SCIEX OS Software User Guide

SCIEX OS Software

Introduction

Bring high-quality data to your drug discovery process quickly and simply. Regardless of scale, our integrated systems include software and services that come together as total solutions to deliver high-quality, rapid results for confident, data-driven decision making.

• To Ensure Compatibility with Your IT Environment
  With the shift to Windows 11, SCIEX OS software is designed to integrate seamlessly into your lab’s infrastructure, helping you stay current without compromising performance or support.
• To Empower Your Lab with Future-Ready Tools
  Your workflows demand software that keeps pace. The transition to SCIEX OS software ensures you have access to streamlined and modern solutions with tools for compliance that can support your evolving scientific needs.
• To Help You Achieve Long-Term Efficiency and Innovation
  SCIEX OS software provides a secure, scalable foundation that supports automation, customization, and regulatory compliance, so your lab can focus on discovery, not disruption.

Who This Guide is For?

• Lab managers
• Analysts/end-users
• Quality/compliance leads
• IT/administrators

Why is This Change Happening

• Transitioning from Analyst software to SCIEX OS software involves a structured migration designed to modernize your LC-MS workflows with minimal operational disruption.
• The scope covers software installation, data, and method migration, instrument connection, user account setup, and verification that the system performs properly in your IT environment. You may opt to purchase from SCIEX Professional Services Consultants and Software Workflow Specialists who guide planning, readiness assessment, and validation activities. The level of effort varies by lab size, but could include preparation steps such as confirming system requirements, completing backups, updating standard operating procedures, and coordinating with IT and quality assurance.
• Users should plan for data integrity checks, configuration reviews, and basic acceptance testing to ensure compliance with internal and regulatory expectations, including 21 CFR Part 11. Training is part of the expected workflow, with SCIEX Now resources and eLearning paths to accelerate user adoption.
• Overall, the transition is a manageable, well-supported process that positions your lab for greater efficiency, compliance, and future software compatibility.

Why Transition to SCIEX OS Software

• Transitioning from Analyst software to SCIEX OS software is about building on your expertise with smarter, more agile tools. Designed for modern labs, SCIEX OS software offers streamlined workflows, enhanced compliance features, and compatibility with Windows 11 LTSC 2024.
• SCIEX OS software is not just a replacement for Analyst, it is the strategic platform SCIEX is building on for the next generation of features, instruments, and digital capabilities. By transitioning now, laboratories position themselves to take advantage of advancements that will only be delivered through SCIEX OS going forward.

Business and Scientific Benefits

• Improved Compliance, Auditability, and Data Integrity
  SCIEX OS software includes enhanced controls for secure access, user management, audit trails, electronic signatures, and record protection, helping labs more easily meet GxP and 21 CFR Part 11 requirements. Built-in features reduce reliance on custom workarounds and manual oversight, making it easier to maintain defensible and traceable LC-MS data during audits and investigations.
• Expanded Automation and Connectivity Options
  Decision Rules, Flagging Rules, Calculated Columns, and automatic data processing/reporting allow analysts to configure workflows that run with minimal supervision. These tools help standardize results, reduce variability, and free up analyst time. SCIEX OS software also integrates more seamlessly with instruments, networks, and downstream systems to support connected lab initiatives.
• Greater Performance and Scalability
  SCIEX OS software is optimized to process larger datasets, handle more complex acquisition methods, and support multi-instrument environments without compromising speed or stability. As your lab expands capacity, adds instruments, or increases sample volume, SCIEX OS provides a foundation that scales with instrument environments without compromising speed or stability.
• Alignment with Evolving Regulatory and Data-Management Requirements
  As regulatory expectations shift toward stronger data governance and as IT environments move to Windows 11 and beyond, SCIEX OS software provides the long-term software continuity needed to stay current. It is built to support future feature releases, instrument innovations, and cloud capabilities, ensuring your lab remains aligned to both compliance trends and digital transformation goals.
• Modern, Intuitive User Interface and Streamlined Workflows
  The interface is designed for faster adoption and fewer manual steps—from method creation to acquisition to data review. Common tasks that require multiple windows or manual configuration in Analyst software are simplified in SCIEX OS software, reducing opportunities for error and improving day-to-day operational efficiency.

Advantages of SCIEX OS Software
This section provides a clear comparison of Analyst software and SCIEX OS software, showing a clear view of how SCIEX OS enhances acquisition, processing, automation, and data integrity capabilities across SCIEX instruments. It highlights the advanced features, streamlined workflows, and integrity capabilities across SCIEX instruments and its aligned architecture that position SCIEX OS as the strategic foundation for performance, usability, and regulatory readiness. The following advantages are summarized directly from the official Analyst to SCIEX OS software comparison document to provide a focused, fact-based view of where SCIEX OS extends capabilities beyond Analyst.

What’s New and Improved in SCIEX OS Software

SCIEX OS software introduces a series of architectural, functional, and workflow-level enhancements that extend well beyond the capabilities of Analyst software. These improvements address automation readiness, data processing consistency, compliance tools, and system-level integration—resulting in a more robust, configurable, and scalable LC-MS environment. The features below represent high-impact technical advancements available only in SCIEX OS software.

1. Decision Rules (Advanced Batch Logic Engine)
   SCIEX OS implements a rule-based logic framework that evaluates analytical results in real time and executes predefined actions without user intervention.
2. Calculated Columns (Custom Computation Engine)
   Calculated Columns provide a built-in computation layer within the quantitation environment.
3. Flagging Rules (Automated QC Criteria Evaluation)
   Flagging Rules allow users to implement automated quality checks that systematically evaluate each result against predefined criteria.
4. Unified Acquisition + Processing Environment
   SCIEX OS consolidates acquisition, processing, and reporting under a single platform with a shared data structure (.wiff2), reducing file fragmentation and synchronization issues.
5. Automated Data Processing and Reporting (Pipeline Level Automation)
   SCIEX OS integrates end-to-end automation for the data processing pipeline.
6. Enhanced MRM Intelligence
   SCIEX OS supports advanced acquisition modes such as Scheduled MRM (sMRM) with improved retention time scheduling logic, Scout-triggered MRM (stMRM) for data-rich acquisition triggered by marker ions, and optimized peak detection and integration algorithms.
7.  Strengthened Compliance Tools and Audit Framework
   SCIEX OS software includes enhanced electronic audit trails, configurable role-based access control, integrated electronic signatures, and centralized workstation and user management (Central Administrator Console).
8. Method Development Improvements
   SCIEX OS software offers more flexible method editors for MS and LC parameters, including improved optimization tools (ACO) and expanded system compatibility (SCIEX Triple Quad, QTRAP, QTOF, ZenoTOF).
9. Metrics Tracker (Trend Analysis Workspace)
   This dedicated workspace for tracking analyte and instrument performance over time helps users identify subtle changes before they impact data quality.

Learning and Enablement Resources

• Webinar Series: Deep-Dive into Benefits of SCIEX OS Software
  SCIEX offers an on-demand webinar series for teams evaluating or transitioning to SCIEX OS software. These sessions provide practical demonstrations of key features such as Decision Rules, Calculated Columns, Flagging Rules, and automated reporting, and explain how these capabilities streamline workflows, reduce manual intervention, and support compliance frameworks. The webinars are especially useful for lab managers, method developers, and QA/RA personnel who want a deeper understanding of the operational improvements SCIEX OS delivers beyond Analyst software.
• Additional Resources Available on SCIEX Now
  With 178 courses in different languages, SCIEX Now online provides centralized, on-demand access to training, documentation, and troubleshooting resources that support labs throughout the migration and daily use of SCIEX OS software.

Key materials available include:

Software user guides and technical documentation Detailed installation guides, configuration instructions, release notes, and technical bulletins for SCIEX OS and compatible instruments. (General SCIEX documentation hub already reflected in SCIEX product pages)

Learning paths and self-paced courses Structured courses for:

•  Quantitation workflows (SCIEX Triple Quad/QTRAP)
• Screening workflows
• SCIEX TripleTOF systems

These paths help users quickly build proficiency with SCIEX OS features and interfaces.

 Application tutorials and how-to videos Step-by-step tutorials covering:

• • MS tune
• Method creation
• Source and compound optimization
• Data acquisition
•  Explorer workspace
• Quantitation and targeted ID
• Flagging Rules and Calculated Columns
• Metrics Tracker for system performance monitoring

Knowledge Base articles
A searchable library of troubleshooting articles, best practice recommendations, configuration tips, and system-specific guidance created by SCIEX specialists.

Software Community forum

• A peer-to-peer discussion space where users can ask questions, share workflows, and learn from other SCIEX OS adopters and SCIEX application experts.
• These SCIEX Now resources help extend learning well beyond the software installation and ensure teams maintain long-term proficiency with SCIEX OS.

Local Language Support
SCIEX Now and our regional service and support teams provide assistance in local languages, ensuring that users receive guidance, troubleshooting, and operational support in the language they are most comfortable with.

Migration process
This section outlines the end-to-end path for moving a single LC-MS workstation from Analyst software to SCIEX OS software. It is organized into three practical stages, Premigration, Migration, and Validation and Acceptance, so lab leadership, IT, QA, and analysts can coordinate tasks, minimize downtime, and maintain compliance from first installation through go live. For detailed procedural instructions, please refer to the Laboratory Director’s guide below, which serves as the primary reference for all steps described in this section.

Premigration (planning and prerequisites)
Premigration confirms that workstations, network permissions, and backups meet SCIEX OS requirements and that CSV/Part 11 expectations (URS, risk assessment, IQ/OQ/PQ scope) are defined; the outcome is a documented
“ready to install” state with verified backups, IT/QA preapprovals, and a scheduled downtime window.

What this covers:

• System and hardware requirements: Verify workstation specs and Windows OS compatibility for SCIEX OS; confirm any dependent drivers or firmware prerequisites.
•  Backups and data protection: Create verifiable backups of Analyst data (methods, projects, user profiles, configurations) and document restore steps.
• Network and permissions: Ensure domain access, storage paths, antivirus exclusions, and role permissions are in place for installation and instrument control.
• Validation considerations (CSV/Part 11): Define URS and risk assessment scope, align on required validation deliverables (IQ/OQ/PQ), and prepare SOP updates and training plans.

Migration (installation and configuration)
Migration executes the installation and licensing of SCIEX OS, transfers or recreates required methods, users, and configurations, and reconnects LC-MS instruments with basic functional test runs; the outcome is a cleanly installed and configured workstation with verified instrument connectivity and initial test acquisitions confirming basic operation.

What this covers:

• Install SCIEX OS software: Perform installation and licensing on the target workstation per the installation guide.
• Migrate data and configurations: Move required data, methods, user accounts, and settings; adapt processing methods as needed (e.g., Decision Rules, Calculated Columns).
• Integrate instruments and verify connections: Reconnect LC-MS hardware, confirm drivers/ firmware, and complete communication tests.
•  Verify data integrity and run test acquisitions:
• Execute quick test runs to confirm acquisition, processing, and reporting behave as expected.

Outcome:
The system is installed, configured, and instrument connected with initial test data confirming basic operation.

Validation and acceptance (compliance and readiness to use)

• This stage runs CSV activities (e.g., IQ/OQ/PQ and 21 CFR
• Part 11 assessment), finalizes SOP updates and role-based training, and prepares documentation for QA approval; the outcome is a QA approved, inspection-ready system cleared for production use with trained users and controlled procedures.

What this covers:

• Software validation before use: Execute CSV activities (e.g., IQ/OQ/PQ, traceability, 21 CFR Part 11 assessment) and archive results.
• SOP updates and user training: Update or author SOPs reflecting SCIEX OS workflows; complete role-based training and record attendance/competency.
• SCIEX professional support (optional): Engage SCIEX services for validation execution, documentation packages, and targeted enablement if needed.

Outcome:
Validation evidence approved by QA, SOPs and training completed, and the system cleared for production work.

Readiness and planning

• Effective preparation is essential for a smooth and lowrisk transition from Analyst software to SCIEX OS software.
• This section outlines how laboratories can get ready  by understanding who will support the migration, what needs to be assessed in advance, and how responsibilities should be divided across the organization. SCIEX provides dedicated
• Professional Services Consultants and Software Workflow Specialists in each region to guide planning, installation, data migration, and early user adoption.
• You will also find a readiness assessment checklist to help confirm system compatibility, IT prerequisites, data protection needs, and compliance considerations before the transition begins. In addition, the section clarifies the roles of Analyst  users, IT, QA, lab leadership, and SCIEX support so each stakeholder knows what to expect and when their involvement is required. Finally, a high-level transition timeline for a single system is provided to set realistic expectations for effort,  sequencing, and validation. Together, these elements ensure your team is fully prepared and aligned before migration activities start.

