rMSIproc: an R package for mass spectrometry imaging data processing

Bioinformatics, vol. 36, pp. 3618–3619

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.

Authors 10

1. Pere Ràfols corresponding

   Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

   Affiliation as printed

   Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain

   Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain

2. Bram Heijs Aachen Center for Proteomics and Metabolomics Department of Pathology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics & Metabolomics , Leiden University Medical Center, Leiden, The Netherlands

   Department of Pathology , Leiden University Medical Center, Leiden, The Netherlands

3. Esteban del Castillo

   Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

   Affiliation as printed

   Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain

4. Óscar Yanes

   Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

   Affiliation as printed

   Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain

   Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain

5. Liam Andrew McDonnell Aachen Center for Proteomics and Metabolomics Department of Pathology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics & Metabolomics , Leiden University Medical Center, Leiden, The Netherlands

   Department of Pathology , Leiden University Medical Center, Leiden, The Netherlands

   Fondazione Pisana per la Scienza ONLUS , Pisa, Italy

6. J. Brezmes

   Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

   Affiliation as printed

   Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain

   Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain

7. Iara Pérez‐Taboada

   Consejo Superior de Investigaciones Científicas · Instituto de Investigaciones Biomédicas Sols-Morreale · Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Universidad Autónoma de Madrid

   Affiliation as printed

   Instituto de Investigaciones Biomédicas Alberto Sols , Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma de Madrid, Madrid, Spain

   Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain

8. Mario Vallejo

   Consejo Superior de Investigaciones Científicas · Instituto de Investigaciones Biomédicas Sols-Morreale · Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Universidad Autónoma de Madrid

   Affiliation as printed

   Instituto de Investigaciones Biomédicas Alberto Sols , Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma de Madrid, Madrid, Spain

   Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain

9. María García‐Altares

   Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

   Affiliation as printed

   Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain

   Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain

10. Xavier Correig

    Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas · Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

    Affiliation as printed

    Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain

    Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain