{"id":"https://openalex.org/W3157953488","doi":"https://doi.org/10.1186/s12859-021-03963-6","title":"Evaluation of open search methods based on theoretical mass spectra comparison","display_name":"Evaluation of open search methods based on theoretical mass spectra comparison","publication_year":2021,"publication_date":"2021-04-01","ids":{"openalex":"https://openalex.org/W3157953488","doi":"https://doi.org/10.1186/s12859-021-03963-6","mag":"3157953488","pmid":"https://pubmed.ncbi.nlm.nih.gov/33902435"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-03963-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03963-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03963-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03963-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087563325","display_name":"Albane Lysiak","orcid":"https://orcid.org/0000-0002-6769-7549"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210099947","display_name":"Biopolym\u00e8res Interactions Assemblages","ror":"https://ror.org/013vjwn12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099947"]},{"id":"https://openalex.org/I4210117005","display_name":"Laboratoire des Sciences du Num\u00e9rique de Nantes","ror":"https://ror.org/02snf8m58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I4210117005","https://openalex.org/I4210124215","https://openalex.org/I4210127572","https://openalex.org/I4210139971","https://openalex.org/I97188460","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Albane Lysiak","raw_affiliation_strings":["CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France","UR BIA, INRAE, 44316, Nantes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I4210117005","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"UR BIA, INRAE, 44316, Nantes, France","institution_ids":["https://openalex.org/I4210099947","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048361747","display_name":"Guillaume Fertin","orcid":"https://orcid.org/0000-0002-8251-2012"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210117005","display_name":"Laboratoire des Sciences du Num\u00e9rique de Nantes","ror":"https://ror.org/02snf8m58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I4210117005","https://openalex.org/I4210124215","https://openalex.org/I4210127572","https://openalex.org/I4210139971","https://openalex.org/I97188460","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Guillaume Fertin","raw_affiliation_strings":["CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France. guillaume.fertin@ls2n.fr","CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France"],"raw_orcid":"https://orcid.org/0000-0002-8251-2012","affiliations":[{"raw_affiliation_string":"CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France. guillaume.fertin@ls2n.fr","institution_ids":["https://openalex.org/I4210117005","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I4210117005","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046031524","display_name":"G\u00e9raldine Jean","orcid":"https://orcid.org/0000-0002-1534-2682"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210117005","display_name":"Laboratoire des Sciences du Num\u00e9rique de Nantes","ror":"https://ror.org/02snf8m58","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I4210117005","https://openalex.org/I4210124215","https://openalex.org/I4210127572","https://openalex.org/I4210139971","https://openalex.org/I97188460","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G\u00e9raldine Jean","raw_affiliation_strings":["CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, LS2N, Universit\u00e9 de Nantes, 44000, Nantes, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I4210117005","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000575007","display_name":"Dominique Tessier","orcid":"https://orcid.org/0000-0003-1503-7693"},"institutions":[{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210099947","display_name":"Biopolym\u00e8res Interactions Assemblages","ror":"https://ror.org/013vjwn12","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4210099947"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Dominique Tessier","raw_affiliation_strings":["BIBS Facility, INRAE, 44316, Nantes, France","UR BIA, INRAE, 44316, Nantes, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIBS Facility, INRAE, 44316, Nantes, France","institution_ids":["https://openalex.org/I4210099947","https://openalex.org/I4210088668"]},{"raw_affiliation_string":"UR BIA, INRAE, 44316, Nantes, France","institution_ids":["https://openalex.org/I4210099947","https://openalex.org/I4210088668"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048361747"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210117005","https://openalex.org/I97188460"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6811,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.6469013,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"22","issue":"S2","first_page":"65","last_page":"65"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9383000135421753,"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":0.9383000135421753,"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":0.01889999955892563,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.008299999870359898,"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/context","display_name":"Context (archaeology)","score":0.703779935836792},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6673595905303955},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6160885095596313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5682740211486816},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.5498278141021729},{"id":"https://openalex.org/keywords/mass-spectrum","display_name":"Mass spectrum","score":0.5302635431289673},{"id":"https://openalex.org/keywords/spectral-line","display_name":"Spectral line","score":0.525583803653717},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4553540050983429},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4377981424331665},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41397517919540405},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3939689099788666},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36087939143180847},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3325093388557434},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.30359548330307007},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.20895767211914062},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18130749464035034},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.11228621006011963},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10095059871673584},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.07838848233222961}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.703779935836792},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6673595905303955},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6160885095596313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5682740211486816},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.5498278141021729},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.5302635431289673},{"id":"https://openalex.org/C4839761","wikidata":"https://www.wikidata.org/wiki/Q212111","display_name":"Spectral