{"id":"https://openalex.org/W2099275584","doi":"https://doi.org/10.1093/bioinformatics/btu717","title":"Mass spectrometry-based protein identification with accurate statistical significance assignment","display_name":"Mass spectrometry-based protein identification with accurate statistical significance assignment","publication_year":2014,"publication_date":"2014-10-31","ids":{"openalex":"https://openalex.org/W2099275584","doi":"https://doi.org/10.1093/bioinformatics/btu717","mag":"2099275584","pmid":"https://pubmed.ncbi.nlm.nih.gov/25362092"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu717","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu717","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4341067","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080166154","display_name":"Gelio Alves","orcid":"https://orcid.org/0000-0002-1595-1445"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gelio Alves","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080970152","display_name":"Yi\u2010Kuo Yu","orcid":"https://orcid.org/0000-0002-6213-7665"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi-Kuo Yu","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6447,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.66802566,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"31","issue":"5","first_page":"699","last_page":"706"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9976000189781189,"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":0.9976000189781189,"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":0.0005000000237487257,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.00039999998989515007,"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/computer-science","display_name":"Computer science","score":0.7125328779220581},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5922767519950867},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.591923177242279},{"id":"https://openalex.org/keywords/shotgun-proteomics","display_name":"Shotgun proteomics","score":0.4728415608406067},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43502047657966614},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.3668307065963745},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16499009728431702}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7125328779220581},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5922767519950867},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.591923177242279},{"id":"https://openalex.org/C68289359","wikidata":"https://www.wikidata.org/wiki/Q7502514","display_name":"Shotgun proteomics","level":4,"score":0.4728415608406067},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43502047657966614},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.3668307065963745},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16499009728431702},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu717","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu717","pdf_url":null,"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:25362092","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25362092","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:pubmedcentral.nih.gov:4341067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4341067","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4341067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4341067","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W87556421","https://openalex.org/W1587447328","https://openalex.org/W1964068488","https://openalex.org/W1964194772","https://openalex.org/W1972631150","https://openalex.org/W1978542424","https://openalex.org/W1980269662","https://openalex.org/W1985560593","https://openalex.org/W1986893074","https://openalex.org/W1988670311","https://openalex.org/W1989217826","https://openalex.org/W2008741852","https://openalex.org/W2015556811","https://openalex.org/W2021106071","https://openalex.org/W2024668145","https://openalex.org/W2026465178","https://openalex.org/W2038581432","https://openalex.org/W2043204396","https://openalex.org/W2062706447","https://openalex.org/W2080741498","https://openalex.org/W2082006641","https://openalex.org/W2085767578","https://openalex.org/W2087481305","https://openalex.org/W2095983933","https://openalex.org/W2096057003","https://openalex.org/W2099314206","https://openalex.org/W2100768052","https://openalex.org/W2102572519","https://openalex.org/W2107115446","https://openalex.org/W2110065044","https://openalex.org/W2114883363","https://openalex.org/W2124606291","https://openalex.org/W2125617877","https://openalex.org/W2135405321","https://openalex.org/W2147640998","https://openalex.org/W2160017921","https://openalex.org/W2161397902","https://openalex.org/W2325827597","https://openalex.org/W2904748943","https://openalex.org/W4205930252","https://openalex.org/W4235043437"],"related_works":["https://openalex.org/W2418091836","https://openalex.org/W2020165683","https://openalex.org/W1543316492","https://openalex.org/W2094017258","https://openalex.org/W2093547725","https://openalex.org/W4236949517","https://openalex.org/W4388717893","https://openalex.org/W3089151658","https://openalex.org/W2327641937","https://openalex.org/W2141343306"],"abstract_inverted_index":{"MOTIVATION:":[0],"Assigning":[1],"statistical":[2],"significance":[3],"accurately":[4],"has":[5],"become":[6],"increasingly":[7],"important":[8],"as":[9],"metadata":[10,29],"of":[11,28,41,49,82,99,113,135,168,173],"many":[12],"types,":[13],"often":[14],"assembled":[15],"in":[16,93,194],"hierarchies,":[17],"are":[18,181],"constructed":[19,73],"and":[20],"combined":[21,157],"for":[22,57,140,165,202],"further":[23],"biological":[24],"analyses.":[25],"Statistical":[26],"inaccuracy":[27],"at":[30,204],"any":[31],"level":[32,66,130],"may":[33],"propagate":[34],"to":[35,105,110],"downstream":[36],"analyses,":[37],"undermining":[38],"the":[39,47,96,106,111,133,159,166,176],"validity":[40],"scientific":[42],"conclusions":[43],"thus":[44],"drawn.":[45],"From":[46],"perspective":[48],"mass":[50],"spectrometry-based":[51],"proteomics,":[52],"even":[53],"though":[54],"accurate":[55,64,128,163],"statistics":[56,67],"peptide":[58,80,101],"identification":[59],"can":[60],"now":[61],"be":[62],"achieved,":[63],"protein":[65,75,85,124,129,147,153],"remain":[68],"challenging.":[69],"RESULTS:":[70],"We":[71,118],"have":[72,119],"a":[74,83,88,145,197],"ID":[76,125,154],"method":[77,126,180],"that":[78,122,151],"combines":[79],"evidences":[81],"candidate":[84],"based":[86],"on":[87,196],"rigorous":[89],"formula":[90,95],"derived":[91],"earlier;":[92],"this":[94,123,152],"database":[97],"P-value":[98],"every":[100],"is":[102,200],"weighted,":[103],"prior":[104],"final":[107],"combination,":[108],"according":[109],"number":[112],"proteins":[114],"it":[115],"maps":[116],"to.":[117],"also":[120],"shown":[121],"provides":[127],"E-value,":[131],"eliminating":[132],"need":[134],"using":[136],"empirical":[137],"post-processing":[138],"methods":[139,185],"type-I":[141],"error":[142],"control.":[143],"Using":[144],"known":[146],"mixture,":[148],"we":[149],"find":[150],"method,":[155],"when":[156],"with":[158,183],"Sori\u0107":[160],"formula,":[161],"yields":[162],"values":[164],"proportion":[167],"false":[169],"discoveries.":[170],"In":[171],"terms":[172],"retrieval":[174],"efficacy,":[175],"results":[177],"from":[178],"our":[179],"comparable":[182],"other":[184],"tested.":[186],"AVAILABILITY":[187],"AND":[188],"IMPLEMENTATION:":[189],"The":[190],"source":[191],"code,":[192],"implemented":[193],"C++":[195],"linux":[198],"system,":[199],"available":[201],"download":[203],"ftp://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/RAId/RAId_Linux_64Bit.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
