MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data

Laurent Gatto; Sebastian Gibb; Johannes Rainer

doi:10.1021/acs.jproteome.0c00313

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data

J Proteome Res. 2021 Jan 1;20(1):1063-1069. doi: 10.1021/acs.jproteome.0c00313. Epub 2020 Sep 28.

Authors

Laurent Gatto¹, Sebastian Gibb², Johannes Rainer³

Affiliations

¹ Computational Biology Unit, de Duve Institute, Université catholique de Louvain, Brussels, 1200, Belgium.
² Department of Anaesthesiology and Intensive Care, University Medicine Greifswald, University of Greifswald, 17475 Greifswald, Germany.
³ Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.

PMID: 32902283
DOI: 10.1021/acs.jproteome.0c00313

Abstract

We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides infrastructure for the manipulation, processing, and visualization of mass spectrometry data. We focus on the new on-disk infrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for elegant data processing, method development, and visualization.

Keywords: Bioconductor; R; mass spectrometry; metabolomics; proteomics; reproducible research; software; visualization.

MeSH terms

Mass Spectrometry
Proteomics*
Software*