Migration support team

• SCIEX has a global team of Professional Services Consultants (PSC) and Software Workflow Specialists (SWS) to support laboratories throughout managed transition to SCIEX OS software.
• Each region has dedicated experts who guide planning, installation, data migration, workflow optimization, and early adoption.
• To connect with your migration support team, please reach out to your local SCIEX sales person or email us at: professionalservices@sciex.com

Readiness assessment checklist

• Before moving from Analyst to SCIEX OS software, it’s essential to confirm your lab, people, and systems are prepared. The readiness assessment ensures your
• IT environment meets requirements, critical data and methods are protected, compliance activities are planned, and stakeholders know their roles. Completing this step reduces migration risk, shortens downtime, and accelerates user adoption  by aligning expectations and resources up front.
• Use the checklist below to validate prerequisites, organize responsibilities, and lock in a realistic transition timeline  for a single system.

System and infrastructure

•  Verify workstation specs meet SCIEX OS requirements (CPU, RAM, storage; Windows 11 LTSC 2024).
•  Confirm network/domain access, required permissions, antivirus exclusions, and backup policies.
•  Align with IT security standards for audit trails, access control, and patching cadence.

Compliance and documentation

• Plan CSV activities (URS, risk assessment, IQ/OQ/PQ, summary report) and update SOPs.
• Map user roles and e-signature policies to 21 CFR Part 11 expectations.
• Prepare acceptance criteria for post migration verification.

Data and configuration

• Back up Analyst software data, methods, user profiles, and system settings.
• Identify methods/templates to be recreated or adapted in SCIEX OS; plan any wiff1 to wiff2 handling.
• Define folder structures, projects, and role mappings for first-day operations.

People and roles

• Confirm availability of Analyst software users, method developers, data reviewers, IT admins, QA, and lab leadership.
• Assign responsibilities across installation, data migration, validation, and sign off.
• Schedule enablement: SCIEX Now tutorials, eLearning paths, and role-based training.

Instruments and workflows

•  Check instrument firmware/driver compatibility and plan reconnect/verification.
• Prioritize critical assays/workflows for first validation passes.
• Draft a minimal acceptance test set (acquisition, processing, reporting).

Timeline and support

•  Set a migration window with defined downtime, milestones, and decision gates.
• Book SCIEX regional support (PSC + Software Workflow Specialists).
• Communicate the plan to stakeholders and confirm rollback contingencies.

For a complete, detailed view of all readiness requirements, please refer to the full SCIEX software readiness checklist.

Project roles and responsibilities
A successful transition from Analyst to SCIEX OS software requires alignment across multiple functions. The roles below outline who is responsible for planning, executing, validating, and approving each part of the migration.

Analyst users / end users

• Identify key methods, workflows, and datasets that must be migrated or rebuilt.
•  Assist in verifying SCIEX OS configurations, method equivalency, and workflow continuity.
• Perform functional checks (acquisition, processing, reporting) during acceptance testing.
•  Provide feedback on usability, workflow gaps, and training needs.
• Update personal workflows and support QA in documenting user-level impacts.

IT / System administrators

• Confirm workstation specifications, Windows 11 readiness, and security compliance.
• Install SCIEX OS software and required dependencies (drivers, permissions, antivirus configuration).
• Set up user accounts, Active Directory roles, and access control policies.
• Ensure network stability for LC-MS connectivity and data storage paths.
• Support data backups, migration of wiff1 files, and folder structures for SCIEX OS projects.

Quality assurance / compliance

• Review and approve validation documents (URS, risk assessment, IQ/OQ/PQ, summary report).
•  Ensure the transition aligns with internal CSV requirements and 21 CFR Part 11 expectations.
•  Approve updated SOPs, training records, and change control documentation.
• Validate audit trail settings, security configurations, and e signature workflows.
• Provide final compliance sign off before the system is used for regulated work.

Lab leadership / management

•  Define project scope, priorities, and resource allocation.
• Approve the migration schedule, system downtime, and training plan.
• Ensure cross-functional alignment between IT, QA, and scientific teams.
•  Make final decisions on go-live readiness and post-migration support needs.
•  Communicate strategy, timelines, and expectations across the organization.

