{"id":"https://openalex.org/W2182208592","doi":"https://doi.org/10.1146/annurev-anchem-071015-041542","title":"Methods for the Analysis of Protein Phosphorylation\u2013Mediated Cellular Signaling Networks","display_name":"Methods for the Analysis of Protein Phosphorylation\u2013Mediated Cellular Signaling Networks","publication_year":2016,"publication_date":"2016-04-07","ids":{"openalex":"https://openalex.org/W2182208592","doi":"https://doi.org/10.1146/annurev-anchem-071015-041542","mag":"2182208592","pmid":"https://pubmed.ncbi.nlm.nih.gov/27049636"},"language":"en","primary_location":{"id":"doi:10.1146/annurev-anchem-071015-041542","doi":"https://doi.org/10.1146/annurev-anchem-071015-041542","is_oa":false,"landing_page_url":"https://doi.org/10.1146/annurev-anchem-071015-041542","pdf_url":null,"source":{"id":"https://openalex.org/S171259723","display_name":"Annual Review of Analytical Chemistry","issn_l":"1936-1327","issn":["1936-1327","1936-1335"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","medline","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320373","host_organization_name":"Annual Reviews","host_organization_lineage":["https://openalex.org/P4310320373"],"host_organization_lineage_names":["Annual Reviews"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annual Review of Analytical Chemistry","raw_type":"journal-article"},"volume":null,"type":"review","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002079869","display_name":"Forest M. White","orcid":"https://orcid.org/0000-0002-1545-1651","observed_orcids":["https://orcid.org/0000-0002-1545-1651"]},"institutions":[{"id":"https://openalex.org/I4390039253","display_name":"Koch Institute for Integrative Cancer Research At MIT","ror":"https://ror.org/01xd6q208","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4390039253","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Forest M. White","raw_affiliation_strings":["Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;","institution_ids":["https://openalex.org/I4390039253","https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078003568","display_name":"Alejandro Wolf\u2010Yadlin","orcid":"https://orcid.org/0000-0003-2909-3880","observed_orcids":["https://orcid.org/0000-0003-2909-3880"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alejandro Wolf-Yadlin","raw_affiliation_strings":["Department of Genome Sciences, University of Washington, Seattle, Washington 98105;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington, Seattle, Washington 98105;","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2039,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.15317919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"1","first_page":"295","last_page":"315"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9848999977111816,"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":0.9848999977111816,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0032999999821186066,"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/T10169","display_name":"Protein Kinase Regulation and GTPase Signaling","score":0.002300000051036477,"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/protein-phosphorylation","display_name":"protein phosphorylation","score":1.0},{"id":"https://openalex.org/keywords/cellular-signaling-networks","display_name":"cellular signaling networks","score":0.8659999966621399},{"id":"https://openalex.org/keywords/phosphorylation-site-identification","display_name":"phosphorylation site identification","score":0.7770000100135803},{"id":"https://openalex.org/keywords/phosphoproteomics","display_name":"phosphoproteomics","score":0.7760000228881836},{"id":"https://openalex.org/keywords/signaling-dynamics","display_name":"signaling dynamics","score":0.6859999895095825},{"id":"https://openalex.org/keywords/signaling-pathway-regulation","display_name":"signaling regulation","score":0.3880000114440918}],"concepts":[{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.8513237237930298},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.6443232297897339},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.5648808479309082},{"id":"https://openalex.org/C150555746","wikidata":"https://www.wikidata.org/wiki/Q210973","display_name":"Cell signaling","level":3,"score":0.5301476716995239},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.5013117790222168},{"id":"https://openalex.org/C2994130171","wikidata":"https://www.wikidata.org/wiki/Q210973","display_name":"Signaling proteins","level":3,"score":0.4746863543987274},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4668736159801483},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.441153347492218},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.1414588987827301}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1146/annurev-anchem-071015-041542","doi":"https://doi.org/10.1146/annurev-anchem-071015-041542","is_oa":false,"landing_page_url":"https://doi.org/10.1146/annurev-anchem-071015-041542","pdf_url":null,"source":{"id":"https://openalex.org/S171259723","display_name":"Annual Review of Analytical Chemistry","issn_l":"1936-1327","issn":["1936-1327","1936-1335"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","medline","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320373","host_organization_name":"Annual Reviews","host_organization_lineage":["https://openalex.org/P4310320373"],"host_organization_lineage_names":["Annual Reviews"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Annual Review of Analytical Chemistry","raw_type":"journal-article"},{"id":"pmid:27049636","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27049636","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":"Annual review of analytical chemistry (Palo Alto, Calif.)