Skip to content

pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library.

Type Information
Nr 39 (Research article)
Authors Röst, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars
Title pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library.
Journal Proteomics (2014) 14 74-7
DOI 10.1002/pmic.201300246
Citations 58 citations (journal impact: 3.97)
Abstract pyOpenMS is an open-source Python-based interface to the C OpenMS library providing facile access to a feature-rich open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS specifically those for file access mzXML mzML TraML mzIdentML among others basic signal processing smoothing filtering de-isotoping and peak-picking and complex data analysis including label-free SILAC iTRAQ and SWATH analysis tools. pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner using the interactive Python interpreter and is also ideally suited for researchers not proficient in C. In addition our code to wrap a complex C library is completely open-source allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at httpspypi.python.orgpypipyopenms while the autowrap tool to create Cython code automatically is available at httpspypi.python.orgpypiautowrap both released under the 3-clause BSD licence.
Synopsis We describe a software implementation that allows access to data structures and algorithm in the OpenMS CPP library from the scripting language python.