{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T14:12:17Z","timestamp":1777990337664,"version":"3.51.4"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,2,28]],"date-time":"2020-02-28T00:00:00Z","timestamp":1582848000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish Ministry of Economy and Competitiveness","award":["TEC2015-69076-P"],"award-info":[{"award-number":["TEC2015-69076-P"]}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["BES-2013-065572"],"award-info":[{"award-number":["BES-2013-065572"]}]},{"name":"Spanish Ministry of Economy and Competitiveness","award":["BFU2017-89336-R"],"award-info":[{"award-number":["BFU2017-89336-R"]}]},{"name":"Direcci\u00f3 General de Recerca of the Government of Catalonia"},{"name":"Spanish Ministry of Education, Culture and Sports","award":["FPU 14\/04457"],"award-info":[{"award-number":["FPU 14\/04457"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>rMSIproc is freely available at https:\/\/github.com\/prafols\/rMSIproc.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>pere.rafols@urv.cat<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa142","type":"journal-article","created":{"date-parts":[[2020,2,25]],"date-time":"2020-02-25T20:16:28Z","timestamp":1582661788000},"page":"3618-3619","source":"Crossref","is-referenced-by-count":34,"title":["rMSIproc: an R package for mass spectrometry imaging data processing"],"prefix":"10.1093","volume":"36","author":[{"given":"Pere","family":"R\u00e0fols","sequence":"first","affiliation":[{"name":"Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bram","family":"Heijs","sequence":"additional","affiliation":[{"name":"Center for Proteomics & Metabolomics , Leiden University Medical Center, Leiden, The Netherlands"},{"name":"Department of Pathology , Leiden University Medical Center, Leiden, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Esteban","family":"del Castillo","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oscar","family":"Yanes","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liam A","family":"McDonnell","sequence":"additional","affiliation":[{"name":"Center for Proteomics & Metabolomics , Leiden University Medical Center, Leiden, The Netherlands"},{"name":"Department of Pathology , Leiden University Medical Center, Leiden, The Netherlands"},{"name":"Fondazione Pisana per la Scienza ONLUS , Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jes\u00fas","family":"Brezmes","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iara","family":"P\u00e9rez-Taboada","sequence":"additional","affiliation":[{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain"},{"name":"Instituto de Investigaciones Biom\u00e9dicas Alberto Sols , Consejo Superior de Investigaciones Cient\u00edficas (CSIC)\/Universidad Aut\u00f3noma de Madrid, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Vallejo","sequence":"additional","affiliation":[{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain"},{"name":"Instituto de Investigaciones Biom\u00e9dicas Alberto Sols , Consejo Superior de Investigaciones Cient\u00edficas (CSIC)\/Universidad Aut\u00f3noma de Madrid, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda","family":"Garc\u00eda-Altares","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xavier","family":"Correig","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering , Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Madrid, 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