Maltcms

Maltcms provides reusable data structures and alignment algorithms for chromatography-mass spectrometry (CMS) data to enable consistent access to mass spectra, chromatograms, and metadata for metabolomics and proteomics analyses.

Key Features:

• File format abstraction: Abstracts from low-level data formats including netCDF, mzXML, mzData, and mzML to provide uniform data access.
• Data structures: Implements reusable and efficient data structures representing mass spectra, chromatograms, and metadata.
• ChromA retention time alignment: Performs retention time alignment using dynamic time warping with customizable local distance and similarity functions.
• Anchored and constrained alignment: Supports user-defined anchors and associated neighborhoods to constrain and accelerate alignment operations.
• Multiple-file alignment: Aligns multiple files using a center-star approximation that selects a reference file for alignment.
• Visualization: Provides visualization options for qualitative interpretation and comparison of aligned CMS data.

Scientific Applications:

• Metabolomics: Processing and retention time alignment of chromatography-mass spectrometry data for metabolomics studies.
• Proteomics: Processing and retention time alignment of chromatography-mass spectrometry data for proteomics studies.
• Comparative analysis: Qualitative interpretation and comparison of aligned chromatograms and mass spectra across samples.

Methodology:

Abstraction from netCDF, mzXML, mzData, and mzML to access mass spectra, chromatograms, and metadata; retention time alignment via dynamic time warping with local distance/similarity functions; user-defined anchors and neighborhoods for constrained alignment; center-star approximation for multiple-file alignment.