{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T04:35:19Z","timestamp":1772685319272,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":995,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Experimental spatial proteomics, i.e. the high-throughput assignment of proteins to sub-cellular compartments based on quantitative proteomics data, promises to shed new light on many biological processes given adequate computational tools.<\/jats:p>\n               <jats:p>Results: Here we present pRoloc, a complete infrastructure to support and guide the sound analysis of quantitative mass-spectrometry-based spatial proteomics data. It provides functionality for unsupervised and supervised machine learning for data exploration and protein classification and novelty detection to identify new putative sub-cellular clusters. The software builds upon existing infrastructure for data management and data processing.<\/jats:p>\n               <jats:p>Availability: \u00a0pRoloc is implemented in the R language and available under an open-source license from the Bioconductor project (http:\/\/www.bioconductor.org\/). A vignette with a complete tutorial describing data import\/export and analysis is included in the package. Test data is available in the companion package pRolocdata.<\/jats:p>\n               <jats:p>Contact: \u00a0lg390@cam.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu013","type":"journal-article","created":{"date-parts":[[2014,1,12]],"date-time":"2014-01-12T01:28:34Z","timestamp":1389490114000},"page":"1322-1324","source":"Crossref","is-referenced-by-count":98,"title":["Mass-spectrometry-based spatial proteomics data analysis using <tt>pRoloc<\/tt> and <tt>pRolocdata<\/tt>"],"prefix":"10.1093","volume":"30","author":[{"given":"Laurent","family":"Gatto","sequence":"first","affiliation":[{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"},{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"}]},{"given":"Lisa M.","family":"Breckels","sequence":"additional","affiliation":[{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"},{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"}]},{"given":"Samuel","family":"Wieczorek","sequence":"additional","affiliation":[{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"}]},{"given":"Thomas","family":"Burger","sequence":"additional","affiliation":[{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"}]},{"given":"Kathryn S.","family":"Lilley","sequence":"additional","affiliation":[{"name":"1 Computational Proteomics Unit and 2Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and 3Universit\u00e9 Grenoble-Alpes, CEA (iRSTV\/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France"}]}],"member":"286","published-online":{"date-parts":[[2014,1,11]]},"reference":[{"key":"2023012710531137200_btu013-B1","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.jprot.2013.02.019","article-title":"The effect of organelle discovery upon sub-cellular protein localisation","volume":"88","author":"Breckels","year":"2013","journal-title":"J. Proteom."},{"key":"2023012710531137200_btu013-B2","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-23780-5_33","article-title":"Perturbo: a new classification algorithm based on the spectrum perturbations of the laplace-beltrami operator","volume-title":"The Proceedings of ECML\/PKDD (1)","author":"Courty","year":"2011"},{"key":"2023012710531137200_btu013-B3","doi-asserted-by":"crossref","first-page":"6518","DOI":"10.1073\/pnas.0506958103","article-title":"Mapping the arabidopsis organelle proteome","volume":"103","author":"Dunkley","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"issue":"1 Pt A","key":"2023012710531137200_btu013-B4","first-page":"42","article-title":"Using R and Bioconductor for proteomics data analysis","volume":"1844","author":"Gatto","year":"2013","journal-title":"Biochim. Biophys. Acta."},{"key":"2023012710531137200_btu013-B5","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bioinformatics\/btr645","article-title":"MSnbase \u2013 an R\/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation","volume":"28","author":"Gatto","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012710531137200_btu013-B6","doi-asserted-by":"crossref","first-page":"3957","DOI":"10.1002\/pmic.201000244","article-title":"Organelle proteomics experimental designs and analysis","volume":"10","author":"Gatto","year":"2010","journal-title":"Proteomics"},{"key":"2023012710531137200_btu013-B7","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023012710531137200_btu013-B8","doi-asserted-by":"crossref","first-page":"1520","DOI":"10.1038\/emboj.2011.63","article-title":"Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods","volume":"30","author":"Jakobsen","year":"2011","journal-title":"EMBO J."},{"key":"2023012710531137200_btu013-B9","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/nrc1274","article-title":"Nuclear transport and cancer: from mechanism to intervention","volume":"4","author":"Kau","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"2023012710531137200_btu013-B10","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/1471-2164-10-122","article-title":"Prediction of disease-related mutations affecting protein localization","volume":"10","author":"Laurila","year":"2009","journal-title":"BMC Genomics"},{"key":"2023012710531137200_btu013-B11","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1104\/pp.112.204263","article-title":"Putative glycosyltransferases and other plant golgi apparatus proteins are revealed by LOPIT proteomics","volume":"160","author":"Nikolovski","year":"2012","journal-title":"Plant Physiol."},{"key":"2023012710531137200_btu013-B12","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1016\/j.cell.2010.07.047","article-title":"The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics","volume":"142","author":"Ohta","year":"2010","journal-title":"Cell"},{"key":"2023012710531137200_btu013-B13","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/msb.2011.29","article-title":"Protein localization as a principal feature of the etiology and comorbidity of genetic diseases","volume":"7","author":"Park","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2023012710531137200_btu013-B14","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1021\/pr800866n","article-title":"Mapping organelle proteins and protein complexes in drosophila melanogaster","volume":"8","author":"Tan","year":"2009","journal-title":"J. Proteome Res."},{"key":"2023012710531137200_btu013-B15","doi-asserted-by":"crossref","first-page":"3625","DOI":"10.1093\/molbev\/mss178","article-title":"PredAlgo: a new subcellular localization prediction tool dedicated to green algae","volume":"29","author":"Tardif","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"2023012710531137200_btu013-B16","doi-asserted-by":"crossref","first-page":"4213","DOI":"10.1002\/pmic.201000359","article-title":"Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions","volume":"10","author":"Trotter","year":"2010","journal-title":"Proteomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/9\/1322\/48922853\/bioinformatics_30_9_1322.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/9\/1322\/48922853\/bioinformatics_30_9_1322.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:33:37Z","timestamp":1674819217000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/9\/1322\/236363"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,11]]},"references-count":16,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2014,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu013","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,5,1]]},"published":{"date-parts":[[2014,1,11]]}}}