QTOF and ZenoTOF 7600/7600+ systems: Install the driver:

• X500 QTOF systems: Browse to the Drivers folder of the DVD or installation package

and then double-click the xTDC4_driver_v1.1.1.exe file to install version 1.1.1.

• ZenoTOF 7600/7600+ systems: Browse to the Drivers folder of the DVD or installation

package and then double-click the Ndigo_driver_v1.5.4.exe file to install version

1.5.4.

6. In the Install folder on the DVD or in the installation package, double-click the

Setup.exe file.

7. Obey the on-screen instructions.

During the installation, prompts to select the type of installation and the modules to be

installed are shown.

• Acquisition + Processing

• Processing

• Administration

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Figure 3-1 Choose Modules for Installation Dialog

Note: ExionLC 2.0 systems: If the SCIEX OS software will be installed on a computer on

which the Analyst software is used for acquisition, then do not install the drivers for the

ExionLC 2.0 system during the installation of the SCIEX OS software.

Note: Make sure that the type of license is correct for the modules selected for installation.

Licenses might be required for optional features and integrated applications.

Note: To prevent installation issues, install the software on a local drive. Do not install the

software on a network or removable drive.

Note: To prevent installation issues, make sure that the path to the installation folder is

118 characters or less. If the path is longer than 118 characters, then installation will not

continue.

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Tip! If an upgrade to the .NET Framework is required, then a prompt for a computer

restart is shown during the installation. Users have the option to continue with the restart

immediately or to postpone the restart until later. However, installation does not continue

until after the restart.

If the installation does not complete successfully, then use the SCIEX OS Installation Repair

Tool to identify the issue. Refer to the section: SCIEX OS Installation Repair Tool.

8. Restart the computer.

9. (Optional) Use the SCIEX OS Installation Confirmation Tool to make sure that the software

was installed correctly:

a. From the Windows Start menu, select SCIEX OS > Installation Confirmation Tool.

b. In the SCIEX OS Installation Confirmation Tool, click Start verifying installed files.

c. After the analysis is complete, click Print Report, select a printer, and then click Print.

10. If the CAC software is used, then configure the Windows firewall on the computer. Refer to

the section: Configure Windows Firewall.

Use TCP ports 63333 and 44144 for communication with the CAC software. The computer

must permit inbound traffic on ports 63333 and 44144 and outbound traffic on port 63333.

11. Open the software.

12. Use the license key to activate the software, including optional features and integrated

applications. Refer to the section: Electronic Licensing.

Note: Supported accurate and nominal mass systems: If the SCIEX OS software 3.4 license

includes licensing for the LibraryView software, then the LibraryView software must be

installed separately.

Note: In addition to the SCIEX OS software license, licenses might be required for optional

features and integrated applications. Make sure to get and activate the licenses before

trying to use these features.

13. (If required) For acquisition computers, run the MS FW Updater to update the MS firmware

and instrument configuration tables. Refer to the sections: MS FW Updater Utility and Mass

Spectrometer Firmware Versions.

Note: To give users access to the SCIEX OS software, add them to the security database.

Refer to the document: Laboratory Director Guide or Help.

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Install the CAC Software

Prerequisites

• Make sure that a license key for the CAC software is available. The license key might be

distributed on a printed activation certificate, or in an e-mail from SCIEX Now. If the license

key is missing, then contact a SCIEX sales representative.

• If a Windows Update is in progress, then wait until the update is finished.

• If a reboot is required after a Windows Update, then reboot the computer before beginning

the installation.

• To use the queue monitoring feature, install a TLS certificate. To get a certificate, contact

the customer IT department. The certificate name must be CACServerCertificate. The

certificate must be installed in the Local Computer/Trusted Root Certification

Authorities store.

Note: To use a different certificate name, edit the IssuedTo property in the C:\Program

Files\SCIEX\SCIEX OS\appsettings.json file.

When installing the software from a DVD, always install it from the official SCIEX DVD and

confirm after the installation that the correct version is installed.

Note: The installation program disables the System Restore task.

Note: To make changes in the installation, deactivate the devices in the SCIEX OS software

before using the Modify option. Refer to the section: Installation Troubleshooting Tips.

1. Log on to the computer as a Windows user with Administrator privileges.

2. Make sure that all applications are closed.

3. To install the software from a DVD, load the DVD in the DVD drive.

4. To install the software from a downloaded file, do these steps:

a. Download the required zip file from the SCIEX website.

Tip! To prevent installation issues, save the file to the local computer, in a location other

than the computer desktop. Then, before the start of the installation, disconnect any

external USB storage devices.

b. After the download is complete, right-click the downloaded file and then click Extract

All to extract the installation package.

5. Double-click Setup.exe in the Install folder on the DVD or in the installation package.

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6. Obey the on-screen instructions. On the Choose Modules for Installation dialog, select

Central Administrator Console.

Figure 3-2 Choose Modules for Installation

Note: To avoid installation issues, install the software on a local drive. Do not install on a

network or removable drive.

Note: To avoid installation issues, make sure that the path to the installation folder is 118

characters or less. If it is longer, then installation will not proceed.

Tip! If an upgrade to .NET is required, then a prompt for a computer restart is shown during

the installation. Users have the option to continue with the restart immediately or select the

option to postpone the restart until later. However, installation does not continue until after

the restart.

If the installation does not complete successfully, then use the SCIEX OS Installation Repair

Tool to identify the issue. Refer to the section: SCIEX OS Installation Repair Tool.

7. If prompted, then restart the computer after the software is installed.

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Note: A restart is recommended after the software is installed for the first time, even if no

prompt is given. A restart is not required after reinstallation of the software.

8. (Optional) Use the SCIEX OS Installation Confirmation Tool to make sure that the software

was installed correctly:

a. From the Windows Start menu, select SCIEX OS > Installation Confirmation Tool.

b. In the SCIEX OS Installation Confirmation Tool, click Start verifying installed files.

c. After the analysis is complete, click Print Report, select a printer, and then click Print.

9. Configure the Windows firewall on the CAC server. Refer to the section: Configure Windows

Firewall.

TCP ports 63333 and 44144 are used for communication with theSCIEX OS software. Open

port 63333 for inbound traffic, and open ports 44144 and 63333 for outbound traffic.

To use the queue monitoring feature, open ports 5000 and 5001 for inbound traffic on the

CAC server.

10. Configure the Windows firewall on the computers with the SCIEX OS software. Refer to the

section: Configure Windows Firewall.

TCP ports 63333 and 44144 are used for communication with the CAC server. Open ports

63333 and 44144 for inbound traffic and port 63333 for outbound traffic.

11. Open the software.

12. Activate the software using the license key. Refer to the section: Electronic Licensing.

13. Configure the CAC software. Refer to the document: CAC Help.

Note: The administration mode can be changed in the CAC or SCIEX OS software. For

instructions for configuring the administration mode in the SCIEX OS software, refer to the

SCIEX OS Software Help System.

Upgrade the Software

A new software license is required to upgrade from versions of SCIEX OS earlier than version

3.4.

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Upgrade SCIEX OS Software to Version 3.4 from Versions 1.4

Through to 3.3.x

Prerequisites

• Make sure that a license key for the SCIEX OS software is available. Eligible customers can

also get an upgrade license key by clicking the Upgrade Software button on the Registered

Software page in SCIEX Now.

• If any Results Tables contain custom columns with the name IF, then change the column

name.

• Make sure that the versions of all vertical applications installed on the computer are

supported. For supported versions, refer to the section: Compatible Software. If required,

update the vertical applications before upgrading the SCIEX OS software. Refer to the

section: Install Optional Vertical Applications.

• If a Windows Update is in progress, then wait until the update is finished.

• If a restart is required after a Windows Update, then restart the computer before beginning

the upgrade.

• ExionLC 2.0 systems: If the SCIEX OS software will be used for acquisition on a computer

that will also have the Analyst software 1.7.3, or the Analyst software 1.7.3 with HotFix 1 or

2 installed, then upgrade the Analyst software and install the HotFixes, if applicable, before

the upgrade of the SCIEX OS software. Analyst 1.7.3 HotFix 3 can be installed before or

after the upgrade of the SCIEX OS software.

The installation program silently removes the patches that are integrated in this version.

While installing the SCIEX OS software, the user selects the modules to be installed, such as

Molecule Profiler or Analytics.

Note: The CAC software is a part of the installation package for the SCIEX OS software.

However, the CAC and SCIEX OS software cannot be installed on the same computer.

1. Deactivate all devices and then close the SCIEX OS software.

2. Make sure that all other applications are closed.

3. Back up the C:\ProgramData\SCIEX folder. Refer to the section: Back up the Data

Folders to a Safe Location.

4. For upgrades from SCIEX OS software 1.4: If the Audit Trail feature is being used, then do

these steps to save the Workstation audit data:

a. Browse to the folder, C:\ProgramData\SCIEX, and then create a folder named

Audit Data. Give System, Users, and Administrators read and write access to the

new folder.

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b. Browse to the folder, SCIEX OS Data\common-project-area\Audit Data, and

then copy the following files:

• WorkstationAuditMap.atms

• WorkstationAuditMapTemplates.atms

• WorkstationAuditTrailData.atds

Note: By default, SCIEX OS Data is installed on D:\.

c. Paste the files in the folder, C:\ProgramData\SCIEX\Audit Data.

5. Log on to the computer as a Windows user with Administrator privileges.

6. Acquisition computers: Do these steps:

a. Open the currently installed SCIEX OS software.

b. Open the MS Tune workspace.

c. Click Positive MS Tuning.

d. Click Save Tuning Settings in the left panel and then click Save settings.

7. Back up the SCIEX OS Data folder. Refer to the section: Back up the Data Folders to a

Safe Location.

8. Do one of the following:

• If the software is being installed from a DVD, then insert the DVD in the DVD drive and

continue with step 12.

• If the software is being installed from a downloaded file, then continue with step 9.

9. Download the required zip file from the SCIEX website.

Tip! To prevent installation issues, save the file to the local computer, in a location other

than the computer desktop. Then, before the start of the installation, disconnect any external

USB storage devices.

10. After the download is complete, right-click the downloaded file and then click Extract All to

extract the installation package.

11. Acquisition computers: Upgrade the drivers.

• X500 QTOF systems: Browse to the Drivers folder of the DVD or installation package

and then double-click xTDC4_driver_v1.1.1.exe to remove the earlier version of the

TDC driver and install version 1.1.1

• ZenoTOF systems: Browse to the Drivers folder of the DVD or installation package and

then double-click the Ndigo_driver_v1.5.4.exe file to remove the earlier version of

the ADC driver and install version 1.5.4.

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12. Double-click Setup.exe on the DVD or in the installation package.

13. Follow the on-screen instructions. When prompted, select the modules to be installed.

Tip! If an upgrade to .NET is required, then a prompt for a computer restart is shown during

the installation. Users have the option to continue with the restart immediately or select the

option to postpone the restart until later. However, installation does not continue until after

the restart.

If the upgrade does not complete successfully, then use the SCIEX OS Installation Repair

Tool to identify the issue. Refer to the section: SCIEX OS Installation Repair Tool.

14. (Optional) Use the SCIEX OS Installation Confirmation Tool to make sure that the software

was installed correctly:

a. From the Windows Start menu, select SCIEX OS > Installation Confirmation Tool.

b. In the SCIEX OS Installation Confirmation Tool, click Start verifying installed files.

c. After the analysis is complete, click Print Report, select a printer, and then click Print.

15. For acquisition computers, run the MS FW Updater utility to update the mass spectrometer

firmware and configuration tables, if required. Refer to the section: MS FW Updater Utility.

For a list of supported firmware versions, refer to the section: Mass Spectrometer Firmware

Versions.

16. If required, install the ExionLC 2.0 system driver.

Upgrade from Earlier Versions of the SCIEX OS Software

To upgrade from versions of the SCIEX OS software earlier than version 1.4, remove the earlier

version of the SCIEX OS software, and then install the new version.

1. Deactivate all devices and then close the SCIEX OS software.

2. Make sure that all other applications are closed.

3. Back up the C:\ProgramData\SCIEX folder. Refer to the section: Back up the Data

Folders to a Safe Location.

4. In the Windows Apps & features control panel, remove the SCIEX OS software.

5. Install the SCIEX OS software 3.4. Refer to the section: Install the SCIEX OS Software.

6. Upgrade any vertical applications. Refer to the section: Install Optional Vertical Applications.

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Migrate from the Analyst Software

Prerequisites

• Complete the SCIEX OS eLearning, available at SCIEX Now Learning Hub.

• Make sure that the acquisition computer meets the requirements for the SCIEX OS

software.

• Purchase the license for the SCIEX OS software.

Customers who use the Analyst software to acquire data from SCIEX 4500, 5500, 5500+,

6500, and 6500+ systems can upgrade to the SCIEX OS software, the new mass spectrometry

software available from SCIEX. An onsite upgrade service is available from SCIEX. For more

information, contact a sales representative or field service employee (FSE).

Note: SCIEX does not support workflows that use both the Analyst and SCIEX OS software to

acquire data from the same mass spectrometer.

1. Install the SCIEX OS software 3.4. Refer to the section: Install the SCIEX OS Software.

2. Use the Instrument Settings Converter to import the mass spectrometer settings from the

Analyst software into the SCIEX OS software. Refer to the document: Instrument Settings

Converter Release Notes.

Tip! The release notes are in the Instrument Settings Converter folder in the

installation package for the SCIEX OS software.

Note: Use the version of the Instrument Settings Converter that is supplied in the installation

package for the SCIEX OS software 3.4.

3. In the MS Method workspace in the SCIEX OS software, click Open > Convert File.

4. Import the MS methods that were made with the Analyst software and convert them to the

format for the SCIEX OS software.

Note: Only MS method information is converted. LC methods must be created manually in

the SCIEX OS software.

5. Review the transferred settings in the SCIEX OS software to make sure that they are

correct.