line","level":2,"score":0.525583803653717},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4553540050983429},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4377981424331665},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41397517919540405},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3939689099788666},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36087939143180847},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3325093388557434},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.30359548330307007},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20895767211914062},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18130749464035034},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.11228621006011963},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10095059871673584},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.07838848233222961},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0}],"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":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-021-03963-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03963-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03963-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33902435","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33902435","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:hal-03318623v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-03318623","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2021, 22 (2 (Special Issue)), pp.65. &#x27E8;10.1186/s12859-021-03963-6&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:HAL:hal-03346887v1","is_oa":false,"landing_page_url":"https://hal.archives-ouvertes.fr/hal-03346887","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1471-2105","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:a15edb81d31d4a378a39cce35f967f22","is_oa":true,"landing_page_url":"https://doaj.org/article/a15edb81d31d4a378a39cce35f967f22","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss S2, Pp 1-17 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8073971","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8073971","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-03963-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03963-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-03963-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4935033833","display_name":null,"funder_award_id":"ANR-18-CE45-004","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6876561401","display_name":null,"funder_award_id":"ANR-18","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3157953488.pdf","grobid_xml":"https://content.openalex.org/works/W3157953488.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1480858518","https://openalex.org/W1553112665","https://openalex.org/W1568341953","https://openalex.org/W1973051173","https://openalex.org/W2080258378","https://openalex.org/W2095983933","https://openalex.org/W2096057003","https://openalex.org/W2107003257","https://openalex.org/W2147788028","https://openalex.org/W2155443196","https://openalex.org/W2205194111","https://openalex.org/W2207277820","https://openalex.org/W2465480251","https://openalex.org/W2494262371","https://openalex.org/W2604478324","https://openalex.org/W2607310450","https://openalex.org/W2728534204","https://openalex.org/W2789457189","https://openalex.org/W2894727674","https://openalex.org/W2930099314","https://openalex.org/W2949278902","https://openalex.org/W2951448848","https://openalex.org/W2964939082","https://openalex.org/W2970104449","https://openalex.org/W2991081046","https://openalex.org/W3111263758","https://openalex.org/W6806115372"],"related_works":["https://openalex.org/W2085384747","https://openalex.org/W2106071040","https://openalex.org/W2088166309","https://openalex.org/W4312133475","https://openalex.org/W4238976562","https://openalex.org/W2276587472","https://openalex.org/W1977853483","https://openalex.org/W2036032105","https://openalex.org/W4238908301","https://openalex.org/W2166757835"],"abstract_inverted_index":{"BACKGROUND:":[0],"Mass":[1],"spectrometry":[2],"remains":[3,50,202,281],"the":[4,13,27,45,59,105,119,125,129,133,137,142,167,177,181,186,200,235,251,257,283],"privileged":[5],"method":[6],"to":[7,40,123,174,231,246],"characterize":[8],"proteins.":[9],"Nevertheless,":[10],"most":[11],"of":[12,26,47,64,66,75,85,121,128,144,226,250,262,264,267,269,276,285],"spectra":[14,67,87,191,287],"generated":[15,132],"by":[16,69,184,211],"an":[17,203],"experiment":[18],"remain":[19],"unidentified":[20],"after":[21],"their":[22,76],"analysis,":[23],"mostly":[24],"because":[25],"modifications":[28],"they":[29],"carry.":[30],"Open":[31],"Modification":[32],"Search":[33],"(OMS)":[34],"methods":[35,71,208,280],"offer":[36],"a":[37,51,82,115,148,222,289],"promising":[38],"answer":[39],"this":[41,111,296],"problem.":[42],"However,":[43],"assessing":[44],"quality":[46,196,274],"OMS":[48,70,94,207,254,279],"identifications":[49,265],"difficult":[52],"task.":[53],"METHODS:":[54],"Aiming":[55],"at":[56],"better":[57,195],"understanding":[58],"relationship":[60],"between":[61,189],"(1)":[62],"similarity":[63],"pairs":[65],"provided":[68],"and":[72,266],"(2)":[73],"relevance":[74,109],"corresponding":[77],"peptide":[78,130],"sequences,":[79],"we":[80,91],"used":[81],"dataset":[83],"composed":[84],"theoretical":[86,286],"only,":[88],"on":[89],"which":[90,249],"applied":[92],"two":[93,99,159,190,252],"strategies.":[95],"We":[96],"also":[97,162],"introduced":[98],"appropriately":[100],"defined":[101],"measures":[102,160,243],"for":[103,292],"evaluating":[104],"above":[106,241],"mentioned":[107,242],"spectra/sequence":[108,228],"in":[110,147,164,206,260,278,295],"context:":[112],"one":[113],"is":[114,141,214,288],"color":[116,218],"classification":[117,219],"representing":[118],"level":[120],"difficulty":[122],"retrieve":[124],"proper":[126],"sequence":[127],"that":[131,154,179,221],"identified":[134],"spectrum":[135],";":[136],"other,":[138,258],"called":[139],"LIPR,":[140],"proportion":[143,225],"common":[145],"masses,":[146],"given":[149],"Peptide":[150],"Spectrum":[151],"Match":[152],"(PSM),":[153],"represent":[155],"dissimilar":[156],"sequences.":[157],"These":[158],"were":[161],"considered":[163],"conjunction":[165],"with":[166],"False":[168],"Discovery":[169],"Rate":[170],"(FDR).":[171],"RESULTS:":[172],"According":[173],"our":[175,217],"measures,":[176],"strategy":[178],"selects":[180],"best":[182],"candidate":[183],"taking":[185],"mass":[187],"difference":[188],"into":[192],"account":[193],"yields":[194],"results.":[197],"Besides,":[198],"although":[199],"FDR":[201],"interesting":[204],"indicator":[205],"(as":[209],"shown":[210],"LIPR),":[212],"it":[213],"questionable:":[215],"indeed,":[216],"shows":[220],"non":[223],"negligible":[224],"relevant":[227],"interpretations":[229],"corresponds":[230],"PSMs":[232,277],"coming":[233],"from":[234],"decoy":[236],"database.":[237],"CONCLUSIONS:":[238],"The":[239],"three":[240],"allowed":[244],"us":[245],"clearly":[247],"determine":[248],"studied":[253],"strategies":[255],"outperformed":[256],"both":[259],"terms":[261],"number":[263],"accuracy":[268],"these":[270],"identifications.":[271],"Even":[272],"though":[273],"evaluation":[275],"challenging,":[282],"study":[284],"favorable":[290],"framework":[291],"going":[293],"further":[294],"direction.":[297]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
