{"id":"https://openalex.org/W2596554155","doi":"https://doi.org/10.1021/acs.jproteome.6b01019","title":"Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification","display_name":"Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification","publication_year":2017,"publication_date":"2017-03-16","ids":{"openalex":"https://openalex.org/W2596554155","doi":"https://doi.org/10.1021/acs.jproteome.6b01019","mag":"2596554155","pmid":"https://pubmed.ncbi.nlm.nih.gov/28299940"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jproteome.6b01019","doi":"https://doi.org/10.1021/acs.jproteome.6b01019","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.6b01019","pdf_url":null,"source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Proteome Research","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059219443","display_name":"Jin-Young Cho","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]},{"id":"https://openalex.org/I4210162080","display_name":"Yonsei Proteome Research Center","ror":"https://ror.org/055yqn475","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210162080"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jin-Young Cho","raw_affiliation_strings":["Yonsei Proteome Research Center, Seoul 03722, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yonsei Proteome Research Center, Seoul 03722, Korea","institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210162080"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113671959","display_name":"Hyoung\u2013Joo Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]},{"id":"https://openalex.org/I4210162080","display_name":"Yonsei Proteome Research Center","ror":"https://ror.org/055yqn475","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210162080"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyoung-Joo Lee","raw_affiliation_strings":["Yonsei Proteome Research Center, Seoul 03722, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yonsei Proteome Research Center, Seoul 03722, Korea","institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210162080"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Seul-Ki Jeong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]},{"id":"https://openalex.org/I4210162080","display_name":"Yonsei Proteome Research Center","ror":"https://ror.org/055yqn475","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210162080"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seul-Ki Jeong","raw_affiliation_strings":["Yonsei Proteome Research Center, Seoul 03722, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yonsei Proteome Research Center, Seoul 03722, Korea","institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210162080"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006448477","display_name":"Young\u2010Ki Paik","orcid":"https://orcid.org/0000-0002-8146-1751","observed_orcids":["https://orcid.org/0000-0002-8146-1751"]},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]},{"id":"https://openalex.org/I4210162080","display_name":"Yonsei Proteome Research Center","ror":"https://ror.org/055yqn475","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210162080"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Young-Ki Paik","raw_affiliation_strings":["Yonsei Proteome Research Center, Seoul 03722, Korea"],"raw_orcid":"https://orcid.org/0000-0002-8146-1751","affiliations":[{"raw_affiliation_string":"Yonsei Proteome Research Center, Seoul 03722, Korea","institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210162080"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006448477"],"corresponding_institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210162080"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.8318,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62889246,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"16","issue":"12","first_page":"4435","last_page":"4445"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9990000128746033,"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":0.9990000128746033,"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":0.0006000000284984708,"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":0.0,"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/spectral-library-search","display_name":"spectral library search","score":0.8240000009536743},{"id":"https://openalex.org/keywords/false-discovery-rate-control","display_name":"false discovery rate control","score":0.8679999709129333},{"id":"https://openalex.org/keywords/sequence-database-searching","display_name":"sequence database searching","score":0.5009999871253967}],"concepts":[{"id":"https://openalex.org/C158007255","wikidata":"https://www.wikidata.org/wiki/Q1055222","display_name":"Spectrum analyzer","level":2,"score":0.5930848717689514},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5001850128173828},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.4244595170021057},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4234102964401245},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41331642866134644},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.3611797094345093},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1399010717868805},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C58226133","wikidata":"https://www.wikidata.org/wiki/Q1324199","display_name":"Pulmonary surfactant","level":2,"score":0.0},{"id":"https://openalex.org/C55352822","wikidata":"https://www.wikidata.org/wiki/Q5558978","display_name":"Gibbs isotherm","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jproteome.6b01019","doi":"https://doi.org/10.1021/acs.jproteome.6b01019","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.6b01019","pdf_url":null,"source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Proteome