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Code availability
All OpenMS source code is available on GitHub (https://github.com/OpenMS/OpenMS) under a permissive three-clause BSD license. Documentation for users (https://openms.readthedocs.io/), Python programmers (https://pyopenms.readthedocs.io/en/latest/index.html), and C++ developers (https://www.openms.org/documentation) can be accessed online.
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Acknowledgements
C.B. was in part supported by the Chan Zuckerberg EOSS program (179). J.P. was funded by Forschungscampus MODAL (project grant 3FO18501). K.J., E.N. and T.S. were supported by the Ministry of Science, Research and Arts Baden-Württemberg. A.S. and A.F. are part of the MSCA-ITN-2020 PROTrEIN project, which received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No: 956148. J.C. was funded by the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-164) and supported by the Ontario Graduate Scholarship. J.C.S. was funded by the European Research Area Network Personalized Medicine Cofund (PerProGlio). A.W. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation TRR 261/1,Z03). S.W. was supported by de.NBI (031A535A), Analytics for Biologics (H2020-MSCA-ITN-2017), the EU H2020 project EPIC-XS (H2020-INFRAIA), TRR (TP Z03), and TUE.AI. S.K. was funded by Horizon 2020 under grant agreement No 686070. M.P.S. was funded by Polish National Science Centre grant no. 2017/26/D/ST6/00304. Y.P.-R. acknowledges funding from EMBL core funding, Wellcome grants (208391/Z/17/Z, 223745/Z/21/Z), and the EU H2020 project EPIC-XS (823839).
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Authors and Affiliations
Contributions
J.P., C.B., S.W., K.J., E.N., A.W., T.D., T.S. wrote the manuscript. All authors contributed to the development of the software.
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Competing interests
L.H. is an employee of Laminlabs. H.W. is an employee of STORM Therapeutics. L.B. is an employee of BioNTech SE. L.N. is an employee of OpenMS Consulting. O.K., T.S. and S.W. are officers in OpenMS Inc., a non-profit foundation that manages the international coordination of OpenMS development. All remaining authors declare no competing interests.
Peer review
Peer review information
Nature Methods thanks Brian Searle and Wen-Feng Zeng for their contribution to the peer review of this work.
Supplementary information
Supplementary Information
Supplementary Note and Figs. 1–7
Supplementary Table
List of all OpenMS tools.
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Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7
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DOI: https://doi.org/10.1038/s41592-024-02197-7