title: pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.
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 https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence).
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Ph.D. Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland.
authors.forename: Hannes L
authors.initials: HL
authors.lastname: Röst
authors.forename: Uwe
authors.initials: U
authors.lastname: Schmitt
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
mesh_terms: D000465:Algorithms; D057225:Data Mining / Q000379:methods; D030562:Databases, Protein; D013058:Mass Spectrometry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D040901:Proteomics; D012984:Software
chemical_list: D011506:Proteins
keywords: Bioinformatics; Data mining; Mass spectra; Proteome maps; Python; Software