{"id":"https://openalex.org/W4296701479","doi":"https://doi.org/10.1093/bioinformatics/btac638","title":"Increasing confidence in proteomic spectral deconvolution through mass defect","display_name":"Increasing confidence in proteomic spectral deconvolution through mass defect","publication_year":2022,"publication_date":"2022-09-20","ids":{"openalex":"https://openalex.org/W4296701479","doi":"https://doi.org/10.1093/bioinformatics/btac638","pmid":"https://pubmed.ncbi.nlm.nih.gov/36130273"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5119/47153740/btac638.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5119/47153740/btac638.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057236072","display_name":"Milan Avila Clasen","orcid":"https://orcid.org/0000-0002-9118-7581"},"institutions":[{"id":"https://openalex.org/I4210154871","display_name":"Funda\u00e7\u00e3o Carlos Chagas","ror":"https://ror.org/051hcjr97","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210154871"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Milan A Clasen","raw_affiliation_strings":["Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-9118-7581","affiliations":[{"raw_affiliation_string":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil","institution_ids":["https://openalex.org/I4210154871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034898438","display_name":"Louise Ulrich Kurt","orcid":"https://orcid.org/0000-0002-9703-7226"},"institutions":[{"id":"https://openalex.org/I4210154871","display_name":"Funda\u00e7\u00e3o Carlos Chagas","ror":"https://ror.org/051hcjr97","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210154871"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Louise U Kurt","raw_affiliation_strings":["Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-9703-7226","affiliations":[{"raw_affiliation_string":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil","institution_ids":["https://openalex.org/I4210154871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035051817","display_name":"Marlon Dias Mariano Santos","orcid":"https://orcid.org/0000-0002-1178-1266"},"institutions":[{"id":"https://openalex.org/I4210154871","display_name":"Funda\u00e7\u00e3o Carlos Chagas","ror":"https://ror.org/051hcjr97","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210154871"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marlon D M Santos","raw_affiliation_strings":["Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-1178-1266","affiliations":[{"raw_affiliation_string":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil","institution_ids":["https://openalex.org/I4210154871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011606492","display_name":"Diogo Borges Lima","orcid":"https://orcid.org/0000-0001-6056-0825"},"institutions":[{"id":"https://openalex.org/I4210099563","display_name":"Leibniz-Forschungsinstitut f\u00fcr Molekulare Pharmakologie","ror":"https://ror.org/010s54n03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210099563"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Diogo B Lima","raw_affiliation_strings":["Department of Structural Biology, Leibniz\u2014Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6056-0825","affiliations":[{"raw_affiliation_string":"Department of Structural Biology, Leibniz\u2014Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany","institution_ids":["https://openalex.org/I4210099563"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371030","display_name":"Fan Liu","orcid":"https://orcid.org/0000-0002-2358-549X"},"institutions":[{"id":"https://openalex.org/I4210099563","display_name":"Leibniz-Forschungsinstitut f\u00fcr Molekulare Pharmakologie","ror":"https://ror.org/010s54n03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210099563"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fan Liu","raw_affiliation_strings":["Department of Structural Biology, Leibniz\u2014Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Structural Biology, Leibniz\u2014Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany","institution_ids":["https://openalex.org/I4210099563"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038331268","display_name":"F\u00e1bio C. Gozzo","orcid":"https://orcid.org/0000-0002-5270-4427"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fabio C Gozzo","raw_affiliation_strings":["Dalton Mass Spectrometry Laboratory, Unicamp , Campinas 13083-970, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalton Mass Spectrometry Laboratory, Unicamp , Campinas 13083-970, Brazil","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080706511","display_name":"Valmir C. Barbosa","orcid":"https://orcid.org/0000-0003-1010-7170"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Valmir C Barbosa","raw_affiliation_strings":["Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro , Rio de Janeiro 21941-972, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-1010-7170","affiliations":[{"raw_affiliation_string":"Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro , Rio de Janeiro 21941-972, Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038367294","display_name":"Paulo C. Carvalho","orcid":"https://orcid.org/0000-0001-6530-3350"},"institutions":[{"id":"https://openalex.org/I4210154871","display_name":"Funda\u00e7\u00e3o Carlos Chagas","ror":"https://ror.org/051hcjr97","country_code":"BR","type":"nonprofit","lineage":["https://openalex.org/I4210154871"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Paulo