What is "openms"

OpenMS is an open-source project for data analysis and processing in protein mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, OS X and Linux.

OpenMS has tools for many common data analysis pipelines used in proteomics, providing algorithms for signal processing, feature finding (including de-isotoping), visualization in 1D (spectra or chromatogram level), 2D and 3D, map mapping and peptide identification. It supports label-free and isotopic-label based quantification (such as iTRAQ and TMT and SILAC). Furthermore, it also supports metabolomics workflows and DIA/SWATH targeted analysis.

To achieve a wide variety of tasks in proteomics, OpenMS provides the The OpenMS Proteomics Pipeline(TOPP) which is a set of computational tools that can be chained together to tailor problem-specific analysis pipelines for HPLC-MS data. It transforms most of the OpenMS functionality into small command line tools that are the building blocks for more complex analysis pipelines.