{"id":"https://openalex.org/W2101411462","doi":"https://doi.org/10.1186/1471-2105-13-288","title":"PAnalyzer: A software tool for protein inference in shotgun proteomics","display_name":"PAnalyzer: A software tool for protein inference in shotgun proteomics","publication_year":2012,"publication_date":"2012-11-05","ids":{"openalex":"https://openalex.org/W2101411462","doi":"https://doi.org/10.1186/1471-2105-13-288","mag":"2101411462","pmid":"https://pubmed.ncbi.nlm.nih.gov/23126499"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-288","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-288","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-288","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/10.1186/1471-2105-13-288","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074495063","display_name":"Gorka Prieto","orcid":"https://orcid.org/0000-0002-6433-8452"},"institutions":[{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gorka Prieto","raw_affiliation_strings":["Department of Communications Engineering, University of the Basque Country (UPV/EHU), Alda, Urquijo s/n, Bilbao, 48013, Spain. gorka.prieto@ehu.es","Department of Communications Engineering, University of the Basque Country (UPV/EHU), Alda, Urquijo s/n, Bilbao, 48013, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Communications Engineering, University of the Basque Country (UPV/EHU), Alda, Urquijo s/n, Bilbao, 48013, Spain. gorka.prieto@ehu.es","institution_ids":["https://openalex.org/I169108374"]},{"raw_affiliation_string":"Department of Communications Engineering, University of the Basque Country (UPV/EHU), Alda, Urquijo s/n, Bilbao, 48013, Spain","institution_ids":["https://openalex.org/I169108374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048578817","display_name":"Kerman Aloria","orcid":"https://orcid.org/0000-0001-7268-7700"},"institutions":[{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Kerman Aloria","raw_affiliation_strings":["Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","institution_ids":["https://openalex.org/I169108374"]},{"raw_affiliation_string":"Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain","institution_ids":["https://openalex.org/I169108374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078334239","display_name":"Nerea Osinalde","orcid":"https://orcid.org/0000-0001-8850-7794"},"institutions":[{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Nerea Osinalde","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), , Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","institution_ids":["https://openalex.org/I169108374"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), , Spain","institution_ids":["https://openalex.org/I169108374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050023206","display_name":"Asier Fullaondo","orcid":"https://orcid.org/0000-0001-5387-4762"},"institutions":[{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Asier Fullaondo","raw_affiliation_strings":["Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","Department of Genetics,Physical Anthropology and Animal Physiology,University of the Basque Country UPV/EHU,Leioa,Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","institution_ids":["https://openalex.org/I169108374"]},{"raw_affiliation_string":"Department of Genetics,Physical Anthropology and Animal Physiology,University of the Basque Country UPV/EHU,Leioa,Spain","institution_ids":["https://openalex.org/I169108374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018619489","display_name":"Jes\u00fas M. Arizmendi","orcid":"https://orcid.org/0000-0002-1412-4042"},"institutions":[{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jesus M Arizmendi","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), , Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain","institution_ids":["https://openalex.org/I169108374"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), , Spain","institution_ids":["https://openalex.org/I169108374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059654999","display_name":"Rune Matthiesen","orcid":"https://orcid.org/0000-0002-6353-2616"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rune Matthiesen","raw_affiliation_strings":["Proteolysis in diseases, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-465, Portugal","Proteolysis in diseases, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Proteolysis in diseases, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, Porto, 4200-465, Portugal","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Proteolysis in diseases, IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074495063"],"corresponding_institution_ids":["https://openalex.org/I169108374"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":1.0198,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.7271141,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"13","issue":"1","first_page":"288","last_page":"288"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9936000108718872,"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":0.9936000108718872,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.0010999999940395355,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.0005000000237487257,"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/shotgun-proteomics","display_name":"Shotgun proteomics","score":0.867242693901062},{"id":"https://openalex.org/keywords/shotgun","display_name":"Shotgun","score":0.7398339509963989},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.6009494662284851},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.544296383857727},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5250765681266785},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4775967597961426},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4425974488258362},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4424426555633545},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3469219207763672},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26845064759254456},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18018200993537903},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1552380919456482},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11329498887062073},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.059986889362335205}],"concepts":[{"id":"https://openalex.org/C68289359","wikidata":"https://www.wikidata.org/wiki/Q7502514","display_name":"Shotgun proteomics","level":4,"score":0.867242693901062},{"id":"https://openalex.org/C2781434637","wikidata":"https://www.wikidata.org/wiki/Q486396","display_name":"Shotgun","level":3,"score":0.7398339509963989},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6009494662284851},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.544296383857727},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5250765681266785},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4775967597961426},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4425974488258362},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4424426555633545},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3469219207763672},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26845064759254456},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18018200993537903},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1552380919456482},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11329498887062073},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.059986889362335205},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057809","descriptor_name":"HEK293 