SCIEX support (field service engineer + PSC + software workflow specialists)

• Guide readiness assessment, system planning, and migration sequencing.
•  Support installation, configuration, and instrument reconnection activities.
• Assist with method translation, workflow mapping, and data processing setup in SCIEX OS software.
•  Provide best practices for validation, acceptance testing, and documentation.
•  Deliver targeted training, troubleshooting, and early adoption support to ensure smooth transition.

Transition timeline summary for one system
The transition timeline provides a concise view of the critical milestones required to move a single LC-MS system from Analyst to SCIEX OS software with minimal business disruption. It is designed to help leadership anticipate resource needs, understand sequencing across technical and compliance activities, and ensure alignment between IT, QA, and scientific teams. By outlining each phase, from planning and installation to validation and final go live, the timeline enables informed decision making, proactive risk management, and efficient coordination. This summary offers a clear, executive level roadmap to keep the transition on schedule, compliant, and operationally smooth.

• SCIEX OS software upgrade from Analyst software
• Perform pre-upgrade testing on old workstation
• Install new computer
• Install SCIEX OS software and license
• Upgrade firmware and configuration
• Install CFR license
• Perform post-upgrade testing on new workstation
• MS IQ/OQ
• LC IQ/OQ
• SW Validation (FIF)
• LCMS – PQ

Pricing implications

Pricing and licensing for SCIEX OS software follow a flexible, modular model that allows laboratories to adopt only the capabilities they need today while maintaining a clear path
for expansion. Costs typically depend on the selected license type, compliance requirements, and any optional services such as validation or training. As part of the transition from Analyst to SCIEX OS, teams can evaluate their current usage and determine the most cost effective configuration moving forward. SCIEX representatives can provide tailored quotations based on your system mix, desired features, and migration plan.

Risk mitigation and assurance

Ensuring system reliability, data integrity, and regulatory readiness is essential when transitioning from Analyst software to SCIEX OS software. This section outlines how SCIEX OS supports a secure, traceable, and resilient operating environment through integrated data integrity controls, security standards, and business continuity safeguards. Together, these capabilities help laboratories minimize operational risk, maintain compliance, and protect critical scientific output throughout and after the migration.

Data integrity and compliance

• SCIEX OS provides structured audit trails, electronic signatures, secure data handling, and traceable system events to help ensure data is preserved, reviewable, and aligned with regulatory expectations. For a deeper explanation of how SCIEX OS can be configured to support 21 CFR Part 11 requirements (including roles/responsibilities, open vs. closed systems, and specific technical/administrative controls), see the SCIEX OS LC-MS software and 21 CFR Part 11 whitepaper. The paper describes a practical approach for configuring SCIEX OS to help meet Part 11 expectations, detailing audit trail behavior, e signatures, security configurations, and validation deliverables (URS, risk assessment, IQ/OQ/PQ) in the context of GLP predicate rules. It clarifies shared responsibilities between supplier and customer and outlines how to document controls so electronic records and signatures remain trustworthy and defensible during audits.
• Security and certifications SCIEX publishes its legal and compliance framework, including software/license terms, trademarks, patents, and related corporate legal notices, through the Legal Information hub; use this page as the authoritative reference for current terms, notices, and applicable policies that underpin software deployment, licensing, and certification statements. The Legal Information area consolidates core references such as patent disclosures and terms and conditions/EULAs, which customers can cite in procurement, validation dossiers, and IT/QA documentation to evidence software provenance and permitted use; consult linked sub pages (e.g., Patents,  Legal Terms and Conditions) for specifics.

Business continuity
SCIEX provides General Security Guidance outlining recommended practices to help protect acquisition and processing computers from malware, unauthorized access, and avoidable downtime, forming an important part of overall business continuity safeguards for SCIEX OS workstations. This guidance details practical measures such as avoiding obsolete operating systems, disabling front panel USB ports, restricting internet and email use, minimizing third party installations, and enforcing strong password policies—steps intended to reduce the attack surface and prevent disruptions caused by infections or system compromise.

Quick start guide

This Quick start guide provides users with direct access to the essential training and self service resources needed to begin operating SCIEX OS software confidently from day one. These materials offer step by step tutorials, short videos, and guided learning paths that cover the core workflows for acquisition, method development, tuning, optimization, and quantitative data processing.

SCIEX OS software overview
A foundational introduction to the SCIEX OS interface, core modules, and navigation structure. Ideal for new users who need a quick understanding of how the platform is organized and where to access key tools. SCIEX OS software overview

MS Tune for SCIEX Triple Quad and QTRAP systems
Shows how to perform instrument tuning, optimize ion source parameters, and verify system readiness. Includes practical demonstrations to help users confidently execute routine performance checks. SCIEX OS software
MS Tune for SCIEX Triple Quad and QTRAP systems

Compound and source optimization
Covers automated and manual approaches for optimizing analytes and source conditions in SCIEX OS. Helps users improve sensitivity and robustness for quantitation workflows. SCIEX OS software – compound and source optimization for SCIEX Triple Quad and QTRAP systems Method creation for SCIEX Triple

Quad and QTRAP systems
Guides users through building MS and LC methods within SCIEX OS, including saving templates and setting acquisition parameters. Useful for both routine methods and more advanced workflows. SCIEX OS software – method creation for SCIEX Triple Quad and QTRAP systems

Scout triggered MRM acquisition
Explains how to configure and apply the scout triggered MRM (stMRM) workflow. Provides practical examples demonstrating how it improves screening efficiency and transition coverage. SCIEX OS software – scout-triggered MRM acquisition

Data acquisition

• Walks users through running batches, monitoring
• acquisitions, and reviewing run status in real time.
• Includes tips for queue management and sample  submission. SCIEX OS software – data acquisition

Explorer workspace
Demonstrates how to access, browse, and inspect  raw data files in the Explorer interface. Shows how to  quickly navigate chromatograms, spectra, and data layers. SCIEX OS software – Explorer workspace

Quantitative data processing
Provides guidance on configuring processing methods, evaluating calibration curves, and reviewing quantitative metrics. Ideal for analysts responsible for data review and batch approval. Quantitative data processing using SCIEX OS software

Quantitation and targeted identification
Combines quantitation steps with targeted screening workflows. Useful for multipurpose methods requiring both quant and identification. Quantitation and targeted identification data processing using SCIEX OS software

Flagging Rules and Custom Columns
Shows how to create automated data quality checks and custom calculations in processing methods. These tools help standardize review criteria and reduce manual review time. Creating Flagging Rules and Custom Columns in SCIEX OS software

System performance monitoring (Metrics Tracker)
Explores how to monitor instrument health and track long term performance trends using Metrics Tracker. Helps labs proactively identify maintenance needs. Using SCIEX OS software to monitor system performance (Metrics Tracker)

Reporter template workflows

• Covers how to use and modify reporting templates to generate consistent, audit ready outputs. Useful for teams aligning reporting across multiple analysts.
• Working with Reporter software templates eLearning courses (screening, quantitation, TripleTOF)
• Self -paced training programs with structured modules and quizzes designed to build end to end workflow competence. Helps teams onboard faster and maintain consistent skill levels. Screening on SCIEX Triple Quad and QTRAP systems using SCIEX OS software | Quantitation on SCIEX Triple Quad and QTRAP systems using SCIEX OS software | SCIEX TripleTOF system

FAQs for Analyst to SCIEX OS migration
Provides answers to the most common transition questions related to installation, compatibility, migration, and validation. A helpful first stop before contacting support.

Knowledge base and community forum
Searchable articles and peer to peer discussions that offer troubleshooting tips, configuration guidance, and workflow insights from SCIEX experts and other users. Ideal for quick problem resolution and best practice sharing. Knowledge Base and Software Community Forum

SCIEX Now support network

SCIEX Now

• Manage your instruments.
• Submit and manage support cases,  track status and view history.
• Access online training courses and articles.
• Manage software licenses linked to your registered instruments.
• View and report critical instrument statistics when connected to Status Scope remote monitoring service.
• Be a part of the SCIEX community by submitting questions and comments.
• Receive notifications from SCIEX with content based on your preferences.

SCIEX Now learning hub

• SCIEX Now learning hub success programs provide LC-MS and CE training customized to meet your exact needs.
• With a selection of training methods and certifications available, you can build a mass spectrometry program that is most suited to your lab and users.
•  Starting with a clear understanding of your desired learning outcomes, we aim to help you improve lab productivity and consistency by designing and delivering a program that is focused on knowledge advancement and retention.