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 difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.
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We gratefully acknowledge the contributions of all OpenMS developers as well as of our users who helped to improve the software. This work was funded by ETH (ETH-30 11-2 to H.L.R.), SNSF (P2EZP3_162268 to H.L.R.), the Swiss Federal Commission for Technology and Innovation CTI (13539.1 PFFLI-LS to G.R.), ERC Proteomics v3.0 (233226 to R.A.), the PhosphonetX project of SystemsX.ch (R.A.), the Swiss National Science Foundation (R.A.), the Wellcome Trust (grant WT098051 to the Sanger Institute/H.W., P.G. and J.S.C.), the German Academic Exchange Service (DAAD, grant 57076385 to X.L.), the European Union (FP7, Predict-IV, GA 202222 to K.R. and C.B.), the Deutsche Forschungsgemeinschaft (SCHI 871/5, SCHI 871/6, SCHI 871/8, SCHI 871/9, GR 1748/6, INST 39/900-1, and SFB850-Project B8 to O.S. and L.N.), the European Research Council (ERC-2011-StG 282111-ProteaSys to O.S. and L.N.), DFG (QBiC to S.N., D.W. and O.K.; SFB685 to M.W. and O.K.), the European Union's Seventh Framework Programme (FP7/2007-2013 under EC-GA No. 263215 “MARINA” to M.R., F.A., S.A., K.R. and O.K.), the European Union (PRIME-XS to M.W., S.N. and O.K.), and BMBF (grant 01GI1104A to E.K. and O.K.; grant 01ZX1301F to E.K., J.P., T.S. and O.K.; grant 031A430C to F.A. and O.K.; grant 0315395B to J.V., L.N. and O.K.; grants 031A367 and 031A535A to O.K., K.R., S.A., J.P. and T.S.). We are deeply grateful for the support of the KNIME team, the Proteome Discoverer team and the Compound Discoverer team.
C.B. is a part-time employee of CodeMS, which operates in the field covered in the Perspective.
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Röst, H., Sachsenberg, T., Aiche, S. et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13, 741–748 (2016). https://doi.org/10.1038/nmeth.3959
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