{"id":"https://openalex.org/W4317702940","doi":"https://doi.org/10.1093/bib/bbad010","title":"Analysis of affinity purification-related proteomic data for studying protein\u2013protein interaction networks in cells","display_name":"Analysis of affinity purification-related proteomic data for studying protein\u2013protein interaction networks in cells","publication_year":2023,"publication_date":"2023-01-22","ids":{"openalex":"https://openalex.org/W4317702940","doi":"https://doi.org/10.1093/bib/bbad010","pmid":"https://pubmed.ncbi.nlm.nih.gov/36682002"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad010","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad010","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad010/49560349/bbad010.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad010/49560349/bbad010.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076871243","display_name":"Rebecca Elizabeth Kattan","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Elizabeth Kattan","raw_affiliation_strings":["Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077711070","display_name":"Deena Ayesh","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deena Ayesh","raw_affiliation_strings":["Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100759568","display_name":"Wenqi Wang","orcid":"https://orcid.org/0000-0003-4053-5088"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wenqi Wang","raw_affiliation_strings":["Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA"],"raw_orcid":"https://orcid.org/0000-0003-4053-5088","affiliations":[{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100759568"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.8492,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.68978967,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9986000061035156,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9986000061035156,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9968000054359436,"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/T13127","display_name":"Biotin and Related Studies","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5722891092300415},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.515151858329773},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.45535850524902344},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.43240439891815186},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36444661021232605},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2670096755027771},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2239992618560791},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09002691507339478}],"concepts":[{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5722891092300415},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.515151858329773},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.45535850524902344},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.43240439891815186},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36444661021232605},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2670096755027771},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2239992618560791},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09002691507339478}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":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},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbad010","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad010","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad010/49560349/bbad010.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36682002","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36682002","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt1pr271bn","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/1pr271bn","pdf_url":"https://escholarship.org/content/qt1pr271bn/qt1pr271bn.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, vol 24, iss 2","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10025443","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10025443","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10025443/pdf/bbad010.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:ark:/13030/qt1pr271bn","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad010","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad010","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad010/49560349/bbad010.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1080478560","display_name":null,"funder_award_id":"UL1 TR001414","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G1096164825","display_name":null,"funder_award_id":"R01GM126048","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1340941988","display_name":null,"funder_award_id":"R01 GM126048","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3203548394","display_name":null,"funder_award_id":"R01 GM143233","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8840615626","display_name":null,"funder_award_id":"R01GM143233","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320337963","display_name":"Institute for Clinical and Translational Science, University of California, Irvine","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4317702940.pdf","grobid_xml":"https://content.openalex.org/works/W4317702940.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W931222270","https://openalex.org/W1575542444","https://openalex.org/W1611787727","https://openalex.org/W1925213563","https://openalex.org/W1964999292","https://openalex.org/W1968063944","https://openalex.org/W1972247888","https://openalex.org/W1979369154","https://openalex.org/W1979853788","https://openalex.org/W1990312420","https://openalex.org/W1990315216","https://openalex.org/W1991953772","https://openalex.org/W1992006348","https://openalex.org/W1996076856","https://openalex.org/W1996722984","https://openalex.org/W2000860171","https://openalex.org/W2020511240","https://openalex.org/W2023096047","https://openalex.org/W2023124677","https://openalex.org/W2023949937","https://openalex.org/W2033303857","https://openalex.org/W2043409309","https://openalex.org/W2047077861","https://openalex.org/W2060705109","https://openalex.org/W2068446924","https://openalex.org/W2078377283","https://openalex.org/W2096057003","https://openalex.org/W2105707485","https://openalex.org/W2106969933","https://openalex.org/W2109993774","https://openalex.org/W2110845720","https://openalex.org/W2125111103","https://openalex.org/W2137531873","https://openalex.org/W2139746915","https://openalex.org/W2142082526","https://openalex.org/W2151364212","https://openalex.org/W2152124140","https://openalex.org/W2155443196","https://openalex.org/W2157198584","https://openalex.org/W2158217645","https://openalex.org/W2158804744","https://openalex.org/W2159675211","https://openalex.org/W2163185745","https://openalex.org/W2165447216","https://openalex.org/W2167844024","https://openalex.org/W2168223461","https://openalex.org/W2223119478","https://openalex.org/W2473061292","https://openalex.org/W2482454958","https://openalex.org/W2537623931","https://openalex.org/W2737189741","https://openalex.org/W2787587553","https://openalex.org/W2887216340","https://openalex.org/W2890289205","https://openalex.org/W2899760200","https://openalex.org/W2915536738","https://openalex.org/W2928665623","https://openalex.org/W2953399152","https://openalex.org/W2990219485","https://openalex.org/W3040718066","https://openalex.org/W3100552275","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3204794438","https://openalex.org/W4205254628","https://openalex.org/W4205788462","https://openalex.org/W4207037002","https://openalex.org/W4220824576"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2088324202","https://openalex.org/W2099982459","https://openalex.org/W2109298101","https://openalex.org/W2007507741","https://openalex.org/W2159860826","https://openalex.org/W3192210502","https://openalex.org/W1981737222"],"abstract_inverted_index":{"During":[0],"intracellular":[1],"signal":[2],"transduction,":[3],"protein-protein":[4],"interactions":[5],"(PPIs)":[6],"facilitate":[7],"protein":[8,13],"complex":[9],"assembly":[10],"to":[11,32,35,57,88],"regulate":[12],"localization":[14],"and":[15,38,60,72,101,114],"function,":[16],"which":[17],"are":[18,105],"critical":[19],"for":[20,119,124],"numerous":[21],"cellular":[22],"events.":[23],"Over":[24],"the":[25,45,78,99],"years,":[26],"multiple":[27],"techniques":[28],"have":[29],"been":[30,52],"developed":[31],"characterize":[33],"PPIs":[34],"elucidate":[36],"roles":[37],"regulatory":[39],"mechanisms":[40],"of":[41,80,84],"proteins.":[42],"Among":[43],"them,":[44],"mass":[46],"spectrometry":[47],"(MS)-based":[48],"interactome":[49],"analysis":[50,79],"has":[51],"increasing":[53],"in":[54,108],"popularity":[55],"due":[56],"its":[58],"unbiased":[59],"informative":[61],"manner":[62],"towards":[63],"understanding":[64],"PPI":[65],"networks.":[66],"However,":[67],"with":[68],"MS":[69],"instrumentation":[70],"advancing":[71],"yielding":[73],"more":[74],"data":[75,87,113],"than":[76],"ever,":[77],"a":[81,116],"large":[82,110],"amount":[83],"PPI-associated":[85],"proteomic":[86,112],"reveal":[89],"bona":[90],"fide":[91],"interacting":[92,122],"proteins":[93,123],"become":[94],"challenging.":[95],"Here,":[96],"we":[97],"review":[98],"methods":[100],"bioinformatic":[102],"resources":[103],"that":[104],"commonly":[106],"used":[107],"analyzing":[109],"interactome-related":[111],"propose":[115],"simple":[117],"guideline":[118],"identifying":[120],"novel":[121],"biological":[125],"research.":[126]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
