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.

The main idea behind PyMS is to provide a set of components for for development and testing of high-throughput processing methods for metabolomics, by decoupling processing methods form visualization and the concept of interactive processing altogether.

PyMS provides functions for reading the raw data files in ANDI-MS format, parsing of peak list files, and manipulation of these objects in Python, including dynamic programming approach for peak alignment (Robinson et al., BMC Bioinformatics 2007, 8:419) Note: this is a new version of PyMS, and some of these features are lacking, currently being ported from the original version.

PyMS consists of three projects:

• pyms -- the PyMS project (this project)
• pyms-docs -- Documentation, including the PDF of the user guide with examples and tutorials
• pyms-test -- Code for tests & examples discussed in the user guide

All three parts of PyMS are hosted on Google Code as separate projects, and are freely available for download.

The data files for examples can be downloaded from here.

The PyMS APIs documentation is available here (for programmers).