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1443670832","display_name":"Vanderbilt Proteome Characterization Center","funder_award_id":"U24CA159988","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2413163874","display_name":"Tumor Cell Networks Center","funder_award_id":"U54CA112967","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4012495672","display_name":"Training Grant in Environmental Toxicology","funder_award_id":"T32ES007020","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G9000891960","display_name":"Cancer Center Support (Core) Grant","funder_award_id":"P30CA014051","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":111,"referenced_works":["https://openalex.org/W948425943","https://openalex.org/W1482622484","https://openalex.org/W1506170988","https://openalex.org/W1508494506","https://openalex.org/W1551209903","https://openalex.org/W1556838039","https://openalex.org/W1605149897","https://openalex.org/W1647597862","https://openalex.org/W1885450701","https://openalex.org/W1946817100","https://openalex.org/W1965807926","https://openalex.org/W1966792579","https://openalex.org/W1967925645","https://openalex.org/W1968654199","https://openalex.org/W1972927753","https://openalex.org/W1974515407","https://openalex.org/W1975338776","https://openalex.org/W1976217821","https://openalex.org/W1978177843","https://openalex.org/W1978254752","https://openalex.org/W1978961627","https://openalex.org/W1981637202","https://openalex.org/W1982478943","https://openalex.org/W1984227596","https://openalex.org/W1984871500","https://openalex.org/W1989022203","https://openalex.org/W1991683095","https://openalex.org/W1993647605","https://openalex.org/W1995403127","https://openalex.org/W1995478292","https://openalex.org/W1996310767","https://openalex.org/W1998521509","https://openalex.org/W1999916343","https://openalex.org/W2001207288","https://openalex.org/W2003462220","https://openalex.org/W2004704197","https://openalex.org/W2009339798","https://openalex.org/W2011147958","https://openalex.org/W2012900739","https://openalex.org/W2015671099","https://openalex.org/W2018126724","https://openalex.org/W2018872127","https://openalex.org/W2020103130","https://openalex.org/W2024575179","https://openalex.org/W2026902836","https://openalex.org/W2038254572","https://openalex.org/W2039058260","https://openalex.org/W2042044881","https://openalex.org/W2045117578","https://openalex.org/W2047552911","https://openalex.org/W2052141890","https://openalex.org/W2054492185","https://openalex.org/W2056467018","https://openalex.org/W2062859898","https://openalex.org/W2063208275","https://openalex.org/W2068481474","https://openalex.org/W2071363300","https://openalex.org/W2073307618","https://openalex.org/W2075754351","https://openalex.org/W2081359173","https://openalex.org/W2085037886","https://openalex.org/W2086150914","https://openalex.org/W2087331879","https://openalex.org/W2091787667","https://openalex.org/W2091824579","https://openalex.org/W2092777410","https://openalex.org/W2093486460","https://openalex.org/W2094399892","https://openalex.org/W2094507968","https://openalex.org/W2099255819","https://openalex.org/W2099374185","https://openalex.org/W2100092346","https://openalex.org/W2104303958","https://openalex.org/W2104366432","https://openalex.org/W2104726963","https://openalex.org/W2105167594","https://openalex.org/W2105928352","https://openalex.org/W2110817748","https://openalex.org/W2111352469","https://openalex.org/W2117629868","https://openalex.org/W2120018526","https://openalex.org/W2121851657","https://openalex.org/W2126910411","https://openalex.org/W2128134586","https://openalex.org/W2129528062","https://openalex.org/W2130717546","https://openalex.org/W2133258252","https://openalex.org/W2136133297","https://openalex.org/W2141091417","https://openalex.org/W2141766988","https://openalex.org/W2142654480","https://openalex.org/W2148691504","https://openalex.org/W2153977008","https://openalex.org/W2154792706","https://openalex.org/W2156842451","https://openalex.org/W2157058776","https://openalex.org/W2157933281","https://openalex.org/W2161811833","https://openalex.org/W2164442321","https://openalex.org/W2164522178","https://openalex.org/W2167089719","https://openalex.org/W2167829261","https://openalex.org/W2168037598","https://openalex.org/W2168691181","https://openalex.org/W2170890534","https://openalex.org/W2171916754","https://openalex.org/W2172111870","https://openalex.org/W2413747597","https://openalex.org/W2417344110","https://openalex.org/W2460123445","https://openalex.org/W2468349180"],"related_works":["https://openalex.org/W1965296166","https://openalex.org/W2167932805","https://openalex.org/W2072389876","https://openalex.org/W2019858779","https://openalex.org/W2029645827","https://openalex.org/W2054800747","https://openalex.org/W1916299160","https://openalex.org/W2021238335","https://openalex.org/W2160406438","https://openalex.org/W1589637437"],"abstract_inverted_index":{"Protein":[0],"phosphorylation-mediated":[1],"cellular":[2,16,56,69],"signaling":[3,106,127],"networks":[4,22],"regulate":[5],"almost":[6],"all":[7],"aspects":[8],"of":[9,29,34,64,76,94,104,112,124],"cell":[10],"biology,":[11],"including":[12,79],"the":[13,44,61,80,102,119],"responses":[14],"to":[15,48,59,67,101],"stimulation":[17],"and":[18,26,31,51,58,89,91,122],"environmental":[19],"alterations.":[20],"These":[21],"are":[23],"highly":[24],"complex":[25,105],"comprise":[27],"hundreds":[28],"proteins":[30,50],"potentially":[32],"thousands":[33],"phosphorylation":[35,53,126],"sites.":[36],"Multiple":[37],"analytical":[38],"methods":[39],"have":[40],"been":[41,99],"developed":[42],"over":[43],"past":[45],"several":[46],"decades":[47],"identify":[49],"protein":[52,125],"sites":[54,66],"regulating":[55],"signaling,":[57],"quantify":[60],"dynamic":[62],"response":[63],"these":[65,77,113],"different":[68],"stimulation.":[70],"Here":[71],"we":[72],"provide":[73,116],"an":[74],"overview":[75],"methods,":[78],"fundamental":[81],"principles":[82],"governing":[83],"each":[84,96,111],"method,":[85],"their":[86],"relative":[87],"strengths":[88],"weaknesses,":[90],"some":[92],"examples":[93],"how":[95],"method":[97],"has":[98],"applied":[100,109],"analysis":[103],"networks.":[107,128],"When":[108],"correctly,":[110],"techniques":[114],"can":[115],"insight":[117],"into":[118],"topology,":[120],"dynamics,":[121],"regulation":[123]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}