PyMS

PyMS is a modular software for processing of chromatography-mass spectrometry data, currently primarily tested on gas chromatography-mass spectrometry (GC-MS) data. PyMS is written in Python, an object oriented, general purpose programming language widely used in scientific computing. PyMS provides functions for reading the raw data files in ANDI-MS and JCAMP-DX formats, noise smoothing, baseline correction, peak detection, peak integration, parsing of peak list files, and manipulation of these objects in Python. PyMS includes an implementation of dynamic programming approach for peak alignment described earlier (Robinson et al., BMC Bioinformatics 2007, 8:419). PyMS implements MPI (Message Passing Interface) based parallel processing, thus enabling processing of metabolomic data on multiple CPUs or computing clusters. PyMS has been extensively tested on gas chromatography--mass spectrometry (GC-MS) data. We are currently working on extending PyMS processing capabilities to liquid chromatography--mass spectrometry (LC-MS) data.

Keywords for this software

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