{"id":"https://openalex.org/W2004806359","doi":"https://doi.org/10.1016/s1672-0229(08)60002-9","title":"Evaluating Peptide Mass Fingerprinting-Based Protein Identification","display_name":"Evaluating Peptide Mass Fingerprinting-Based Protein Identification","publication_year":2007,"publication_date":"2007-12-01","ids":{"openalex":"https://openalex.org/W2004806359","doi":"https://doi.org/10.1016/s1672-0229(08)60002-9","mag":"2004806359","pmid":"https://pubmed.ncbi.nlm.nih.gov/18267296","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054195"},"language":"en","primary_location":{"id":"doi:10.1016/s1672-0229(08)60002-9","doi":"https://doi.org/10.1016/s1672-0229(08)60002-9","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(08)60002-9","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1672022908600029/pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.sciencedirect.com/science/article/pii/S1672022908600029/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035318333","display_name":"Senthilkumar Damodaran","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Senthilkumar Damodaran","raw_affiliation_strings":["Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY, 14214 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY, 14214 , USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076358242","display_name":"Troy D. Wood","orcid":"https://orcid.org/0000-0002-2556-8511","observed_orcids":["https://orcid.org/0000-0002-2556-8511"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Troy D. Wood","raw_affiliation_strings":["Department of Chemistry, University at Buffalo , Buffalo, NY, 14260 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University at Buffalo , Buffalo, NY, 14260 , USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013945697","display_name":"Priyadharsini Nagarajan","orcid":"https://orcid.org/0000-0002-5346-2669","observed_orcids":["https://orcid.org/0000-0002-5346-2669"]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Priyadharsini Nagarajan","raw_affiliation_strings":["Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY, 14214 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY, 14214 , USA","institution_ids":["https://openalex.org/I63190737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111930866","display_name":"Richard A. Rabin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard A. Rabin","raw_affiliation_strings":["Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY, 14214 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo , Buffalo, NY, 14214 , USA","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5035318333"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":{"value":3850,"currency":"USD","value_usd":3850},"apc_paid":{"value":3850,"currency":"USD","value_usd":3850},"fwci":1.2349,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.74463453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"3-4","first_page":"152","last_page":"157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9951000213623047,"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":0.9951000213623047,"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":0.00419999985024333,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/peptide-mass-fingerprinting","display_name":"peptide mass mapping","score":0.9980000257492065},{"id":"https://openalex.org/keywords/protein-identification","display_name":"protein identification","score":0.9929999709129333},{"id":"https://openalex.org/keywords/identification-confidence","display_name":"identification confidence","score":0.7429999709129333},{"id":"https://openalex.org/keywords/high-throughput-proteomics","display_name":"high-throughput proteomics","score":0.7770000100135803},{"id":"https://openalex.org/keywords/false-positive-reduction","display_name":"false positive reduction","score":0.3619999885559082}],"concepts":[{"id":"https://openalex.org/C27420735","wikidata":"https://www.wikidata.org/wiki/Q5968721","display_name":"Peptide mass fingerprinting","level":4,"score":0.8381020426750183},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.656255841255188},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.4101219177246094},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40235060453414917},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3643953800201416},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3409678339958191},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2549561858177185},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.20916220545768738},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19261261820793152},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07605358958244324},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1016/s1672-0229(08)60002-9","doi":"https://doi.org/10.1016/s1672-0229(08)60002-9","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(08)60002-9","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1672022908600029/pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:4016535","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054195","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5054195","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5054195","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,"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":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics Proteomics Bioinformatics","raw_type":"Text"},{"id":"pmid:18267296","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18267296","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":"Genomics, proteomics & bioinformatics","raw_type":"Evaluation Study"}],"best_oa_location":{"id":"doi:10.1016/s1672-0229(08)60002-9","doi":"https://doi.org/10.1016/s1672-0229(08)60002-9","is_oa":true,"landing_page_url":"https://doi.org/10.1016/s1672-0229(08)60002-9","pdf_url":"https://www.sciencedirect.com/science/article/pii/S1672022908600029/pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-140"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics & Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2004806359.pdf","grobid_xml":"https://content.openalex.org/works/W2004806359.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1964443249","https://openalex.org/W1964972981","https://openalex.org/W1973954667","https://openalex.org/W1977371828","https://openalex.org/W1981593008","https://openalex.org/W1984044921","https://openalex.org/W1984320466","https://openalex.org/W1985560593","https://openalex.org/W2001401425","https://openalex.org/W2036185109","https://openalex.org/W2039438504","https://openalex.org/W2055063265","https://openalex.org/W2057847093","https://openalex.org/W2092523771","https://openalex.org/W2099622361","https://openalex.org/W2123248121","https://openalex.org/W2149412648","https://openalex.org/W2156118778","https://openalex.org/W2168843933"],"related_works":["https://openalex.org/W1588229361","https://openalex.org/W2279726639","https://openalex.org/W598815947","https://openalex.org/W2011987459","https://openalex.org/W3041137985","https://openalex.org/W104604325","https://openalex.org/W2120412864","https://openalex.org/W1989317755","https://openalex.org/W2026936025","https://openalex.org/W2079608781"],"abstract_inverted_index":{"Identification":[0],"of":[1,28,55,72],"proteins":[2,56,87],"by":[3,18],"mass":[4,21],"spectrometry":[5],"(MS)":[6],"is":[7,15,63],"an":[8],"essential":[9],"step":[10],"in":[11,82,103],"proteomic":[12,73],"studies":[13,74],"and":[14,57,98],"typically":[16],"accomplished":[17],"either":[19],"peptide":[20],"fingerprinting":[22],"(PMF)":[23],"or":[24],"amino":[25,140],"acid":[26,141],"sequencing":[27],"the":[29],"peptide.":[30],"Although":[31],"sequence":[32,142],"information":[33],"from":[34,144],"MS/MS":[35,61,109,145],"analysis":[36],"can":[37,134],"be":[38,48,135],"used":[39,84],"to":[40,85,91,100],"validate":[41],"PMF-based":[42,104,131],"protein":[43,94,105,132],"identification,":[44],"it":[45],"may":[46],"not":[47,64],"practical":[49],"when":[50,58,130],"analyzing":[51],"a":[52,69,121],"large":[53],"number":[54],"high-":[59],"throughput":[60],"instrumentation":[62],"readily":[65],"available.":[66],"At":[67],"present,":[68],"vast":[70],"majority":[71],"employ":[75],"PMF.":[76,89],"However,":[77],"there":[78],"are":[79,114],"huge":[80],"disparities":[81],"criteria":[83],"identify":[86],"using":[88,96],"Therefore,":[90],"reduce":[92],"incorrect":[93],"identification":[95,106,133],"PMF,":[97],"also":[99],"increase":[101],"confidence":[102],"without":[107,138],"accompanying":[108,139],"analysis,":[110],"definitive":[111],"guiding":[112],"principles":[113],"essential.":[115],"To":[116],"this":[117],"end,":[118],"we":[119],"propose":[120],"value-based":[122],"scoring":[123],"system":[124],"that":[125],"provides":[126],"guidance":[127],"on":[128],"evaluating":[129],"deemed":[136],"sufficient":[137],"data":[143],"analysis.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}