mspack

mspack compresses mass spectrometry (MS) data to reduce storage footprint for proteomics and metabolomics analyses.

Key Features:

• Dual Compression Modes: mspack supports both lossless and lossy compression modes to trade data fidelity against file size.
• Redundancy Exploitation: mspack exploits additional redundancy across scans within a single MS file to improve compression efficiency.
• Format Support: mspack is compatible with the mzML and mzXML file formats.
• Preprocessing Transforms: mspack applies several lossless preprocessing transforms followed by optional lossy transforms that are configurable in error tolerance.
• General-purpose Compressors: mspack integrates with general-purpose compressors such as gzip and bsc to achieve higher compression ratios.
• Performance Metrics: with the bsc backend mspack achieves average file-size reductions of 76% for lossless and 94% for lossy compression versus original files, reduces lossless sizes 10–60% more than MassComp, and compresses 36–60% better than MSNumpress for lossy compression at the same error level while maintaining comparable accuracy and running time.

Scientific Applications:

• Proteomics: reduces storage requirements for mass spectrometry datasets generated in proteomics studies.
• Metabolomics: reduces storage requirements for mass spectrometry datasets generated in metabolomics studies.

Methodology:

Implemented in C++, mspack applies lossless preprocessing transforms followed by optional configurable lossy transforms, exploits redundancy across scans, and uses general-purpose compressors (gzip, bsc) to compress mzML and mzXML files in lossless or lossy modes.