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mpwR: An R package for comparing performance of mass spectrometry-based proteomic workflows.
Bioinformatics 39:3 (2023)
SUMMARY: mpwR is an R package for a standardized comparison of mass spectrometry (MS)-based proteomic label-free workflows recorded by data-dependent or data-independent spectral acquisition. The user-friendly design allows easy access to compare the influence of sample preparation procedures, combinations of liquid chromatography (LC)-MS setups, as well as intra- and inter-software differences on critical performance measures across an unlimited number of analyses. mpwR supports outputs of commonly used software for bottom-up proteomics, such as ProteomeDiscoverer, Spectronaut, MaxQuant, and DIA-NN. AVAILABILITY AND IMPLEMENTATION: mpwR is available as an open-source R package. Release versions can be accessed on CRAN (https://CRAN.R-project.org/package=mpwR) for all major operating systems. The development version is maintained on GitHub (https://github.com/okdll/mpwR) and full documentation with examples and workflow templates is provided via the package website (https://okdll.github.io/mpwR/).
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Publication type
Article: Journal article
Document type
Scientific Article
ISSN (print) / ISBN
1367-4803
Journal
Bioinformatics
Quellenangaben
Volume: 39,
Issue: 6,
Article Number: 3
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
CF Metabolomics & Proteomics (CF-MPC)
Grants
German Ministry for Science and Education funding action CLINSPECT-M