Mass Spectrometry Data Processing for Metabolomics and Lipidomics

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Features

  • New features
    • DecoIMDIA Module:
      • Deconvolution: Added support for deconvoluting LC-IM-MS data based on MS/MS spectra
      • Isotope Removal: Enables the removal of isotopes using a C13 distribution model
    • Annotation Export: Added functionality to export data specifically for ion annotation
  • Updates
    • MSConvert: updated from version 3.0.25116 to 3.0.25129 (supporting Sciex ZenoTOF 8600)
    • TDF-SDK: updated from version from 2.21.0 to 3.3.6 (supporting Bruker TIMS Metabo)
    • Parameter Optimization: optimized parameter set specifically for LC-IM-MS data processing.
    • File Management: implemented automatic removal of temporary converted files generated by MSConvert.
  • Bug Fixes
    • Collision Energy Notes: Corrected the display in Lipid4DAnalyzer for Orbitrap (changed from 45±20 to SNCE 20-40-60)
    • Fragment Annotation: Fixed a typo in the lipidomics library (corrected H20 to H2O)
  • Release history
    • v 2.6 Jun. 24, 2026
  • CAUTION
    • Met4DX 2.6 is not compatible with previous versions (Met4DX 2.3 series and before) temp results. Please clear previous temp results before starting new analysis with the new version
    • It was highly recommanded to clear temp results before prcessing already processed data for minor updated versions

Other versions

Met4DX 2.5
  • Released on Jan. 26, 2026
  • Features
    • MS/MS Deconvolution: Implemented advanced MS/MS deconvolution and peak processing capabilities
    • Enhanced I/O Operations: Added file hashing to pwiz output filenames, enhanced pwiz reader with timeout and retry mechanism
    • Configuration System: Added logging configuration, release mode control, and enhanced versioning logic for release branches
  • Updates
    • I/O Enhancements: Improved CSV encoding detection and error handling, updated mzML reader capabilities
    • Logging System: Replaced old LogManager with loguru-based LogManager2 for better logging capabilities
  • Bug Fixes
    • Fixed bugx in mzML reader in reading mzML data
    • Fixed I/O to handle empty MS1 scan window records
Met4DX 2.4
  • Released on Jul. 14, 2025
  • Features
    • Expanded Instrument Compatibility: Support added for commonly used instrument providers. Refer to Data Format Available for details.
    • Optimized Data Handling: Introduced a new raw data structure based on HDF5 for high-efficiency storage and access.
    • Lipidomics Library Integration: Added support for Thermo Orbitrap instruments within the lipid identification workflows in Lipid4DAnalyzer.
    • Update the sorting methods to ensure consistent results across both Met4DX Desktop and Met4DX Server versions. The server version can be retrieved via request.
Met4DX 2.3.2
  • Released on Mar. 21, 2025
  • Features
    • Add Lipid4DAnalyzer as tool software for lipidomics identification and interactive data view
    • Add library manager for library data view (preparing for the following up managing the library added by users) 
    • Enable to add experiment with processed data (e.g., importing results from XCMS, MS-DIAL, mzMine, etc) 
    • Enable to view logs and report bugs via the Help menu
    • Locking experiment type and acquisition method in adding experiments after the first experiment was created
Met4DX 2.2.0
  • Enable LC-IM-MS (4D) data processing for Bruker timsPro
    • Support PASEF-DDA data, Agilent/Waters MS1-only data 
    • Both MS1 and MS2 oriented button-up peak assembly is supported for 4D data
    • Only detect peaks with 'Extrema' method is supported for 4D data ('centWave' for LC-MS data only)
    • Supports sample alignment using 'Obi-warp' and 'Landmarks' for 4D data
  • Memory cost optimization for data analysis
  • Peak target finding optimization in LC-MS data analysis
  • Enable ms2 acquisition method setup
  • Disable polarity swith mode for Q-Tof acquisition
  • Enable auto span increasing for failed loess regression 
Met4DX 2.1.2
  • Enable LC-IM-MS (4D) data processing for Bruker timsPro
    • Only PASEF-DDA data supported. 
    • Both MS1 and MS2 oriented button-up peak assembly is supported for 4D data
    • Only detect peaks with 'Extrema' method is supported for 4D data ('centWave' for LC-MS data only)
    • Supports sample alignment using 'Obi-warp' and 'Landmarks' for 4D data
Met4DX 2.0.3
  • Enable LC-IM-MS (4D) data processing for Bruker timsPro
  • Only PASEF-DDA data supported. 
  • Only MS2 oriented button-up peak assembly is supported for 4D data
  • Only detect peaks with 'Extrema' method is supported for 4D data ('centWave' for LC-MS data only)
Met4DX 1.2.0
  • Supprt both 3D LC-MS data
  • User-friendly graphic user interface (GUI) 
  • Pre-defined parameter sets for different instruments and data acquistion methods
  • One-click for all data processing steps
  • Export results to other tools (MetDNA, MetTracer, and MetFlow)
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