General Security Guidance


This guidance provides supplemental instructions for protecting your SCIEX acquisition and processing computers. This guidance is intended to supplement rather than replace your current IT policies, requirements, and practices. We suggest that you consult with your IT department before implementing any of the recommended changes.


Although SCIEX computers are released with a general use operating system, we recommend that you treat the computer as a specialized system that is an extension of the instrument itself. To safeguard the computer, use the computer only to perform the steps required for your workflows, not for additional purposes. We recommend that you follow the security best practices outlined in this document for both acquisition and processing computers.

Do not use obsolete operating systems

Obsolete operating systems have vulnerabilities and security gaps that can be exploited by attackers. To protect the computer, make sure that it is running Windows 7 or Windows 10. These operating systems have enhanced security features.

Disable USB ports

USB devices can be programmed to spread viruses to any computer they touch. They can infect computers at the boot stage, before antivirus tools can intervene. To protect the computer, disable the USB ports on the front panel of the computer. Make sure that the USB ports on the back panel remain enabled for Service use.

Do not browse the Internet from the computer

Browsing the Internet from your computer greatly increases the risk of a malware infection. Certain malware can automatically infect your computer by visiting a compromised website without any operator intervention. Downloading and installing applications from the Internet greatly increases the surface area of attack and is strongly discouraged.

Do not use email on the computer

Email is the number one vector of attack for delivering malware. Most malware is delivered via email attachments or malicious links within emails. Using email on the computer greatly increases the risk of a potential malware infection. We strongly recommend that no email activity be performed on the computer.

Do not install any unnecessary third-party software

Installing additional software on your computer increases the attack surface for potential infections. Malware authors often exploit vulnerabilities in third-party applications (like Adobe Flash) to exploit the underlying operating system. We recommend that, whenever possible, you do not perform additional work on the acquisition computer. Instead, use a computer that is intended and protected for such use. If third-party applications must be installed, then we recommend that they be kept up-to-date with the latest security patches.

Establish strong password policies

Make sure that your password is at least 8, and preferably 10, characters long and a mixture of uppercase, lowercase, alphanumeric, and special characters. Enable a screen saver password and inactivity timeout. We recommend that the timeout be 10 minutes. Lock the computer when stepping away from it. Do not share your password with others.

Enable Windows Update

Making sure that critical security patches are installed is essential to maintaining the security of the computer. Our recommended setting is to notify you about the availability of updates and to allow you to select which patches to install and when. This option provides the flexibility to ensure that the installation does not negatively affect acquisition from the instrument. Organizations must balance their security needs and risk tolerance with their need to apply usability patches immediately on release. However, we also recommend that you do not run any Windows updates during SCIEX software acquisition and data processing.

Install antivirus software

While it is a widely acknowledged good practice to employ antivirus and backup software, these applications can interfere with the real-time nature of the SCIEX acquisition software. Some antivirus and backup applications are configured by default to automatically scan and archive a file immediately after creation. Because SCIEX acquisition software can perform multiple writes to a single data file during an acquisition sequence, these real-time features must be disabled to prevent the antivirus or backup software from locking the data file while it is still needed by the SCIEX software application. Many widely-used applications can be configured to either disable real-time protection or ignore certain file-types and paths. Failure to do so might result in either failed acquisitions or acquisitions that take longer to complete than expected.

Follow these guidelines when configuring antivirus software on the acquisition computer:

  • Disable real-time scanning and archiving of files.
  • Ignore the following file types:
    atmsc, rdb, atds, scan, journal, wiff, qsession, wiff2
  • Ignore the following folders and paths:
    For Analyst® software installations:
    • 32-bit: C:\Program Files\Analyst
    • 64-bit: C:\Program Files (x86)\Analyst
    • D:\Analyst Data

    For SCIEX OS installations:
    • C:\Program Data\SCIEX
    • C:\Program Files\SCIEX
    • D:\SCIEX OS Data

Also ignore any folders containing drivers for connected devices, such as Eksigent LC systems.

Note: The default installation location for the Analyst Data folders is D:\. These folders might be installed on a different drive.