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057809","descriptor_name":"HEK293 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057809","descriptor_name":"HEK293 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-13-288","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-288","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-288","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:23126499","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23126499","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2564032","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3548767","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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3548767","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3548767","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"},{"id":"pmh:oai:addi.ehu.es:10810/10070","is_oa":true,"landing_page_url":"http://hdl.handle.net/10810/10070","pdf_url":null,"source":{"id":"https://openalex.org/S4306400469","display_name":"Communities in ADDI (Universidad del Pais Vasco)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210131160","host_organization_name":"Material Physics Center","host_organization_lineage":["https://openalex.org/I4210131160"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:159279edb21b41fbb382a7327b709184","is_oa":true,"landing_page_url":"https://doaj.org/article/159279edb21b41fbb382a7327b709184","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 13, Iss 1, p 288 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-288","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-288","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-288","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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.5}],"awards":[{"id":"https://openalex.org/G1826257621","display_name":null,"funder_award_id":"Ci\u00eancia 2007","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2726856368","display_name":null,"funder_award_id":"IE09-256","funder_id":"https://openalex.org/F4320321705","funder_display_name":"Eusko Jaurlaritza"}],"funders":[{"id":"https://openalex.org/F4320321705","display_name":"Eusko Jaurlaritza","ror":"https://ror.org/00pz2fp31"},{"id":"https://openalex.org/F4320321919","display_name":"Euskal Herriko Unibertsitatea","ror":"https://ror.org/000xsnr85"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101411462.pdf","grobid_xml":"https://content.openalex.org/works/W2101411462.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1597678601","https://openalex.org/W1981536086","https://openalex.org/W1986887325","https://openalex.org/W2007520071","https://openalex.org/W2015556811","https://openalex.org/W2023096047","https://openalex.org/W2038977068","https://openalex.org/W2095983933","https://openalex.org/W2111846704","https://openalex.org/W2116582554","https://openalex.org/W2148364245","https://openalex.org/W2155443196"],"related_works":["https://openalex.org/W2036789867","https://openalex.org/W4299663967","https://openalex.org/W2371475667","https://openalex.org/W2971480178","https://openalex.org/W2046727518","https://openalex.org/W1998648829","https://openalex.org/W2121165269","https://openalex.org/W4254600462","https://openalex.org/W2157839186","https://openalex.org/W1662072142"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"inference":[2,150,276],"from":[3],"peptide":[4,81,106],"identifications":[5],"in":[6,28,49,66,98,180,202,273],"shotgun":[7,50,153],"proteomics":[8,51],"must":[9],"deal":[10,267],"with":[11,268],"ambiguities":[12,270],"that":[13,271],"arise":[14,272],"due":[15],"to":[16,42,58,74,79,129,226,250,266,298],"the":[17,43,55,62,86,90,95,110,116,148,159,181,186,203,232,252,269,274],"presence":[18],"of":[19,61,115,152,185,234,244,254],"peptides":[20],"shared":[21],"between":[22],"different":[23,171],"proteins,":[24],"which":[25],"is":[26,54,248,295],"common":[27],"higher":[29],"eukaryotes.":[30],"Recently":[31],"data":[32,45,70,284],"independent":[33],"acquisition":[34,47],"(DIA)":[35],"approaches":[36,64],"have":[37],"emerged":[38],"as":[39,220],"an":[40,296],"alternative":[41],"traditional":[44],"dependent":[46],"(DDA)":[48],"experiments.":[52],"MSE":[53,69,134,198,242,283],"term":[56],"used":[57,65],"name":[59],"one":[60],"DIA":[63],"QTOF":[67],"instruments.":[68],"require":[71,119],"specialized":[72],"software":[73,87,127,144,191,264,303],"process":[75,151],"acquired":[76],"spectra":[77],"and":[78,82,113,162,200,217,229,256,290,301],"perform":[80],"protein":[83,149,177,275],"identifications.":[84],"However":[85],"available":[88],"at":[89],"moment":[91],"does":[92],"not":[93],"group":[94],"identified":[96,160],"proteins":[97,161],"a":[99,126,143,235,245,263],"transparent":[100],"way":[101],"by":[102,193,208,286],"taking":[103],"into":[104],"account":[105],"evidence":[107,172],"categories.":[108,173],"Furthermore":[109],"inspection,":[111],"comparison":[112],"report":[114,125],"obtained":[117],"results":[118,253],"tedious":[120],"manual":[121],"intervention.":[122],"Here":[123],"we":[124,140],"tool":[128,145,265],"address":[130],"these":[131],"limitations":[132],"for":[133,196,282],"data.":[135],"RESULTS:":[136],"In":[137],"this":[138],"paper":[139],"present":[141,262],"PAnalyzer,":[142],"focused":[146],"on":[147],"proteomics.":[154],"Our":[155],"approach":[156],"considers":[157],"all":[158],"groups":[163],"them":[164],"when":[165],"necessary":[166],"indicating":[167],"their":[168,197],"confidence":[169],"using":[170],"PAnalyzer":[174,255,294],"can":[175,212],"read":[176,215],"identification":[178],"files":[179,211],"XML":[182],"output":[183],"format":[184,205],"ProteinLynx":[187,257,287],"Global":[188,258,288],"Server":[189,289],"(PLGS)":[190],"provided":[192],"Waters":[194],"Corporation":[195],"data,":[199],"also":[201,213],"mzIdentML":[204,230,237],"recently":[206],"standardized":[207],"HUPO-PSI.":[209],"Multiple":[210],"be":[214],"simultaneously":[216],"are":[218,224,280],"considered":[219],"technical":[221,291],"replicates.":[222],"Results":[223],"saved":[225],"CSV,":[227],"HTML":[228],"(in":[231],"case":[233],"single":[236],"input":[238],"file)":[239],"files.":[240],"An":[241],"analysis":[243,285],"real":[246],"sample":[247],"presented":[249],"compare":[251],"Server.":[259],"CONCLUSIONS:":[260],"We":[261],"process.":[277],"Key":[278],"contributions":[279],"support":[281],"replicates":[292],"integration.":[293],"easy":[297],"use":[299],"multiplatform":[300],"free":[302],"tool.":[304]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}