{"id":"https://openalex.org/W4414777573","doi":"https://doi.org/10.1038/s43588-025-00880-z","title":"Proteoform search from protein database with top-down mass spectra","display_name":"Proteoform search from protein database with top-down mass spectra","publication_year":2025,"publication_date":"2025-10-03","ids":{"openalex":"https://openalex.org/W4414777573","doi":"https://doi.org/10.1038/s43588-025-00880-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/41044386"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-025-00880-z","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00880-z","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","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/A5088703050","display_name":"Kunyi Li","orcid":"https://orcid.org/0000-0001-5089-2543"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Kunyi Li","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013405579","display_name":"Baozhen Shan","orcid":"https://orcid.org/0000-0002-8757-5493"},"institutions":[{"id":"https://openalex.org/I4210109217","display_name":"Bioinformatics Solutions (Canada)","ror":"https://ror.org/01jzb6k09","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210109217"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Baozhen Shan","raw_affiliation_strings":["Bioinformatics Solutions Inc, Waterloo, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Solutions Inc, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I4210109217"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lei Xin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109217","display_name":"Bioinformatics Solutions (Canada)","ror":"https://ror.org/01jzb6k09","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210109217"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lei Xin","raw_affiliation_strings":["Bioinformatics Solutions Inc, Waterloo, Ontario, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Solutions Inc, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I4210109217"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351398","display_name":"Ming Li","orcid":"https://orcid.org/0000-0002-2157-2775"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CA","CN"],"is_corresponding":true,"raw_author_name":"Ming Li","raw_affiliation_strings":["Central China Institute of Artificial Intelligence, Zhengzhou, China. mli@uwaterloo.ca","David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada. mli@uwaterloo.ca","Central China Institute of Artificial Intelligence, Zhengzhou, China","David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada"],"raw_orcid":"https://orcid.org/0000-0002-2157-2775","affiliations":[{"raw_affiliation_string":"Central China Institute of Artificial Intelligence, Zhengzhou, China. mli@uwaterloo.ca","institution_ids":["https://openalex.org/I4210100255"]},{"raw_affiliation_string":"David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada. mli@uwaterloo.ca","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Central China Institute of Artificial Intelligence, Zhengzhou, China","institution_ids":["https://openalex.org/I4210100255"]},{"raw_affiliation_string":"David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065315257","display_name":"Lusheng Wang","orcid":"https://orcid.org/0000-0002-4344-8791"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I4210105229","display_name":"City University of Hong Kong, Shenzhen Research Institute","ror":"https://ror.org/00xc0ma20","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210105229"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Lusheng Wang","raw_affiliation_strings":["City University of Hong Kong Shenzhen Research Institution, Shenzhen, China. cswangl@cityu.edu.hk","Department of Computer Science, City University of Hong Kong, Hong Kong, China. cswangl@cityu.edu.hk","City University of Hong Kong Shenzhen Research Institution, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-4344-8791","affiliations":[{"raw_affiliation_string":"City University of Hong Kong Shenzhen Research Institution, Shenzhen, China. cswangl@cityu.edu.hk","institution_ids":["https://openalex.org/I168719708","https://openalex.org/I4210105229"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Hong Kong, China. cswangl@cityu.edu.hk","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"City University of Hong Kong Shenzhen Research Institution, Shenzhen, China","institution_ids":["https://openalex.org/I168719708","https://openalex.org/I4210105229"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5065315257","https://openalex.org/A5100351398"],"corresponding_institution_ids":["https://openalex.org/I151746483","https://openalex.org/I168719708","https://openalex.org/I4210100255","https://openalex.org/I4210105229"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21150103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":"11","first_page":"998","last_page":"1009"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9958999752998352,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9944000244140625,"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":0.6696000099182129},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5164999961853027},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47279998660087585},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4489000141620636},{"id":"https://openalex.org/keywords/basis","display_name":"Basis (linear algebra)","score":0.43479999899864197},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.39489999413490295}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.6696000099182129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6661999821662903},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5164999961853027},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4844000041484833},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4729999899864197},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47279998660087585},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4489000141620636},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.43479999899864197},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.39489999413490295},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.38960000872612},{"id":"https://openalex.org/C48000682","wikidata":"https://www.wikidata.org/wiki/Q5227411","display_name":"Database search engine","level":3,"score":0.36559998989105225},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33629998564720154},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.314300000667572},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.3089999854564667}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-025-00880-z","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00880-z","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:41044386","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41044386","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":"Nature computational science","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4455729470","display_name":null,"funder_award_id":"OGP0046506","funder_id":"https://openalex.org/F4320321487","funder_display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6428773170","display_name":null,"funder_award_id":"NSFC: 61972329","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321487","display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1480858518","https://openalex.org/W2015392253","https://openalex.org/W2025955263","https://openalex.org/W2041230108","https://openalex.org/W2043828494","https://openalex.org/W2058135122","https://openalex.org/W2081465448","https://openalex.org/W2117262948","https://openalex.org/W2131381861","https://openalex.org/W2135581618","https://openalex.org/W2146482199","https://openalex.org/W2286617058","https://openalex.org/W2462197865","https://openalex.org/W2507222891","https://openalex.org/W2516677235","https://openalex.org/W2562897054","https://openalex.org/W2743289556","https://openalex.org/W2775217183","https://openalex.org/W2783149164","https://openalex.org/W2892321323","https://openalex.org/W2943223113","https://openalex.org/W3007615379","https://openalex.org/W4205584480","https://openalex.org/W4378469362","https://openalex.org/W4392928770","https://openalex.org/W4393981121","https://openalex.org/W4399645310","https://openalex.org/W4404458588","https://openalex.org/W6930791422","https://openalex.org/W6949652604","https://openalex.org/W6958753107"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
