SCIEX OS

SCIEX OS software is a unified platform designed to control and manage SCIEX mass spectrometry systems. It covers acquisition, data processing, and operations management within a single environment, and is intended for laboratory scientists running workflows on instruments such as the SCIEX Triple Quad 7500, ZenoTOF 8600, X500 series QTOF, and other supported SCIEX systems. Version 4.0 adds Windows 11 support to help labs meet IT security policies and reduce cybersecurity vulnerabilities.

Labs transitioning from Analyst software or MultiQuant software can import existing acquisition and processing methods directly into SCIEX OS, reducing transcription errors and method development time. A dedicated migration guide provides steps and tips for maintaining data integrity during the transition.

Version 4.0 Enhancements (All Supported Systems)

• Windows 11 support to meet internal and external IT security requirements and reduce cybersecurity risk
• Enhanced Decision Rules with logic-based criteria to drive intelligent, automated actions throughout the analytical workflow
• APIs to support high-throughput data analysis needs
• Automatic compound optimization (ACO)
• Precision printing and OCR for compliance purposes

ZenoTOF 8600 Specific Enhancements

• ZT Scan 2.0 correlates precursors and fragments using the Q1 4th dimension for improved effective speed
• Updated Metrics Tracker providing real-time updates and notifications on assay stability and reproducibility, with a tracking range of up to five years
• EAD MS/MS spectra viewable in the LibraryView workspace
• Analyte ID confidence enhanced using two complementary fragmentation modes; auto-selection of fragments reduces processing time from approximately one hour to one to two minutes for 40–100 analytes
• Updated library functionality including viewing fragmentation mode in SCIEX .wiff files, storage of key EAD parameters, support for flexible EAD vs. library EAD MS/MS searches, handling of mixed MS/MS mode data in Analytics, and a stand-alone LibraryView database with MS/MS spectra

Acquisition Features

• Batch workspace: Used to create and submit samples, entering MS and LC methods, autosampler values (rack position, plate type, vial position, injection volume), processing methods, and results file directory. Supports auto-calibrate functionality for accurate mass systems and direct import of Analyst software methods. Batches can be saved and reopened.
• Queue workspace: Displays real-time acquisition status, estimated start times, and details from the Batch workspace. Allows the user to start and stop the queue.
• MS Method workspace: Supports creation of MRM, MRMHR, SWATH, TOF MS, and other experiment types. Configures source parameters for Turbo V and OptiFlow Pro ion sources. Guided method creators assist with developing methods for new analytes. Acquisition methods from Analyst software can be converted directly within this workspace.
• LC Method workspace: Builds separate LC methods with configuration of flow rates, autosampler conditions, column oven temperature, PDA wavelengths, and auto-purge settings. One LC method can be used across multiple MS methods.
• MS Tune workspace: Supports multiple tuning procedures including detector optimization. Automated tuning is available for the Triple Quad 7500 and X500 series QTOF systems, calibrating all scans across all modes using a single calibrant for both positive and negative mode, with built-in acceptance criteria.
• Scheduled MRM (sMRM): Accounts for retention time drifts, allows single-click RT updates, identifies single dwell time instances for low-intensity ions, and provides interactive plots that update dynamically with method changes.
• Automated compound optimization: Supports infusion, flow injection, on-column, and MRM3 approaches for quantification, with options for signal-to-noise ratio or intensity-based parameter selection.
• Decision Rules: Continuously checks against user-defined criteria during acquisition to detect failures and trigger corrective actions in real time, reducing sample loss and eliminating the need to wait until post-acquisition review.

Data Processing and Management Features

• Explorer workspace: Opens acquired data files and provides navigation tools for reviewing total ion chromatograms (TIC), extracted ion chromatograms (XIC), and IDA explorer data. Includes graph customization, baseline smoothing, and Bio Tool Kit for peptide sequencing. PeakView software is accessible from within the Explorer workspace.
• Analytics workspace: Supports data analysis, custom calculations, and exception review. Key capabilities include:
  • AutoPeak integration algorithm using a second-generation, 3 Gaussian peak model for reliable integration across samples, batches, and analytes without manual re-integration
  • Custom workspace layouts that save column settings, filtering, graphs, and docking preferences, with the option to set a default project layout
  • Automatic outlier removal from calibration curves based on user-specified criteria
  • Calculated columns and flagging rules, including support for "IF" statements, nested "IF" statements, numeric and non-numeric queries, confidence flag queries, and formula files in .frml format that can be shared
• Library workspace: Provides access to and import of spectral libraries.
• Molecule Profiler: Uses MS and MS/MS data analysis combined with extensive libraries to support workflows for determining impurities and biotransformations.
• Biologics Explorer: Delivers workflows for characterizing protein biotherapeutics using current acquisition techniques.
• MarkerView: A statistical data visualization tool for exploring sample groupings and trends in mass spectral data, with direct connections back to raw data. Applicable to metabolomics, lipidomics, proteomics, food authenticity, and water testing.

Operations Management Features

• Configurations: Allows customization of SCIEX OS to meet laboratory-specific needs.
• Audit trail: Tracks data integrity across every run.
• Event log: Records key system events for review.

SCIEX OS software supports API integration for labs with high-throughput data analysis requirements. The platform includes compliance-oriented features such as audit trails, precision printing, and OCR. Automated overnight data acquisition and processing is supported by incorporating processing methods directly into batches, so results are ready for review when analysts return to the lab.