Mass Spectrometry Data Processing for Metabolomics and Lipidomics

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Features

New 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
Release history
- v 2.5 Jan. 26, 2026
CAUTION
- Met4DX 2.5 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
Roadmap
- 4D data processing for DIA mode (e.g., PASEF-DIA in Bruker TIMS instruments)
- User library management for identification

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

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)