OpenMS

OpenMS is a cross-platform (Linux, Windows, macOS) software framework based around a core open source C++ library, which implements all data structures and algorithms required for mass spectroscopic (MS) data analyses. It was created in 2006, is currently at release 2.6 and is licensed under the three clause BSD license. Our contributors are computational mass spectrometrists, bioinformaticians, and data scientists. Among our users are large data repositories like MAssIVE and PRIDE, individuals that value the flexibility and open-source nature of OpenMS and companies in need of customized solutions to their analytical problems. OpenMS was cited in ~900 scientific publications in 2020, and its tools were used ~3,000 times per month by unique users in the first quarter of 2021. We have seen strong interest in our workshops, and over the last years, we have trained between 80 to 120 participants annually (2020 numbers are lower due to COVID-19 travel restrictions). Numerous downstream tools such as MSstats, aLFQ, QCloud2 and Skyline have integrated their tools with OpenMS.

Mass spectrometry is a sensitive high-throughput technique capable of direct quantitative and qualitative measurement of proteins, which perform essentially all cellular tasks required for life. For example, direct protein interactions between SARS-CoV-2 and human proteins are essential for virulence (such as the viral spike protein and human ACE2); mass spectrometry has produced a full map of 332 pairwise protein interactions. OpenMS is used not only for proteins but also metabolites. In addition, MS is used for more specialized purposes like analysis of cross-linked molecules (both protein-protein and protein-nucleic acid) and nucleic acid identification and quantification.