C Carvalho","raw_affiliation_strings":["Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-6530-3350","affiliations":[{"raw_affiliation_string":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz\u2014Paran\u00e1 81310-020, Brazil","institution_ids":["https://openalex.org/I4210154871"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038367294","https://openalex.org/A5057236072"],"corresponding_institution_ids":["https://openalex.org/I4210154871"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.257,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.76666667,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"22","first_page":"5119","last_page":"5120"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9684000015258789,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9684000015258789,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.012400000356137753,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.9147261381149292},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5599067807197571},{"id":"https://openalex.org/keywords/confidence-interval","display_name":"Confidence interval","score":0.5125986933708191},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34518977999687195},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3211129307746887},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.28224605321884155},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.27917587757110596},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21007627248764038},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20700958371162415}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.9147261381149292},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5599067807197571},{"id":"https://openalex.org/C44249647","wikidata":"https://www.wikidata.org/wiki/Q208498","display_name":"Confidence interval","level":2,"score":0.5125986933708191},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34518977999687195},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3211129307746887},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.28224605321884155},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.27917587757110596},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21007627248764038},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20700958371162415}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5119/47153740/btac638.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36130273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36130273","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:arca.fiocruz.br:icict/55813","is_oa":true,"landing_page_url":"https://arca.fiocruz.br/handle/icict/55813","pdf_url":null,"source":{"id":"https://openalex.org/S7407055450","display_name":"Arca - Reposit\u00f3rio Institucional da Fiocruz","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:www.arca.fiocruz.br:icict/55813","is_oa":true,"landing_page_url":"https://www.arca.fiocruz.br/handle/icict/55813","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"reponame:Reposit\u00f3rio Institucional da FIOCRUZ (ARCA)","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac638","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac638","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5119/47153740/btac638.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4296701479.pdf"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W2025955263","https://openalex.org/W2115007450","https://openalex.org/W3007615379","https://openalex.org/W3037320409","https://openalex.org/W4223418536"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4251527294","https://openalex.org/W3090782779","https://openalex.org/W4296701479","https://openalex.org/W2037261263","https://openalex.org/W3149087629","https://openalex.org/W4231036715","https://openalex.org/W2032074591","https://openalex.org/W1986156575","https://openalex.org/W4242983818"],"abstract_inverted_index":{"MOTIVATION:":[0],"Confident":[1],"deconvolution":[2,28,64,94],"of":[3,43],"proteomic":[4],"spectra":[5],"is":[6,76,101,113],"critical":[7],"for":[8,78,104],"several":[9],"applications":[10],"such":[11],"as":[12],"de":[13],"novo":[14],"sequencing,":[15],"cross-linking":[16],"mass":[17,22,33,56,72],"spectrometry":[18],"and":[19,85],"handling":[20],"chimeric":[21],"spectra.":[23],"RESULTS:":[24],"In":[25],"general,":[26],"all":[27],"algorithms":[29],"may":[30],"eventually":[31],"report":[32],"peaks":[34,69],"that":[35,66],"are":[36],"not":[37],"compatible":[38],"with":[39,70,80],"the":[40],"chemical":[41],"formula":[42],"any":[44,93],"peptide.":[45],"We":[46,58],"show":[47],"how":[48],"to":[49],"remove":[50,68],"these":[51],"artifacts":[52],"by":[53],"considering":[54],"their":[55],"defects.":[57,73],"introduce":[59],"Y.A.D.A.":[60,99],"3.0,":[61],"a":[62],"fast":[63],"algorithm":[65],"can":[67,88],"unacceptable":[71],"Our":[74],"approach":[75],"effective":[77],"polypeptides":[79],"less":[81],"than":[82],"10":[83],"kDa,":[84],"its":[86],"essence":[87],"be":[89],"easily":[90],"incorporated":[91],"into":[92],"algorithm.":[95],"AVAILABILITY":[96],"AND":[97],"IMPLEMENTATION:":[98],"3.0":[100],"freely":[102],"available":[103,114],"academic":[105],"use":[106],"at":[107,115],"http://patternlabforproteomics.org/yada3.":[108],"SUPPLEMENTARY":[109],"INFORMATION:":[110],"Supplementary":[111],"information":[112],"Bioinformatics":[116],"online.":[117]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-07-21T08:15:58.654021","created_date":"2025-10-10T00:00:00"}