Research","raw_type":"journal-article"},{"id":"pmid:28299940","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28299940","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,"listed_in":[],"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":"Journal of proteome research","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3333756443","display_name":null,"funder_award_id":"HI16C0257","funder_id":"https://openalex.org/F4320310848","funder_display_name":"Ministry of Health and Welfare"},{"id":"https://openalex.org/G6898511280","display_name":null,"funder_award_id":"HI13C2098","funder_id":"https://openalex.org/F4320310848","funder_display_name":"Ministry of Health and Welfare"}],"funders":[{"id":"https://openalex.org/F4320310848","display_name":"Ministry of Health and Welfare","ror":"https://ror.org/024w0ge69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1977972652","https://openalex.org/W1981593008","https://openalex.org/W1985524611","https://openalex.org/W1986873950","https://openalex.org/W1991343446","https://openalex.org/W1997504014","https://openalex.org/W2005900663","https://openalex.org/W2008214517","https://openalex.org/W2026433130","https://openalex.org/W2026465178","https://openalex.org/W2028673251","https://openalex.org/W2033079433","https://openalex.org/W2049092511","https://openalex.org/W2051978415","https://openalex.org/W2053827324","https://openalex.org/W2067074165","https://openalex.org/W2073229999","https://openalex.org/W2073637473","https://openalex.org/W2075645900","https://openalex.org/W2080752012","https://openalex.org/W2082006641","https://openalex.org/W2089273345","https://openalex.org/W2090968821","https://openalex.org/W2091375086","https://openalex.org/W2091377998","https://openalex.org/W2112143438","https://openalex.org/W2113765377","https://openalex.org/W2117327695","https://openalex.org/W2130706354","https://openalex.org/W2137144192","https://openalex.org/W2139987858","https://openalex.org/W2148490163","https://openalex.org/W2152180036","https://openalex.org/W2160110467","https://openalex.org/W2165711628","https://openalex.org/W2170892735","https://openalex.org/W2221358813","https://openalex.org/W2286437341","https://openalex.org/W2313734891","https://openalex.org/W2345735224","https://openalex.org/W2409617262","https://openalex.org/W2417287503","https://openalex.org/W2501450358"],"related_works":["https://openalex.org/W2068199476","https://openalex.org/W2293199826","https://openalex.org/W4303444681","https://openalex.org/W2079294091","https://openalex.org/W1732544349","https://openalex.org/W1601672496","https://openalex.org/W1986873950","https://openalex.org/W2073637473","https://openalex.org/W7096626168","https://openalex.org/W244723841"],"abstract_inverted_index":{"Mass":[0],"spectrometry":[1],"(MS)":[2],"is":[3,62,207],"a":[4,38,131,140,177,220,244],"widely":[5],"used":[6,29],"proteome":[7,88,249],"analysis":[8,250],"tool":[9,144,246],"for":[10,230,247],"biomedical":[11],"science.":[12],"In":[13,134],"an":[14,63],"MS-based":[15],"bottom-up":[16],"proteomic":[17],"approach":[18],"to":[19,126,147],"protein":[20,159],"identification,":[21],"sequence":[22,39,70,226],"database":[23],"(DB)":[24],"searching":[25,37,61,72,125],"has":[26,86,176],"been":[27],"routinely":[28],"because":[30],"of":[31,69,77,96,151],"its":[32],"simplicity":[33],"and":[34,54,73,98,121,157,172,181,187,196,232,256],"convenience.":[35],"However,":[36],"DB":[40,71,227],"with":[41,80,209],"multiple":[42,119,164,253],"variable":[43],"modification":[44],"options":[45],"can":[46,242],"increase":[47],"processing":[48],"time,":[49],"false-positive":[50],"errors":[51],"in":[52,91,93,102,130,185,236],"large":[53],"complicated":[55],"MS":[56,193],"data":[57,194],"sets.":[58],"Spectral":[59],"library":[60,124,166],"alternative":[64],"solution,":[65],"avoiding":[66],"the":[67,75,94,112,149,153,204,210,215],"limitations":[68,92],"allowing":[74],"detection":[76,95],"more":[78],"peptides":[79],"high":[81],"sensitivity.":[82],"Unfortunately,":[83],"this":[84,135],"technique":[85],"less":[87],"coverage,":[89],"resulting":[90],"novel":[97],"whole":[99,128],"peptide":[100],"sequences":[101],"biological":[103,132,237],"samples.":[104,238],"To":[105],"solve":[106],"these":[107],"problems,":[108],"we":[109,137],"previously":[110],"developed":[111,139],"\"Combo-Spec":[113],"Search\"":[114],"method,":[115,213],"which":[116],"uses":[117],"manually":[118],"references":[120],"simulated":[122],"spectral":[123,165,254],"analyze":[127],"proteomes":[129],"sample.":[133],"study,":[136],"have":[138],"new":[141],"analytical":[142],"interface":[143,180,206],"called":[145,214],"\"Epsilon-Q\"":[146],"enhance":[148],"functions":[150],"both":[152],"Combo-Spec":[154,211],"Search":[155],"method":[156],"label-free":[158,257],"quantification.":[160,258],"Epsilon-Q":[161,205,216,240],"performs":[162],"automatically":[163],"searching,":[167],"class-specific":[168],"false-discovery":[169],"rate":[170],"control,":[171],"result":[173],"integration.":[174],"It":[175],"user-friendly":[178],"graphical":[179],"demonstrates":[182],"good":[183],"performance":[184],"identifying":[186,231],"quantifying":[188,233],"proteins":[189,235],"by":[190,200,223],"supporting":[191],"standard":[192],"formats":[195],"spectrum-to-spectrum":[197],"matching":[198],"powered":[199],"SpectraST.":[201],"Furthermore,":[202],"when":[203],"combined":[208],"search":[212,228],"system,":[217],"it":[218],"shows":[219],"synergistic":[221],"function":[222],"outperforming":[224],"other":[225],"engines":[229],"low-abundance":[234],"The":[239],"system":[241],"be":[243],"versatile":[245],"comparative":[248],"based":[251],"on":[252],"libraries":[255]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2017-03-23T00:00:00"}