{"id":"https://openalex.org/W4313526956","doi":"https://doi.org/10.1109/bibm55620.2022.9995258","title":"Deep Learning Based MS2 Feature Detection for Data-Independent Shotgun Proteomics","display_name":"Deep Learning Based MS2 Feature Detection for Data-Independent Shotgun Proteomics","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313526956","doi":"https://doi.org/10.1109/bibm55620.2022.9995258","pmid":"https://pubmed.ncbi.nlm.nih.gov/37635836"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995258","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9995258","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10457098/pdf/nihms-1874655.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004324451","display_name":"Jonathan He","orcid":null},"institutions":[{"id":"https://openalex.org/I123534392","display_name":"University of North Texas","ror":"https://ror.org/00v97ad02","country_code":"US","type":"education","lineage":["https://openalex.org/I123534392"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathan He","raw_affiliation_strings":["Univeristy of North Texas,Department of Computer Science and Engineering,Denton,USA","Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA"],"affiliations":[{"raw_affiliation_string":"Univeristy of North Texas,Department of Computer Science and Engineering,Denton,USA","institution_ids":["https://openalex.org/I123534392"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA","institution_ids":["https://openalex.org/I123534392"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066917066","display_name":"Olivia Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I123534392","display_name":"University of North Texas","ror":"https://ror.org/00v97ad02","country_code":"US","type":"education","lineage":["https://openalex.org/I123534392"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olivia Liu","raw_affiliation_strings":["Univeristy of North Texas,Department of Computer Science and Engineering,Denton,USA","Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA"],"affiliations":[{"raw_affiliation_string":"Univeristy of North Texas,Department of Computer Science and Engineering,Denton,USA","institution_ids":["https://openalex.org/I123534392"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA","institution_ids":["https://openalex.org/I123534392"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075184660","display_name":"Xuan Guo","orcid":"https://orcid.org/0000-0002-2777-4482"},"institutions":[{"id":"https://openalex.org/I123534392","display_name":"University of North Texas","ror":"https://ror.org/00v97ad02","country_code":"US","type":"education","lineage":["https://openalex.org/I123534392"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xuan Guo","raw_affiliation_strings":["Univeristy of North Texas,Department of Computer Science and Engineering,Denton,USA","Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA"],"affiliations":[{"raw_affiliation_string":"Univeristy of North Texas,Department of Computer Science and Engineering,Denton,USA","institution_ids":["https://openalex.org/I123534392"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA","institution_ids":["https://openalex.org/I123534392"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5004324451"],"corresponding_institution_ids":["https://openalex.org/I123534392"],"apc_list":null,"apc_paid":null,"fwci":3.7034,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.9382716,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"9","issue":null,"first_page":"2342","last_page":"2348"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":1.0,"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":1.0,"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":0.9994999766349792,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9940000176429749,"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":0.6850231885910034},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.555773138999939},{"id":"https://openalex.org/keywords/shotgun-proteomics","display_name":"Shotgun proteomics","score":0.4955242872238159},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.49471279978752136},{"id":"https://openalex.org/keywords/tandem-mass-spectrometry","display_name":"Tandem mass spectrometry","score":0.45643675327301025},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4520190358161926},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4505768120288849},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.44678911566734314},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.4373672306537628},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.43368443846702576},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.339620977640152},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33801203966140747},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.19977426528930664},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.12188804149627686}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6850231885910034},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.555773138999939},{"id":"https://openalex.org/C68289359","wikidata":"https://www.wikidata.org/wiki/Q7502514","display_name":"Shotgun