{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T13:00:36Z","timestamp":1767963636594,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: rTANDEM is an R\/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to\/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS\/MS-based proteomic pipeline in R\/Bioconductor.<\/jats:p>\n               <jats:p>Availability and implementation: rTANDEM and shinyTANDEM are distributed in R\/Bioconductor, http:\/\/bioconductor.org\/packages\/release\/bioc\/ . The packages are under open licenses (GPL-3 and Artistice-1.0).<\/jats:p>\n               <jats:p>Contact: \u00a0frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu178","type":"journal-article","created":{"date-parts":[[2014,4,4]],"date-time":"2014-04-04T01:54:59Z","timestamp":1396576499000},"page":"2233-2234","source":"Crossref","is-referenced-by-count":10,"title":["rTANDEM, an R\/Bioconductor package for MS\/MS protein identification"],"prefix":"10.1093","volume":"30","author":[{"given":"Fr\u00e9d\u00e9ric","family":"Fournier","sequence":"first","affiliation":[{"name":"1 Proteomics Center and 2 Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles","family":"Joly Beauparlant","sequence":"additional","affiliation":[{"name":"1 Proteomics Center and 2 Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ren\u00e9","family":"Paradis","sequence":"additional","affiliation":[{"name":"1 Proteomics Center and 2 Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arnaud","family":"Droit","sequence":"additional","affiliation":[{"name":"1 Proteomics Center and 2 Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada"},{"name":"1 Proteomics Center and 2 Department of Molecular Medicine, CHUQ Research Center, Laval University, Quebec G1V 4G2, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,4,3]]},"reference":[{"key":"2023012711521596500_btu178-B1","volume-title":"topGO: Enrichment Analysis for Gene Ontology","author":"Alexa","year":"2010"},{"key":"2023012711521596500_btu178-B2","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4684-6306-4","volume-title":"Programming with Data: A Guide to the S Language","author":"Chambers","year":"1998"},{"key":"2023012711521596500_btu178-B3","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-75936-4","volume-title":"Software for Data Analysis: Programming with R","author":"Chambers","year":"2008"},{"key":"2023012711521596500_btu178-B4","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"TANDEM: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012711521596500_btu178-B13","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012711521596500_btu178-B5","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt","volume":"4","author":"Durinck","year":"2009","journal-title":"Nat. Protoc."},{"key":"2023012711521596500_btu178-B7","doi-asserted-by":"crossref","first-page":"R80","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":"2023012711521596500_btu178-B8","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100024","article-title":"A uniform proteomics MS\/MS analysis platform utilizing open XML file formats","volume":"1","author":"Keller","year":"2005","journal-title":"Mol. Syst. Biol."},{"key":"2023012711521596500_btu178-B9","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1093\/bioinformatics\/btt642","article-title":"PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modifications of proteins in MS\/MS spectra","volume":"30","author":"Kertesz-Farkas","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012711521596500_btu178-B10","doi-asserted-by":"crossref","first-page":"4627","DOI":"10.1021\/pr4005794","article-title":"Quantitative proteomic analysis of micordissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed and targeted MS approaches","volume":"12","author":"Liu","year":"2013","journal-title":"J. Proteome Res."},{"key":"2023012711521596500_btu178-B11","doi-asserted-by":"crossref","first-page":"2830","DOI":"10.1093\/bioinformatics\/btl379","article-title":"General framework for developing and evaluating database scoring algorithms using the TANDEM search engine","volume":"22","author":"MacLean","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012711521596500_btu178-B12","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1093\/bioinformatics\/bts708","article-title":"RamiGO: an R\/Bioconductor package providing an AmiGO visualize interface","volume":"29","author":"Schr\u00f6der","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/15\/2233\/48924794\/bioinformatics_30_15_2233.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/15\/2233\/48924794\/bioinformatics_30_15_2233.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:09:24Z","timestamp":1674821364000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/15\/2233\/2390529"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,4,3]]},"references-count":12,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2014,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu178","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,8,1]]},"published":{"date-parts":[[2014,4,3]]}}}