Tip! Use the Verify MS scans option in the MS Scan Tuning procedure in the MS Tune

workspace to review the settings. Expected results should be the same regardless of the

control software that is installed.

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Install Optional Vertical Applications

The integrated applications, the MarkerView and Molecule Profiler software, are installed with

the SCIEX OS software. For instructions, refer to the section: Install the SCIEX OS Software.

Note: These applications are activated with a separate license file.

Install the following applications after installation of the SCIEX OS software:

• Biologics Explorer software

• LibraryView software

Note: For supported versions, refer to the section: Compatible Software.

Note: If newer versions of the applications are available, then contact sciex.com/request-support

to verify software compatibility.

Prerequisite Procedures

• Install the SCIEX OS Software

• Make sure that the SCIEX OS software is closed, and then install the optional applications.

Note: For instructions, refer to the documentation for the optional application: Biologics

Explorer Software Release Notes or LibraryView Software Installation Guide.

Downgrade to Earlier Versions of the SCIEX OS

Software

Do this procedure to downgrade from the SCIEX OS software 3.4 to the SCIEX OS software

1.6.1 or later. To downgrade to earlier versions of the SCIEX OS software, contact sciex.com/

request-support.

1. In the Windows Apps & features control panel, remove the SCIEX OS software 3.4.

2. Remove all Microsoft C++ Redistributable packages from 2014 to 2019.

3. Install the earlier version of the SCIEX OS software.

Note: If the installation fails, then do the cleanup procedure. Refer to the section: Installation

Cleanup.

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Remove the SCIEX OS Software

Prerequisites

• Remove any SCIEX OS HotFixes.

1. Log on to the computer as a user with Administrator privileges.

2. Click Start > Control Panel > Programs and Features.

Tip! If the control panel components are shown by Category, then click Start > Control

Panel > Programs > Programs and Features > Uninstall a program.

3. Select SCIEX OS, and then click Uninstall.

The software is removed. User intervention is not required.

Note: The license file is not removed and can be used if the SCIEX OS software is installed

again.

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MS FW Updater Utility

The SCIEX OS software requires that a supported firmware version be installed on the

connected mass spectrometer. Use this utility to upgrade the firmware version on the mass

spectrometer.

For a list of supported versions, refer to the section: Mass Spectrometer Firmware Versions.

Prerequisites

• The SCIEX OS software 3.4 or later is installed.

• The mass spectrometer is active in the Devices workspace.

• The computer is connected to the mass spectrometer.

• The user is logged on as an Administrator in Windows as well as an Administrator in the

User database for the SCIEX OS software.

1. Stop all acquisitions and then clear the queue.

Make sure that there are no samples waiting in the queue.

2. Close the SCIEX OS software.

3. In the installation package for the SCIEX OS software, browse to the \FirmwareUpdater\

folder, and then double-click the MS FW Updater.exe file.

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Figure 4-1 MS FW Updater Utility

4. In the Select Update list, select the mass spectrometer and software version.

5. Click Run Update and then follow the on-screen instructions.

Figure 4-2 MS FW Updater Progress Bar

6. After the update completes, click OK on the progress bar, and then close the utility.

Note: The event log in the SCIEX OS software shows that the firmware was updated

successfully.

7. Wait 30 seconds and then restart the mass spectrometer. Refer to the document: System

User Guide.

8. Open the SCIEX OS software and then open the Devices page in the Configuration

workspace.

The mass spectrometer device has been deleted from the list.

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9. Add the mass spectrometer to the Device list and then activate the required devices.

The MS FW Updater utility can be used to go back to a firmware version that is supported

by an earlier version of the SCIEX OS software. Start the Firmware Updater utility again,

select the required version, and then click Run Update.

Note: X500 QTOF systems: The MS FW Updater cannot go back to firmware versions that

are supported by SCIEX OS software versions earlier than version 1.2. To go back to earlier

versions, contact sciex.com/request-support.

Note: SCIEX 7500 systems: The MS FW Updater cannot go back to firmware versions that

are supported by SCIEX OS software versions earlier than version 2.0. Earlier versions of

the SCIEX OS software do not support the SCIEX 7500 system.

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Electronic Licensing

The SCIEX OS software supports node-locked licensing for both acquisition and processing

workstations. A node-locked license can only be used on one computer. Server-based licensing

is only supported for processing workstations. Install the license files for the SCIEX OS software

3.4 and any optional features and applications in the C:\Program Files\SCIEX\SCIEX OS

folder on the computer where the SCIEX OS software is installed.

Note: For the Central Administrator Console (CAC) software, only node-locked licensing is

supported.

Note: If the computer date and time must be changed, then do so before activating the license.

Otherwise, the software might not operate.

Note: If the license file is edited, then it becomes invalid and cannot be recovered.

Activate a Server-Based License

Note: This procedure is not applicable for the Central Administrator Console (CAC) software.

For a server-based license, contact the IT department to do the following tasks:

1. Set up a license server:

a. Ask the IT department to download the License-Server-Setup.zip file. Go

to sciex.com/software-downloads, and then click Additional Downloads > License

Server Setup > License Server Setup Software.

b. Follow the instructions in the License Server Setup Guide contained in the downloaded

package.

2. Make a license file for the client computers.

3. Install the license file on each client computer where the SCIEX OS software is installed.

Activate a Node-Locked License

Prerequisites

• A license key is available.

1. On the desktop, double-click the SCIEX OS icon.

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Figure 5-1 License Message

2. In step 1 of the SCIEX OS Activation dialog, type the license key.

The license key might be supplied on a printed activation certificate or in an e-mail from

SCIEX Now. If the license key is missing, then contact a SCIEX sales representative.

Note: The license key starts with AID and is followed by 32 characters: 8 segments of

4-digit codes separated by hyphens.

3. In the SCIEX OS Activation dialog, click the link in step 3.

The SCIEX Login web page opens.

4. To log on to a SCIEX account, click Log In, or click Create an Account.

When account creation or log on is complete, the SCIEX software activation web page

opens. The first name, last name, and e-mail address of the user are shown in the first three

fields.

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If a license will be activated for the SCIEX OS software on this computer, then the License

Key field shows the correct information.

5. In the Select Your Instrument field, select and type the required information.

Note: To activate a node-locked license for a processing workstation, use a serial number

for any SCIEX instrument. Contact SCIEX Support at sciex.com/contact-us if an instrument

serial number is not available.

6. If a license is being activated for the SCIEX OS software on a different computer, then

type the computer ID, which is the MAC address of the network port used to connect the

computer to the network, and the license key.

7. Click Submit.

A message shows that an e-mail with the license file will be sent.

8. After the e-mail is received, save the attached license file in the

C:\Program Files\SCIEX\SCIEX OS folder.

9. Use the SCIEX Now web page to get and activate licenses for optional features

and applications, such as CFR, Scout triggered MRM (stMRM) acquisition, the Central

Administrator Console (CAC) software, and the Molecule Profiler software. For more

information, contact Technical Support at sciex.com/request-support.

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Troubleshooting

SCIEX OS Installation Repair Tool

Prerequisites

• Repair the installation of the SCIEX OS software: Start the installation program (Install/

Setup.exe), and then select the Repair option.

If the repair does not complete successfully, then do this procedure.

Note: The SCIEX OS Installation Repair Tool cannot be used for installations of the Central

Administrator Console (CAC) software.

1. To view the status of the installation, in the installation package for the SCIEX OS

software, browse to the Installation Repair Tool folder, and then double-click

Sciex.Installer.Repair.exe.

• In the list of Installed SCIEX Modules, modules that installed successfully are marked

with a green check mark ( ) and modules that were not installed are marked with a red

× (

). All modules selected during installation should be marked as passed.

• On the SCIEX OS Prerequisites tab in the Installer Packages pane, packages shown in

red text were not installed or are the incorrect version.

• On the Subsystem Components tab in the Installer Packages pane, subsystems shown

in red text were not installed or are the incorrect version.

2. Close the SCIEX OS Installation Repair Tool.

3. In the Windows Apps & features control panel, remove the following applications, if present,

in this order:

• LibraryView software

• SCIEX OS software

• LibraryView Framework

• Microsoft Access Database Engine

• Reporter

4. If applicable, remove all of the SQL server applications.

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Note: Do not remove the SQL server applications if they are used by existing libraries.

For new installations and upgrades from the SCIEX OS software 1.6.1 and later versions,

remove the following applications:

• Microsoft SQL Server 2008 Setup Support Files

• Microsoft SQL Server 2012 (64-bit)

• Microsoft SQL Server 2012 Native Client

• Microsoft SQL Server 2012 Setup (English)

• Microsoft SQL Server 2012 Transact_SQL ScriptDom

• Microsoft SQL Server Compact 3.5 SP2 ENU

• Microsoft SQL Server Compact 3.5 SP2 x64 ENU

• SQL Server Browser for SCL Server 2012

• Microsoft VSS Writer for SQL Server 2012

For upgrades from the SCIEX OS software 1.5 and earlier versions, remove the following

applications:

• Microsoft SQL Server 2008 R2 (64-bit)

• Microsoft SQL Server 2008 R2 Native Client

• Microsoft SQL Server 2008 R2 Setup (English)

• Microsoft SQL Server 2008 R2 Setup Support Files

• Microsoft SQL Server Browser

• Microsoft SQL Server Compact 3.5 SP2 ENU

• Microsoft SQL Server Compact 3.5 SP2 x64 ENU

• Microsoft SQL Server VSS Writer

5. Restart the computer.

6. Open the SCIEX OS Installation Repair Tool.

7. If the Clean up SCIEX OS button is active, then click it.

8. After the cleanup is complete, close the SCIEX OS Installation Repair Tool.

9. Install the SCIEX OS software. Refer to the section: Install the SCIEX OS Software or Install

the CAC Software.

10. If the issues cannot be resolved, then follow the instructions in the section: Installation

Cleanup.

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Installation Troubleshooting Tips

Note: The software in this procedure can be either the Central Administrator Console (CAC) or

SCIEX OS software.

Table 6-1 Installation Issues

Error or Warning Message Possible Cause Corrective Action

The installation could

not be completed. Refer

to the figure: Figure 6-1.

Various causes are possible. Do the procedure in the

section: Installation Cleanup.

The installed

version of the

Microsoft Visual C+

+ Redistributable has

not been validated

with the SCIEX OS

software. Refer to the

figure: Figure 6-2.

The version of Microsoft

Visual C++ Redistributable

that is installed on the

computer is later than the

version distributed with the

software.

If this computer is to be used

for acquisition, then remove

the Microsoft Visual C++

Redistributable version shown

in the warning message, and

then install the software again.

No action is required if this

computer is to be used for

processing only.

Microsoft.Practices.Pr

ism.

Regions.UpdateRegions

Exception: An

exception occurred

while trying to create

region objects.

This version of the

LibraryView Framework

installed on the computer

is not compatible with the

software.

1. Remove the software.

2. Remove the

LibraryViewFramework.

3. Rename

C:\ProgramData\SCIEX

C:\ProgramData

\SCIEX_Removed.

4. Install the software.

Setup.exe

- .NET Framework

Initialization Error.

Refer to the figure: Figure 6-3.

.NET Framework Version 4.x

is not installed.

Install .NET Framework

by running Install/

NDP472-KB4054530-x86-

x64-AllOS-ENU.exe,

included in the installation

package.

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Table 6-1 Installation Issues (continued)

Error or Warning Message Possible Cause Corrective Action

The software does not

start after the installation is

changed with the Modify

option in the installation

program.

The software was installed

while devices were active.

To prevent this issue, before

using the Modify option,

deactivate all devices.

If the issue occurs, then delete

the file:

C:\ProgramData\SCIEX\C

learcore2.Acquisition\

HardwareProfile.hwp.

After this file is deleted, the

software will open properly.

Figure 6-1 Installation Error (Example)

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Figure 6-2 Microsoft Visual C++ Redistributable Error

Figure 6-3 .NET Framework Initialization Error

Installation Cleanup

Use this procedure to do an installation cleanup if the SCIEX OS Installation Repair Tool could

not complete a cleanup. Refer to the section: SCIEX OS Installation Repair Tool.

1. If the following applications are installed, then in the Windows Apps & features control

panel, remove the applications, in this order:

• LibraryView software

• SCIEX OS software

• LibraryView Framework

• Microsoft Access Database Engine

• Reporter

2. If applicable, then remove all of the SQL server applications.

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Note: If the SQL server applications are used by active libraries, then do not remove the

applications.

For new installations and upgrades from the SCIEX OS software 1.6.1 and later versions,

remove the following applications:

• Microsoft SQL Server 2008 Setup Support Files

• Microsoft SQL Server 2012 (64-bit)

• Microsoft SQL Server 2012 Native Client

• Microsoft SQL Server 2012 Setup (English)

• Microsoft SQL Server 2012 Transact_SQL ScriptDom

• Microsoft SQL Server Compact 3.5 SP2 ENU

• Microsoft SQL Server Compact 3.5 SP2 x64 ENU

• SQL Server Browser for SCL Server 2012

• Microsoft VSS Writer for SQL Server 2012

For upgrades from the SCIEX OS software 1.5 and earlier versions, remove the following

applications:

• Microsoft SQL Server 2008 R2 (64-bit)

• Microsoft SQL Server 2008 R2 Native Client

• Microsoft SQL Server 2008 R2 Setup (English)

• Microsoft SQL Server 2008 R2 Setup Support Files

• Microsoft SQL Server Browser

• Microsoft SQL Server Compact 3.5 SP2 ENU

• Microsoft SQL Server Compact 3.5 SP2 x64 ENU

• Microsoft SQL Server VSS Writer

3. Back up and then delete all of the SQL server files in the following folders:

• SCIEX OS software 1.6.1 or later: C:\Program Files\Microsoft SQL

Server\MSSQL11.sqlexpress\MSSQL\Data

• SCIEX OS software 1.5 or earlier: C:\Program Files\Microsoft SQL

Server\MSSQL.1\MSSQL\Data or C:\Program Files\Microsoft SQL

Server\MSSQL10-50.sqlexpress\MSSQL\Data

4. In the Windows Apps & features control panel, remove the Update for Microsoft Windows

(KB4054590).

