rMSIproc: an R package for mass spectrometry imaging data processing

• Published in: Bioinformatics Vol. 36; no. 11; pp. 3618 - 3619
• Main Authors: Ràfols, Pere, Heijs, Bram, del Castillo, Esteban, Yanes, Oscar, McDonnell, Liam A, Brezmes, Jesús, Pérez-Taboada, Iara, Vallejo, Mario, García-Altares, María, Correig, Xavier
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.06.2020
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btaa142

Abstract Summary Mass spectrometry imaging (MSI) can reveal biochemical information directly from a tissue section. MSI generates a large quantity of complex spectral data which is still challenging to translate into relevant biochemical information. Here, we present rMSIproc, an open-source R package that implements a full data processing workflow for MSI experiments performed using TOF or FT-based mass spectrometers. The package provides a novel strategy for spectral alignment and recalibration, which allows to process multiple datasets simultaneously. This enables to perform a confident statistical analysis with multiple datasets from one or several experiments. rMSIproc is designed to work with files larger than the computer memory capacity and the algorithms are implemented using a multi-threading strategy. rMSIproc is a powerful tool able to take full advantage of modern computer systems to completely develop the whole MSI potential. Availability and implementation rMSIproc is freely available at https://github.com/prafols/rMSIproc. Contact pere.rafols@urv.cat Supplementary information Supplementary data are available at Bioinformatics online.