{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T02:22:36Z","timestamp":1784600556294,"version":"3.55.0"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2022,9,21]],"date-time":"2022-09-21T00:00:00Z","timestamp":1663718400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fiocruz, Funda\u00e7\u00e3o Arauc\u00e1ria, Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"},{"DOI":"10.13039\/501100003593","name":"Conselho nacional de desenvolvimento cient\u00edfico e tecnol\u00f3gico","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Funda\u00e7\u00e3o de Amparo a Pesquisa do Estado de S\u00e3o Paulo","award":["2014\/17264-3"],"award-info":[{"award-number":["2014\/17264-3"]}]},{"name":"Funda\u00e7\u00e3o de Amparo a Pesquisa do Estado de S\u00e3o Paulo","award":["2014\/50867-3"],"award-info":[{"award-number":["2014\/50867-3"]}]},{"name":"National Institute of Science and Technology in Bioanalitics"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10\u2009kDa, and its essence can be easily incorporated into any deconvolution algorithm.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Y.A.D.A. 3.0 is freely available for academic use at http:\/\/patternlabforproteomics.org\/yada3.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary information is available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac638","type":"journal-article","created":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T13:24:13Z","timestamp":1663680253000},"page":"5119-5120","source":"Crossref","is-referenced-by-count":18,"title":["Increasing confidence in proteomic spectral deconvolution through mass defect"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9118-7581","authenticated-orcid":false,"given":"Milan A","family":"Clasen","sequence":"first","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9703-7226","authenticated-orcid":false,"given":"Louise U","family":"Kurt","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1178-1266","authenticated-orcid":false,"given":"Marlon D M","family":"Santos","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6056-0825","authenticated-orcid":false,"given":"Diogo B","family":"Lima","sequence":"additional","affiliation":[{"name":"Department of Structural Biology, Leibniz\u2014Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Structural Biology, Leibniz\u2014Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabio C","family":"Gozzo","sequence":"additional","affiliation":[{"name":"Dalton Mass Spectrometry Laboratory, Unicamp , Campinas 13083-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1010-7170","authenticated-orcid":false,"given":"Valmir C","family":"Barbosa","sequence":"additional","affiliation":[{"name":"Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro , Rio de Janeiro 21941-972, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6530-3350","authenticated-orcid":false,"given":"Paulo C","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,21]]},"reference":[{"key":"2022112014190868700_btac638-B1","doi-asserted-by":"crossref","first-page":"2734","DOI":"10.1093\/bioinformatics\/btp489","article-title":"YADA: a tool for taking the most out of high-resolution spectra","volume":"25","author":"Carvalho","year":"2009","journal-title":"Bioinformatics"},{"key":"2022112014190868700_btac638-B2","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.cels.2020.01.003","article-title":"FLASHDeconv: ultrafast, High-Quality feature deconvolution for top-down proteomics","volume":"10","author":"Jeong","year":"2020","journal-title":"Cell Syst"},{"key":"2022112014190868700_btac638-B3","doi-asserted-by":"crossref","first-page":"2772","DOI":"10.1074\/mcp.M110.002766","article-title":"Deconvolution and database search of complex tandem mass spectra of intact proteins","volume":"9","author":"Liu","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2022112014190868700_btac638-B4","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1038\/s41596-022-00690-x","article-title":"Simple, efficient and thorough shotgun proteomic analysis with PatternLab V","volume":"17","author":"Santos","year":"2022","journal-title":"Nat. Protoc"},{"key":"2022112014190868700_btac638-B5","doi-asserted-by":"crossref","first-page":"10335","DOI":"10.1038\/s41598-020-67113-3","article-title":"Proteomics pinpoints alterations in grade I meningiomas of male versus female patients","volume":"10","author":"Silva","year":"2020","journal-title":"Sci. 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