This is the .NET Framework 4.7.2.

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5. If applicable, then in the Windows Apps & features control panel, remove the following

software:

• BPV Flex software

• BioPharmaView software

• MetabolitePilot software

Note: These applications are not supported by the SCIEX OS software 3.4.

6. Back up and then delete the following folders:

• C:\Program Files\SCIEX\LibraryView

• C:\Program Files\SCIEX\SCIEX OS

• D:\SCIEX OS Data

7. Back up and then delete the C:\ProgramData\SCIEX folder.

8. Start the computer again.

9. Open the Windows Services control panel, and then make sure that there are no SQL or

LibraryViewHost services in the list.

10. If the ClearCore2 service is shown in the Windows Services control panel, then open a

Command Prompt window, type the following command, and then press Enter:

sc DELETE "Clearcore2.Service.exe"

11. Install the software again. If applicable, then start the computer again when the prompt is

shown.

12. After the software is installed, restore these files from the backup:

• C:\ProgramData\SCIEX\Clearcore2.Acquisition

• C:\ProgramData\SCIEX\Clearcore2.Client

• C:\ProgramData\SCIEX\MassSpec\InstrumentData\Current.dat

• C:\ProgramData\SCIEX\MassSpec\InstrumentData\Current_Backup.dat

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Mass Spectrometer Firmware

Versions

Note: For SCIEX Triple Quad and QTRAP systems, the version of the instrument controller

board (ICB) that is installed on the system controls the versions of the supported firmware and

configuration table.

Table A-1 Firmware and Configuration Table Versions

Mass Spectrometer Firmware Version Configuration Table Version

X500R QTOF system with LT-

ICU1

ATLAS_QTOF_ICX_v0_r04 CONFIG_X500R_v0_r05

X500R QTOF system with LT-

ICU2

AION_X500_ICX64_v2_r01 CONFIG_X500R_v2_r01

X500B QTOF system with LT-

ICU1

ATLAS_QTOF_ICX_v0_r04 CONFIG_X500B_v0_r04

X500B QTOF system with LT-

ICU2

AION_X500_ICX64_v2_r01 CONFIG_X500B_v2_r01

ZenoTOF 7600 system AION_QTOF_ICX64_v0_r05 CONFIG_Zeno-

TOF-7600_v0_r08

ZenoTOF 7600+ system AION_QTOF_ICX64_v0_r05 CONFIG_ZenoTOF-7600+_v0

_r01

SCIEX Triple Quad 4500

system with ICB3/ICB4

TripleQuad4500_PIL2007 FWTripleQuad4500R22

SCIEX Triple Quad 4500

system with ICB5

TripleQuad4500_QIL0101 FWTripleQuad4500R522

QTRAP 4500 system with

ICB3/ICB4

QTrap4500_PIL2007 FWQTrap4500R21

QTRAP 4500 system with

ICB5

QTrap4500_QIL0101 FWQTrap4500R521

SCIEX Triple Quad 5500

system with ICB3/ICB4

TripleQuad5500_PIL2007 FWTripleQuad5500R08

SCIEX Triple Quad 5500

system with ICB5

TripleQuad5500_QIL0101 FWTripleQuad5500R508

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Table A-1 Firmware and Configuration Table Versions (continued)

Mass Spectrometer Firmware Version Configuration Table Version

QTRAP 5500 system with

ICB3/ICB4

QTrap5500_PIL2007 FWQTrap5500R07

QTRAP 5500 system with

ICB5

QTrap5500_QIL0101 FWQTrap5500R507

SCIEX Triple Quad 5500+

system with ICB3/ICB4

TripleQuad5500+_PIL2007 FWTripleQuad5500+R02

SCIEX Triple Quad 5500+

system with ICB5

TripleQuad5500+_QIL0101 FWTripleQuad5500+R502

SCIEX Triple Quad 6500

system with ICB3/ICB4

TripleQuad6500_PIL2007 FWTripleQuad6500R05

SCIEX Triple Quad 6500

system with ICB5

TripleQuad6500_QIL0101 FWTripleQuad6500R505

QTRAP 6500 system with

ICB3/ICB4

QTrap6500_PIL2007 FWQTrap6500R04

QTRAP 6500 system with

ICB5

QTrap6500_QIL0101 FWQTrap6500R504

SCIEX Triple Quad 6500+

system with ICB3/ICB 4 and

the oil-sealed roughing pump

TripleQuad6500+_PIL2007 FWTripleQuad6500+R04

SCIEX Triple Quad 6500+

system with ICB3/ICB4 and

the dry pump

TripleQuad6500+_PIL2007 FWTripleQuad6500+R31

SCIEX Triple Quad 6500+

system with ICB5 and the oil-

sealed roughing pump

TripleQuad6500+_QIL0101 FWTripleQuad6500+R504

SCIEX Triple Quad 6500+

system with ICB5 and the dry

pump

TripleQuad6500+_QIL0101 FWTripleQuad6500+R531

QTRAP 6500+ system with

ICB3/ICB4 and the oil-sealed

roughing pump

QTrap6500+_PIL2007 FWQTrap6500+R03

QTRAP 6500+ system with

ICB3/ICB4 and the dry

roughing pump

QTrap6500+_PIL2007 FWQTrap6500+R31

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Table A-1 Firmware and Configuration Table Versions (continued)

Mass Spectrometer Firmware Version Configuration Table Version

QTRAP 6500+ system with

ICB5 and the dry pump

QTrap6500+_QIL0101 FWQTrap6500+R503

QTRAP 6500+ system with

ICB5 and the dry pump

QTrap6500+_QIL0101 FWQTrap6500+R531

SCIEX 7500 system with

ICB3/ICB4 and the oil-sealed

roughing pump

TripleQuad7500_PIL2007 FWTripleQuad7500QTRR03

SCIEX 7500 system with

ICB3/ICB4 and the dry pump

TripleQuad7500_PIL2007 FWTripleQuad7500QTRR30

SCIEX 7500 system with ICB5

and the oil-sealed roughing

pump

TripleQuad7500_QIL0101 FWTripleQuad7500QTRR503

SCIEX 7500 system with ICB5

and the dry pump

TripleQuad7500_QIL0101 FWTripleQuad7500QTRR530

SCIEX 7500+ system with the

oil-sealed roughing pump

SCIEX7500+system_QIL0201 FWSCIEX7500+systemR501

SCIEX 7500+ system with the

dry pump

SCIEX7500+system_QIL0201 FWSCIEX7500+systemR531

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Devices and Firmware

The SCIEX OS software 3.4 supports the following devices.

In most cases, more recent firmware versions from the device manufacturer will operate with the

SCIEX OS software 3.4. If issues occur, then change the device firmware to the version listed

in the table. For information about firmware verification or upgrades, refer to the documentation

that was supplied by the device manufacturer or contact a SCIEX Field Service Employee

(FSE). For information about device installation and configuration, refer to the document:

Devices Setup Guide.

Note: For information about drivers for Waters ACQUITY UPLC systems, contact Waters

Support.

Note: For information about drivers for Thermo multichannel LC systems, contact Thermo

Support.

Table B-1 Echo

MS and Echo

MS+ Systems

Device Component Firmware

Echo

MS module

2.0

Echo

MS+ module

2.0

Table B-2 M5 MicroLC System

Device Component Tested Firmware or Software

M5 MicroLC SCIEX OS Driver

1.0

Eksigent Control software 4.3

LC pump 2.48

CTC PAL3 autosampler 2.4.18031.1655

Table B-3 ExionLC 2.0 Systems

Peripheral Device Model Tested Firmware Communication

Cable Required

LPG Pump LPGP-200 1.07 Ethernet

If a firmware upgrade is required, then contact an FSE.

For migration from the Analyst software to SCIEX OS, contact an FSE.

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Table B-3 ExionLC 2.0 Systems (continued)

Peripheral Device Model Tested Firmware Communication

Cable Required

Binary Pump BP-200 1.07 Ethernet

Binary Pump+ BP-200+ 1.02 Ethernet

Autosampler AS-200 1.22 Ethernet

Autosampler+ AS-200+ 1.22 Ethernet

Column Switching

(Valve drive)

DR-200 6.20 Ethernet

Column Oven CO-200 2.02 Ethernet

Multiwavelength

Detector

MWD-200 01.11.282 Ethernet

Diode Array Detector DAD-200 01.11.282 Ethernet

Diode Array Detector -

DADHS-200 1.24.03 Ethernet

Wash System WS-200 1.14 Ethernet

Table B-4 ExionLC AE Systems

Model Tested Firmware Communication Cable

Required

ExionLC AE Controller 1.65 Ethernet

ExionLC AE Pump 1.12 Optic

ExionLC AE Multiplatesampler 3.30 Optic

ExionLC AE Autosampler 1.17 Optic

ExionLC AE Column Oven 1.03 Optic

ExionLC AE PDA Detector 2.08 Ethernet

ExionLC AE UV Detector 1.11 Optic

The PDA detector requires a switching hub to connect to the system controller and the acquisition computer.

Refer to the document: SCIEX OS Devices Setup Guide.

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Table B-5 ExionLC AC/ExionLC AD Systems

Peripheral Device Tested Firmware (Other

Firmware

)

Communication Cable

Required

ExionLC Controller 3.61 (2.0, 3.01, 3.40) Ethernet

ExionLC AC Pump 5.001 (2.04) Optic

ExionLC AC Autosampler 5.00 (2.05, 3.12) Optic

ExionLC AC Column Oven 3.21 Optic

ExionLC AD Pump 3.30 (2.04, 3.11, 3.21) Optic

ExionLC AD Autosampler 3.15 (3.12) Optic

ExionLC AD Multiplate

Sampler

3.30 (3.15) Optic

ExionLC PDA Detector 4.02 Ethernet

ExionLC UV Detector 2.03 Optic

ExionLC Rack Changer 2.0 Optic

ExionLC Degasser N/A N/A

ExionLC Solvent Selection

Valve

N/A N/A

Table B-6 Agilent 1290 Infinity and Infinity II Devices

Peripheral Device Model Tested Firmware

(Other Firmware

)

Communication

Cable Required

1290 Infinity Devices

Binary pump G4220A B.06.73, A.06.73,

B.07.01),

Ethernet or CAN

Standard autosampler G4226A (A.07.01, A.06.54,

A.07.01)

Ethernet or, if the

system contains a

DAD, then CAN

Column compartment G1316C (A.07.01, A.06.53) CAN

DAD G4212A A.06.73, B.06.30 Ethernet

1290 Infinity II Devices

Not tested but expected to work.

The PDA Detector requires a switching hub to connect to the system controller and the acquisition computer.

Refer to the document: SCIEX OS Devices Setup Guide.

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Table B-6 Agilent 1290 Infinity and Infinity II Devices (continued)

Peripheral Device Model Tested Firmware

(Other Firmware

)

Communication

Cable Required

High-speed pump G7120A (B.07.10) CAN or Ethernet

Flexible pump G7104A (B.07.10) CAN or Ethernet

Vialsampler G7129B (B.07.10) CAN

Multisampler G7167B (D.07.17) CAN or Ethernet

Multicolumn-

thermostat

G7116B D.07.10 CAN

DAD G7117B D.07.23 (D.07.10) Ethernet

Table B-7 Agilent 1260 Infinity II Devices

Peripheral Device Model Tested Firmware

(Other Firmware

)

Communication

Cable Required

Infinity II Devices

Flexible pump G7104C (B.07.25) Ethernet or, if the

system contains a

DAD, then CAN

Binary pump G7112B D07.33 CAN or Ethernet

Quarternary pump G7111B D.07.24 CAN or Ethernet

Bio-inert pump G5654A (D.07.13) CAN or Ethernet

Vialsampler G7129C (D.07.26) CAN

Multisampler G7167A (D.07.16) Ethernet or, if the

system contains a

DAD, then CAN

Bio-inert multisampler G5668A (D.07.16) Ethernet or, if the

system contains a

DAD, then CAN

Multicolumn

thermostat

G7116A D.07.13, D.07.16 CAN

DAD G7117C D.07.10 Ethernet

DAD WR G7115A D.07.25 Ethernet

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Table B-7 Agilent 1260 Infinity II Devices (continued)

Peripheral Device Model Tested Firmware

(Other Firmware

)

Communication

Cable Required

FLD spectra (Bio-

inert)

G7121B D.07.25 Ethernet

Table B-8 Shimadzu Devices

Peripheral Device Tested Firmware (Other

Firmware

)

Communication Cable

Required

CBM-20 A with Ethernet

switch (system controller with

8 fiber optic ports)

3.61 (2.81, 3.01, 3.11, 3.31) Ethernet

CBM-40 system controller 1.30 (0.31) Ethernet

CBM-40 Lite system controller 1.30 Ethernet

SCL-40 system controller 1.30 Ethernet

SIL-20ACXR autosampler 2.05 (1.20, 1.22, 1.23, 1.25) Optic

SIL-30AC autosampler 3.12 Optic

SIL-30ACMP autosampler 3.21 (3.15) Optic

SIL-40 autosampler 1.05 Optic

SIL-40C autosampler 1.05 Optic

SIL-40C X3 autosampler 1.05 (1.04) Optic

SIL-40C XR autosampler 1.05 (1.08) Optic

LC-20AB binary solvent

delivery unit

N/A N/A

LC-20AD pump 3.11 (1.04, 1.10, 1.07) Optic

LC-20AD XR pump 1.21 (1.20) Optic

LC-30AD pump 3.21 (3.11) Optic

LC-40D pump 1.06 Optic

LC-40D XR pump 1.06 (1.04) Optic

LC-40B XR pump 1.04 Optic

LC-40D X3 pump 1.04 Optic

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Table B-8 Shimadzu Devices (continued)

Peripheral Device Tested Firmware (Other

Firmware

)

Communication Cable

Required

LC-40B X3 pump 1.06 (1.04) Optic

CTO-20AC column oven 2.10 (2.03) Optic

CTO-30A column oven 3.11 Optic

CTO-40C column oven 1.01 (1.00) Optic

CTO-40S column oven 1.01 (1.00) Optic

SPD-20A UV-Vis detector 1.04 Optic

SPD-40V UV-Vis detector 1.06 (1.04) Optic

SPD-M30A UV detector 3.11, 4.02 Ethernet

SPD-M40 PDA detector 2.00 Ethernet

RF-20A XS fluorescence

detector

2.02 Optic

FCV-12AH valve N/A N/A

FCV-13AL valve N/A N/A

FCV-32AH valve N/A N/A

FCV-0206[H/H3] flow channel

selection valve with drive

N/A N/A

FCV-0607[H/H3] flow channel

selection valve with drive

N/A N/A

FCV-S flow channel selection

valve with drive (1 box,

1 valve)

1.02 N/A

FCV-DR (drive) 1.02 N/A

LPGE-40 (no mixer) 1.02 N/A

LC-40 reservoir switching

valve

1.02 N/A

FCV-11ALS solvent selection

valve for LC-40 (1 pump)

1.02 N/A

The detector requires a switching hub to connect to the system controller and the acquisition computer.

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Table B-8 Shimadzu Devices (continued)

Peripheral Device Tested Firmware (Other

Firmware

)

Communication Cable

Required

FCV-11AL solvent selection

valve for LC-40 (3 pumps)

1.02 N/A

Rack Changer II 2.0 Optic

Nexera Plate Changer 1.05 N/A

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Windows Operating System

Configuration

Only the English Language setting is supported.

The English, German, French, and Italian Region settings are supported.

Note: If the computer is connected to the Internet, then follow the recommended security

guidelines. Go to sciex.com/productsecurity. Make sure that adequate virus protection is in place

to prevent virus corruption of system functionality.

Windows Update

Making sure that critical security patches are installed is essential to maintaining the security of

the computer. Follow these guidelines for the configuration and use of Windows Update:

• Windows 10: Configure Windows Update to notify only. Do not download and install updates

automatically as this may impact systems during data acquisition.

• Download and install updates as soon as possible after notification is received.

• Before installing updates:

• Wait until acquisition and processing is finished.

• Deactivate the devices and stop the ClearCore2 service.

• Install all updates. If an issue occurs as the result of an update, report it to SCIEX at

sciex.com/contact-us or sciex.com/request-support as soon as possible.

System Restore

By default, the Windows Task Scheduler runs the System Restore task at midnight and when

the computer starts. The installation program disables the System Restore task, to optimize

acquisition performance in IDA mode.

The System Restore task might slow down the system when it is active. If it is active during

acquisition in IDA mode, the cycle time might be longer, increasing from milliseconds to

seconds. This might result in fewer points across a chromatographic peak. Therefore, we

recommend that the System Restore task be disabled, for optimum performance.

Note: System Restore does not impact performance for regular operations or for data

processing.

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Customer Security Guidance: Backups

Backup of customer data is the responsibility of the customer. Although SCIEX service and

support personnel might provide advice and recommendations about customer data backup, it

is up to the customer to make sure the data is backed up according to the policies, needs, and

regulatory requirements of the customer. The frequency and coverage of customer data backup

should be commensurate with organizational requirements and the criticality of the data that is

generated.

Customers should make sure that backups are functional, because backups are a vital

component of overall data management and essential to recovery in the event of a malicious

attack, hardware failure, or software failure. Do not back up the computer during data

acquisition, or else make sure that files being acquired are ignored by the backup software.

We strongly recommend that a full backup be taken of the computer before any security updates

are installed or any computer repairs are performed. This will facilitate a rollback in the rare case

that a security patch affects any application functionality.

User Account Control Settings

We recommend the use of the default User Account Control Settings when the SCIEX OS

3.4 software is installed on the Windows 10, 64-bit, operating system. For the Administrator,

the default setting is Default - Notify me only when programs try to make changes to my

computer. For standard users, it is Always notify me.

The acquisition computer comes configured with the default User Account Control Settings.

1. Open Control Panel.

2. Click Security and Maintenance > Change User Account Control settings.

The User Account Control Settings dialog opens.

3. Move the slider bar to the required level.

4. For the Administrator, select Notify me only when programs try to make changes to my

computer (default), and then click OK.

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Figure C-1 User Account Control Settings: Administrator

5. For standard users, select Always notify me when, and then click OK.

Region Settings

Note: Setting the Format field to a different value might cause the software to show the file

information or the audit trail information incorrectly.

1. Open Control Panel.

2. Click Region.

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Figure C-2 Region Dialog

3. Make sure that the Format field is set to English (United States), French (France), or

German (Germany).

4. Click Apply.

5. Click OK.

Language Settings

Note: Setting the Windows display language to a different value might cause the software to

show the file information or the audit trail information incorrectly.

1. Open Control Panel.

2. Click Region.

3. Click Language preferences.

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Figure C-3 Language Dialog

4. For the Windows display language, select English (United States).

Local Settings

Only the local settings shown in the following figure are supported.

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Figure C-4 Local Settings

Label Supported in the SCIEX OS Software

Decimal symbol Either '.' or ',' is supported.

No. of digits after

decimal

Controlled by the number format in the SCIEX OS software.

Digit grouping symbol Not supported.

Digit grouping Not supported.

Negative sign symbol Controlled by the SCIEX OS software.

Negative number

format

Not supported.

Display leading zeros Not supported.

List separator Not supported.

Measurement system Not supported.

Standard digits Not supported.

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Label Supported in the SCIEX OS Software

Use native digits Not supported.

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Configure Windows Firewall

The SCIEX OS software connects to the Central Administrator Console (CAC) server with TCP

ports 63333 and 44144. Use the procedures in this section to open the Windows firewall ports

on the CAC server and the computer with the SCIEX OS when Windows Defender is used as

firewall software (default). If different firewall software is used, then use instructions specific to

that software to open the ports.

If the queue monitoring feature will be used, then ports 5000 and 5001 must be opened for

inbound traffic on the CAC server.

Configure Incoming Connections

On the computer with the SCIEX OS software, ports 63333 and 44144 must be open for inbound

traffic. On the Central Administrator Console (CAC) server, port 63333 must be open for inbound

traffic.

To use the queue monitoring feature, open ports 5000 and 5001 on the CAC server.

1. Open the Windows Defender Firewall with Advanced Security.

2. Right-click the Inbound Rules menu, and then click New Rule.

The Rule Type page opens.

3. Select Port, and then click Next.

The Protocol and Ports page opens.

4. Set Specific local ports as required, and then click Next.

• SCIEX OS software: Set Specific local ports to 63333,44144.

• CAC software: Set Specific local ports to 5000, 5001, and 63333.

Note: Ports 5000 and 5001 are required only if the queue monitoring feature will be used.

The Action page opens.

5. Select Allow the connection, and then click Next.

The Profile page opens.

Note: Make sure that Domain, Private, and Public profiles are selected.

6. Click Next.

The Name page opens.

