OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O.
High-resolution mass spectrometry (Ms) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of Ms data makes transparent, accurate and reproducible analysis dif cult. We present OpenMs 2.0 (http:// www.openms.de), a robust, open-source, cross- platform software speci cally designed for the exible and reproducible analysis of high-throughput Ms data. the extensible OpenMs software implements common mass spectrometric data processing tasks through a well-de ned application programming interface in c++ and python and through standardized open data formats. OpenMs additionally provides a set of 185 tools and ready-made work ows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.
