{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T12:30:14Z","timestamp":1761395414601,"version":"3.37.3"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,4]],"date-time":"2019-02-04T00:00:00Z","timestamp":1549238400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Brazilian National Research Council"},{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Graduate Studies Agency"},{"DOI":"10.13039\/501100002322","name":"CAPES","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-15-CE18-0021"],"award-info":[{"award-number":["ANR-15-CE18-0021"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/patternlabforproteomics.org\/tdgc, freely available for academic use.<\/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\/btz085","type":"journal-article","created":{"date-parts":[[2019,2,2]],"date-time":"2019-02-02T12:16:17Z","timestamp":1549109777000},"page":"3489-3490","source":"Crossref","is-referenced-by-count":5,"title":["Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra"],"prefix":"10.1093","volume":"35","author":[{"given":"Diogo B","family":"Lima","sequence":"first","affiliation":[{"name":"Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur , Paris, France"}]},{"given":"Andr\u00e9 R F","family":"Silva","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1, Brazil"}]},{"given":"Mathieu","family":"Dupr\u00e9","sequence":"additional","affiliation":[{"name":"Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur , Paris, France"}]},{"given":"Marlon D M","family":"Santos","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1, Brazil"}]},{"given":"Milan A","family":"Clasen","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1, Brazil"}]},{"given":"Louise U","family":"Kurt","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1, Brazil"}]},{"given":"Priscila F","family":"Aquino","sequence":"additional","affiliation":[{"name":"Le\u00f4nidas and Maria Deane Institute , Fiocruz, Amazonas, Brazil"}]},{"given":"Valmir C","family":"Barbosa","sequence":"additional","affiliation":[{"name":"Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro , Rio de Janeiro, Brazil"}]},{"given":"Paulo C","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1, Brazil"}]},{"given":"Julia","family":"Chamot-Rooke","sequence":"additional","affiliation":[{"name":"Mass Spectrometry for Biology Unit, CNRS USR 2000, Institut Pasteur , Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2019,2,4]]},"reference":[{"key":"2023013108062519200_btz085-B1","doi-asserted-by":"crossref","first-page":"4152","DOI":"10.1021\/acs.analchem.5b00162","article-title":"Benchmarking multiple fragmentation methods on an orbitrap fusion for top-down phospho-proteoform characterization","volume":"87","author":"Brunner","year":"2015","journal-title":"Anal. 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Proteome Res"},{"key":"2023013108062519200_btz085-B5","doi-asserted-by":"crossref","first-page":"1883","DOI":"10.1093\/bioinformatics\/btx093","article-title":"DiagnoProt: a tool for discovery of new molecules by mass spectrometry","volume":"33","author":"Silva","year":"2017","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/18\/3489\/48975772\/bioinformatics_35_18_3489.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/18\/3489\/48975772\/bioinformatics_35_18_3489.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T13:50:02Z","timestamp":1675173002000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/18\/3489\/5306329"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,2,4]]},"references-count":5,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2019,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz085","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,9,15]]},"published":{"date-parts":[[2019,2,4]]}}}