7. Type CAC inbound connections in the Name field.

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8. Click Finish.

Configure Outgoing Connections

On the computer with the SCIEX OS software, ports 63333 must be open for outbound traffic.

On the Central Administrator Console (CAC) server, port 44144 must be open for outbound

traffic.

1. Open the Windows Defender Firewall with Advanced Security.

2. Right-click the Outbound Rules menu, and then click New Rule.

The Rule Type page opens.

3. Select Port, and then click Next.

The Protocol and Ports page opens.

4. Set Specific local ports as required, and then click Next.

• SCIEX OS software: Set Specific local ports to 63333.

• CAC server: Set Specific local ports to 44144 and 63333.

The Action page opens.

5. Select Allow the connection, and then click Next.

The Profile page opens.

Note: Make sure that Domain, Private, and Public profiles are selected.

6. Click Next.

The Name page opens.

7. Type CAC inbound connections in the Name field.

8. Click Finish.

Configure Windows Firewall

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Install the Software Using a

Deployment Tool

Use the command lines in this procedure for the modular installation of the SCIEX OS software.

User can install, change, repair or remove the software modules by running the silent mode or

passive mode commands from the installation files location using the deployment tool.

setup.exe {/quiet | /passive} [/install=modules] [/add=modules] [/

repair=all] [/remove=modules] [/uninstall=all]

Table E-1 Elements and Attributes

Value String Comment

/quiet

Runs the installation in silent mode without any user

interaction.

/passive

Runs the software installation in unattended mode. The user

sees only a progress bar.

/install=module1,

module2

To install one or more than one software module. For a list of

the module codes, refer to the table: Table E-2.

/add=module1,module2 To install one or more than one software module in an existing

installation of this software version. For a list of the module

codes, refer to the table: Table E-2.

/repair=all

To repair installed software modules.

/remove=module1,module2 To uninstall one or more than one software module from an

existing installation of this software version. For a list of the

module codes, refer to the table: Table E-2.

/uninstall=all

To remove the SCIEX OS software.

Table E-2 Software Modules

Code Software Module

AG Agilent drivers

AN Analytics workspace (Processing)

AQ Acquisition workspaces

CC Central Administrator Console (CAC) (Administration)

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Table E-2 Software Modules (continued)

Code Software Module

EC Echo

MS system

EX ExionLC system

M5 M5 MicroLC system

MP Molecule Profiler software (Processing)

MV MarkerView software (Processing)

SH Shimadzu drivers

Example: Quiet Install Command

Setup.exe /quiet /Install=MP

Example: Quiet Add and Remove Command

Setup.exe /quiet /Add=AQ,AG,SH,AN /Remove=MP

Example: Quiet Repair Command

Setup.exe /quiet /Repair=all

Example: Quiet Uninstall Command

Setup.exe /quiet /Uninstall=all

Example: Passive Install Command

Setup.exe /passive /Install=MP

Example: Passive Add and Remove Command

Setup.exe /passive /Add=AQ,AG,SH,AN /Remove=MP

Example: Passive Repair Command

Setup.exe /passive /Repair=all

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Example: Passive Uninstall Command

Setup.exe /passive /Uninstall=all

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Documentation for the SCIEX OS

Software

For a list of the software guides that are installed with the SCIEX OS software, refer to the table:

Table F-1. These guides can be accessed at the following locations: Start > SCIEX OS.

The software guides are installed in <drive>:\Program Files\SCIEX\SCIEX

OS\Documentation\.

Table F-1 Software Documentation

Document Description

Software Installation Guide Supplies procedures for installation of the software.

Installed with the software.

Release Notes Gives a description of new features and any software

issues. Installed with the software.

Laboratory Director Guide Gives a description of the security and audit

functionality of the SCIEX OS software. Installed with

the software.

SCIEX OS Help System Supplies procedures for setting up and using the

SCIEX OS software to create methods, acquire

samples, and analyze data. Installed with the software.

To see the Help System, click the Help button in the

SCIEX OS software.

CAC Help

Supplies procedures for using the Central Administrator

Console (CAC) software to manage users, workgroups,

workstations, and projects. Installed with the software.

To see the Help, click the Help button in the CAC

software.

Devices Setup Guide

Supplies procedures for configuration of devices for

operation with the mass spectrometer and control

by the SCIEX OS software. Available at sciex.com/

customer-documents.

Explorer for TOF Systems Tutorial

Supplies procedures for using the Explorer workspace

to analyze data that was acquired by TOF systems.

Available at sciex.com/customer-documents.

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Hardware guides are distributed on the Customer Reference DVDs for the system and ion

source. The following table lists these guides.

Table F-2 Hardware Documentation

Document Description

System User Guide Supplies information about operation and maintenance

of the mass spectrometer and using the SCIEX OS

software.

Qualified Maintenance Person Guide Supplies procedures for cleaning and maintenance of

the mass spectrometer.

Note: Only qualified operators should perform the

procedures in this guide.

Devices Setup Guide

Supplies procedures for connection of devices to the

computer and instrument.

Site Planning Guide Supplies information about how to prepare the site,

as well as materials required for installation of the

instrument.

Turbo V Ion Source Operator Guide X500 QTOF and ZenoTOF systems: Supplies

procedures for installation and maintenance of the ion

source.

IonDrive Turbo V Ion Source Operator

Guide

Supplies procedures for installation and maintenance

the ion source.

OptiFlow Turbo V Ion Source

Operator Guide

ZenoTOF systems: Supplies procedures for installation

and maintenance the ion source.

OptiFlow Pro Ion Source Operator

Guide

SCIEX 7500 systems: Supplies procedures for

installation and maintenance the ion source.

Echo

MS Core Module User Guide Echo

MS systems: Supplies procedures for operation

and maintenance of the Echo

MS core module.

Echo

MS+ System User Guide Echo

MS+ systems: Supplies procedures for

operation and maintenance of the Echo

MS+ system.

Note: The latest versions of the documentation are available on the SCIEX website, at

sciex.com/customer-documents.

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Customer Training

• In North America: NA.CustomerT[email protected]

• In Europe: Europe.CustomerT[email protected]

• Outside the EU and North America, visit sciex.com/education for contact information.

Online Learning Center

• SCIEX Now Learning Hub

SCIEX Support

SCIEX and its representatives have a global staff of fully-trained service and technical

specialists. They can supply answers to questions about the system or any technical issues

that might occur. For more information, go to the SCIEX website at sciex.com or use one of the

following links to contact us.

• sciex.com/contact-us

• sciex.com/request-support

Cybersecurity

For the latest guidance on cybersecurity for SCIEX products, visit sciex.com/productsecurity.

Documentation

This version of the document supersedes all previous versions of this document.

To find software product documentation, refer to the release notes or software installation guide

that comes with the software.

To find hardware product documentation, refer to the documentation that comes with the system

or component.

The latest versions of the documentation are available on the SCIEX website, at sciex.com/

customer-documents.

Note: To request a free, printed version of this document, contact sciex.com/contact-us.

Software Installation Guide

RUO-IDV-02-7371-Z

SCIEX OS Software 3.4

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