For example, in the Symantec Endpoint software, the following settings have been found to improve performance during data acquisition:

  • Virus and Spyware Protection:
    • Auto-Protect > Advanced > Scan files when: Scan when a file is modified.
    • Early Launch Anti-Malware: Disable Symantec Early Launch Anti-Malware.
  • Exceptions > Security Risk Exceptions:
    • Extensions: Make sure that the Extensions list includes the previously specified extensions.
    • Folder: Add the previously specified folders.
  • Proactive Threat Protection Settings:
    • General: Disable SONAR.
    • Suspicious Behavior Detection: Disable Suspicious Behavior Detection.
  • Network and Host Exploit Mitigation Settings
    • Firewall: Disable Smart DHCP, Smart DNS, and Smart WINS.
    • Memory Exploit Mitigation Policy: Disable Memory Exploit Mitigation.

For users running IDA and Scheduled MRM™ workflow on TripleTOF®, QTRAP®, and X500 QTOF systems, antivirus software might interfere with data acquisition and cause delays with acquisition of data points. We recommend that either you disable real-time antivirus protection, antivirus scheduled scans, and other data-intensive background tasks for these acquisition scenarios or perform validation for your specific antivirus and use case scenarios. After acquisition is complete, re-enable the real-time antivirus.

For instructions on how best to configure your particular antivirus or backup software, contact your antivirus or backup software provider.

Enable Windows Firewall (currently enabled by default)

As an additional layer of security, we recommend that the Windows Firewall remain enabled. The Windows Firewall has been turned on by default and is set to allow only a minimal number of necessary Windows services.

Keep other applications up to date

The SCIEX computer comes with Adobe Reader to allow operators to view our guides and documentation. We recommend that updates be installed as required, to reduce possible attack vectors. We recommend that the user guides and documentation be viewed on a computer other than the acquisition computer.

Leave network discovery turned off

Network discovery allows the computer to discover other computers on the network, but it also allows other computers to discover the computer. If the computer is discoverable, then it can be scanned for vulnerabilities. Keeping this setting disabled has little impact on your ability to access any resources.

Turn off AutoPlay (currently enabled for CD/DVDs and not removable drives)

Malware can take advantage of the AutoPlay (auto run) functionality as a mechanism to infect a computer. Because of the large-scale global outbreak of the Conflicker virus in 2008, Microsoft changed the behavior of AutoPlay for removable devices only. We recommend disabling AutoPlay for all media types, including removable and CD/DVD devices.


The frequency of backup of computers should be commensurate with organizational requirements and the criticality of the data that is generated. Making sure that backups are functional is 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 make sure that the files mentioned previously are ignored by the backup software. We strongly recommend that a full backup be taken of the computer prior to installation of any security updates. This will facilitate a rollback in the rare case that a security patch affects any application functionality.

Enable Internet Explorer security settings (if browsing the Internet is absolutely required)

While we strongly recommend that Internet browsing not be conducted on the computer, if you choose to do so then you should enable security settings that will help to protect your computer. These include:

  • Enable Internet Explorer Enhanced Protected Mode

    To enable Internet Explorer to protect your computer and personal data, Enhanced Protected Mode isolates untrusted web content in a restricted environment known as an AppContainer. This mode limits how much access malware, spyware, and other potentially harmful code has to your system.
  • Enable SmartScreen Filter

    SmartScreen Filter helps you to identify reported phishing and malware websites and also helps you to make informed decisions about downloads. Set the security for the Internet zone to High, if possible. Setting this zone to High maximizes all safeguards available in the browser. As a result, however, the browsing experience will be limited. For example, this setting prevents running of scripts and downloading of files.
  • Security Event Log Auditing

    Security event log auditing is a powerful tool that logs and tracks system activity. The logs can be used to make sure that regulatory compliance requirements are met, to monitor critical user activity, to detect anomalous behavior, and more. Because auditing plays a key role in providing evidence for regulatory compliance, consult with the appropriate personnel prior to making any of the recommended changes. To provide a secure baseline, we recommend the following customized auditing settings:


Audit Policy SettingLog on SuccessLog on Failure
Audit Credential ValidationYesNo
Audit Computer Account ManagementYesNo
Audit Other Account Management EventsYesNo
Audit Security Group ManagementYesNo
Audit Process CreationYesNo
Audit LogoffYesNo
Audit LogonYesNo
Audit Audit Policy ChangeYesYes
Audit Security State ChangeYesYes
Audit Security System ExtensionYesYes

If you have any questions regarding the security of your system, please contact SCIEX Support at

If you would like to arrange for SCIEX Service to perform on-site securing of your system, please email