proteomics","level":4,"score":0.4955242872238159},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.49471279978752136},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.45643675327301025},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4520190358161926},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4505768120288849},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.44678911566734314},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4373672306537628},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.43368443846702576},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.339620977640152},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33801203966140747},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19977426528930664},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.12188804149627686},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibm55620.2022.9995258","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9995258","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmid:37635836","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37635836","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":"Proceedings. IEEE International Conference on Bioinformatics and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10457098","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10457098","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10457098/pdf/nihms-1874655.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10457098","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10457098","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10457098/pdf/nihms-1874655.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings (IEEE Int Conf Bioinformatics Biomed)","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2161374474","display_name":null,"funder_award_id":"R15LM013460","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4880614305","display_name":null,"funder_award_id":"R15LM013460","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G7544851979","display_name":null,"funder_award_id":"LM013460","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"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":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4313526956.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W639708223","https://openalex.org/W1516333482","https://openalex.org/W1995115647","https://openalex.org/W2008631073","https://openalex.org/W2027974246","https://openalex.org/W2050758433","https://openalex.org/W2080752012","https://openalex.org/W2313734891","https://openalex.org/W2317856197","https://openalex.org/W2404881327","https://openalex.org/W2510334816","https://openalex.org/W2526449353","https://openalex.org/W2586644082","https://openalex.org/W2589013025","https://openalex.org/W2623106170","https://openalex.org/W2724889495","https://openalex.org/W2736859409","https://openalex.org/W2770788665","https://openalex.org/W2772184539","https://openalex.org/W2776525063","https://openalex.org/W2887566220","https://openalex.org/W2932867787","https://openalex.org/W2964121718","https://openalex.org/W2967730427","https://openalex.org/W2990072002","https://openalex.org/W3041584148","https://openalex.org/W4324356200"],"related_works":["https://openalex.org/W2418091836","https://openalex.org/W1543316492","https://openalex.org/W2094017258","https://openalex.org/W2093547725","https://openalex.org/W1539981706","https://openalex.org/W1485011350","https://openalex.org/W4236949517","https://openalex.org/W4388717893","https://openalex.org/W2327641937","https://openalex.org/W3089151658"],"abstract_inverted_index":{"Accuracy":[0],"of":[1,14,24,29,54,90,129,162,176],"peptide":[2,30],"identification":[3],"in":[4,18,33,57,66],"LC-MS":[5,68],"analysis":[6,69],"is":[7,37,82],"crucial":[8,63],"for":[9,49],"information":[10],"regarding":[11],"the":[12,22,50,67,87,174],"aspects":[13],"proteins":[15],"that":[16,41,71,95,125,141,170],"aid":[17],"biomarker":[19],"discovery":[20],"and":[21,80,92,109,149],"profiling":[23],"complex":[25],"proteomes.":[26],"The":[27],"detection":[28,154],"fragment":[31],"ions":[32],"tandem":[34],"mass":[35],"spectrometry":[36],"still":[38],"challenging":[39,84],"given":[40],"current":[42],"tools":[43],"were":[44],"not":[45],"created":[46],"or":[47],"tested":[48],"low-abundance,":[51],"low-peak":[52],"fragments":[53],"peptides":[55,73,91],"found":[56],"MS2":[58,135],"data.":[59],"Feature":[60],"detection,":[61],"a":[62,103,116,159],"pre-processing":[64],"step":[65],"pipeline":[70],"quantifies":[72],"by":[74],"their":[75],"mass-to-charge":[76],"ratio,":[77],"retention":[78],"time,":[79],"intensity,":[81],"particularly":[83],"due":[85],"to":[86,133],"overlapping":[88],"nature":[89],"weak":[93],"signals":[94],"are":[96],"often":[97],"indistinguishable":[98],"from":[99],"noises,":[100],"thus":[101],"creating":[102],"reliance":[104],"on":[105],"rigid":[106],"mathematical":[107],"structures":[108],"heuristics.":[110],"In":[111],"this":[112],"study,":[113],"we":[114,168],"developed":[115],"deep-learning-based":[117],"model":[118,143,172],"with":[119],"an":[120],"innovative":[121],"sliding":[122],"window":[123],"process":[124],"enables":[126],"high-resolution":[127],"processing":[128],"quantitative":[130],"MS/MS":[131],"data":[132],"conduct":[134],"feature":[136,153],"detection.":[137],"Experimental":[138],"results":[139],"show":[140],"our":[142,171],"can":[144],"produce":[145],"more":[146],"accurate":[147],"values":[148],"identifications":[150],"than":[151],"existing":[152],"tools,":[155],"as":[156,158],"well":[157],"high":[160],"rate":[161],"true":[163],"positive":[164],"features":[165],"quantified.":[166],"Therefore,":[167],"believe":[169],"illustrates":[173],"advantages":[175],"deep":[177],"learning":[178],"techniques":[179],"applied":[180],"towards":[181],"computational":[182],"proteomics.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}