OpenMS – A platform for reproducible analysis of mass spectrometry data

Abstract

OpenMS will continue to increase its ease of use for developers as well as users with improved continuous integration/deployment strategies, regular trainings with updated training materials and multiple sources of support. The active developer community ensures the incorporation of new features to support state of the art research.

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

“…To perform the benchmarking, we built a workflow using OpenMS (18, 28) in which raw files were converted from Thermo Scientific RAW files to mzML using the msconvert tool from ProteoWizard (14) on the one hand, and with ThermoRawFileParser on the other hand. The resulting spectra were centroided and searched using MS-GF+ (v2018.01.30) (29), executed via the OpenMS search engine wrapper MSGFPlusAdapter, allowing 10 ppm precursor mass tolerance, and setting carbamidomethylation of cysteine as fixed, and methionine oxidation as variable modification.…”

“…While the Thermo cross-platform library thus enables specially-developed software to access Thermo Raw files on diverse operating systems, most open-source computational proteomics workflows (e.g. OpenMS (18), Galaxy (19), and the Trans-Proteomics pipeline (TPP) (20)) are based on generic, open data formats such as Mascot Generic File (MGF) or mzML. In order to allow these tools to benefit maximally from the cross-platform access to Thermo Raw files, we here present ThermoRawFileParser, an open-source, cross-platform tool that converts Thermo RAW files into open file formats such as MGF and mzML similar to other tools such as msconvert (14) and RawTools (21).…”

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon

“…OpenMS [57] workflow as described by Wright et al [39] and Weisser et al [58] The spectra were search against a sequence database composed of all GENCODE v27 protein coding transcripts and PhyloCSF Candidate Coding Regions [29]; an equally sized decoy database generated using DecoyPYrat [59] was concatenated and used to control FDR. Peptides were filtered to a posterior error probability of less than 0.01 and required to be significant in multiple search engines; a minimum and maximum length of 6 and 30 amino acids respectively was set; a maximum of 2 missed cleavages were allowed, and peptides containing certain modifications, such as deamidation were excluded.…”

Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines

“…Multiple tools and modules can be packaged into the same framework (e.g. OpenMS [34]) but all of them should be executable independently and interchangeably (through adequate exchange intermediate formats). A component-based software framework is a branch of software development that emphasizes the separation of concerns with respect to the wide-ranging functionality available throughout a given software system.…”

“…In MS-based proteomics three different frameworks have been designed from the beginning on component-based architecture: OpenMS [34], Trans-proteomics pipeline [35] and OpenSWATH [24]. OpenMS and OpenSWATH provide a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.…”