{"id":"https://openalex.org/W1614433858","doi":"https://doi.org/10.7907/z9qc01d9","title":"Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging","display_name":"Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging","publication_year":2015,"publication_date":"2015-05-29","ids":{"openalex":"https://openalex.org/W1614433858","doi":"https://doi.org/10.7907/z9qc01d9","mag":"1614433858"},"language":"en","primary_location":{"id":"pmh:oai:thesis.library.caltech.edu:8891","doi":null,"is_oa":false,"landing_page_url":"https://thesis.library.caltech.edu/8891/9/Table%202.S2.xlsx","pdf_url":null,"source":{"id":"https://openalex.org/S4306402402","display_name":"CaltechTHESIS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},"volume":null,"type":"dissertation","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.7907/z9qc01d9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066589781","display_name":"John D. Bagert","orcid":"https://orcid.org/0000-0001-7768-2853","observed_orcids":["https://orcid.org/0000-0001-7768-2853"]},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bagert, John David","raw_affiliation_strings":["California Institute of Technology"],"raw_orcid":"https://orcid.org/0000-0001-7768-2853","affiliations":[{"raw_affiliation_string":"California Institute of Technology","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066589781"],"corresponding_institution_ids":["https://openalex.org/I122411786"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9351000189781189,"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":0.9351000189781189,"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/T11440","display_name":"Click Chemistry and Applications","score":0.03889999911189079,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.00430000014603138,"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/boncat","display_name":"BONCAT","score":0.8920000195503235},{"id":"https://openalex.org/keywords/nascent-protein-synthesis","display_name":"nascent protein synthesis","score":0.8519999980926514},{"id":"https://openalex.org/keywords/time-resolved-proteomics","display_name":"time-resolved proteomics","score":0.9430000185966492},{"id":"https://openalex.org/keywords/small-rna-regulation","display_name":"small RNA regulation","score":0.8119999766349792},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.9129999876022339},{"id":"https://openalex.org/keywords/vibrio-harveyi","display_name":"Vibrio harveyi","score":0.9810000061988831},{"id":"https://openalex.org/keywords/quorum-sensing","display_name":"quorum sensing","score":0.9990000128746033},{"id":"https://openalex.org/keywords/iron-homeostasis","display_name":"iron homeostasis","score":0.9919999837875366}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6966677904129028},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.643638014793396},{"id":"https://openalex.org/C118687296","wikidata":"https://www.wikidata.org/wiki/Q905754","display_name":"Quorum sensing","level":4,"score":0.5528009533882141},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.49609026312828064},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.4945933520793915},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.4235067069530487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39246031641960144},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34276682138442993},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:thesis.library.caltech.edu:8891","doi":null,"is_oa":false,"landing_page_url":"https://thesis.library.caltech.edu/8891/9/Table%202.S2.xlsx","pdf_url":null,"source":{"id":"https://openalex.org/S4306402402","display_name":"CaltechTHESIS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},{"id":"doi:10.7907/z9qc01d9","doi":"https://doi.org/10.7907/z9qc01d9","is_oa":true,"landing_page_url":"https://doi.org/10.7907/z9qc01d9","pdf_url":null,"source":{"id":"https://openalex.org/S7407050848","display_name":"Caltech Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"thesis"},{"id":"mag:1614433858","doi":null,"is_oa":false,"landing_page_url":"http://gradworks.proquest.com/37/05/3705521.html","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.7907/z9qc01d9","doi":"https://doi.org/10.7907/z9qc01d9","is_oa":true,"landing_page_url":"https://doi.org/10.7907/z9qc01d9","pdf_url":null,"source":{"id":"https://openalex.org/S7407050848","display_name":"Caltech Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1115769823","display_name":null,"funder_award_id":"W911NF-09-0001","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G226397104","display_name":null,"funder_award_id":"W911NF\u201009\u20100001","funder_id":"https://openalex.org/F4320338502","funder_display_name":"Institute for Collaborative Biotechnologies"},{"id":"https://openalex.org/G4950536974","display_name":null,"funder_award_id":"-0001","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6754950289","display_name":"Proteome Exploration Laboratory","funder_award_id":"GBMF775","funder_id":"https://openalex.org/F4320306202","funder_display_name":"Gordon and Betty Moore Foundation"},{"id":"https://openalex.org/G713862231","display_name":"New Amino Acids for Protein Engineering","funder_award_id":"R01GM062523","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7452299184","display_name":null,"funder_award_id":"W911NF","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"}],"funders":[{"id":"https://openalex.org/F4320306202","display_name":"Gordon and Betty Moore Foundation","ror":"https://ror.org/006wxqw41"},{"id":"https://openalex.org/F4320309398","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055"},{"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/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"},{"id":"https://openalex.org/F4320338502","display_name":"Institute for Collaborative Biotechnologies","ror":"https://ror.org/04kz4p343"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2746664096","https://openalex.org/W4285048550","https://openalex.org/W2279738089","https://openalex.org/W2500470069","https://openalex.org/W6978451217","https://openalex.org/W4410361352","https://openalex.org/W4413138710","https://openalex.org/W4414747457","https://openalex.org/W7098620813","https://openalex.org/W3015379326"],"abstract_inverted_index":{"Bio-orthogonal":[0],"non-canonical":[1,37],"amino":[2,38],"acid":[3,39],"tagging":[4],"(BONCAT)":[5],"is":[6,43],"an":[7,92,111],"analytical":[8],"method":[9,107],"that":[10,88,143,166,290],"allows":[11],"the":[12,16,36,85,105,114,123,130,193,197,219,223,234,238,245],"selective":[13],"analysis":[14,253,287],"of":[15,18,50,84,161,175,196,222,237,301],"subset":[17],"newly":[19,155],"synthesized":[20,156],"cellular":[21],"proteins":[22,58,257,269],"produced":[23],"in":[24,45,48,76,81,126,133,151,202,271],"response":[25],"to":[26,62,153,182,191,232,250,279,282,296],"a":[27,117,146,298],"biological":[28,131,194,302],"stimulus.":[29],"In":[30,185,226],"BONCAT,":[31],"cells":[32],"are":[33,59],"treated":[34],"with":[35,99,258],"L-azidohomoalanine":[40],"(Aha),":[41],"which":[42],"utilized":[44],"protein":[46,162,176],"synthesis":[47,177],"place":[49],"methionine":[51],"by":[52],"wild-type":[53],"translational":[54],"machinery.":[55],"Nascent,":[56],"Aha-labeled":[57],"selectively":[60],"ligated":[61],"affinity":[63],"tags":[64],"for":[65,95,113],"enrichment":[66],"and":[67,82,108,129,136,212,268,288],"subsequently":[68],"identified":[69],"via":[70],"mass":[71],"spectrometry.":[72],"The":[73],"work":[74,276],"presented":[75],"this":[77,167,275],"thesis":[78,115],"exhibits":[79],"advancements":[80,125],"applications":[83,132],"BONCAT":[86,106,145,169,190,231,281],"technology":[87],"establishes":[89],"it":[90],"as":[91,110,116],"effective":[93],"tool":[94,148],"analyzing":[96],"proteome":[97],"dynamics":[98],"time-resolved":[100,285],"precision.":[101],"Chapter":[102,127,138,186,227],"1":[103],"introduces":[104],"serves":[109],"outline":[112],"whole.":[118],"I":[119,164,188,205,229],"discuss":[120],"motivations":[121],"behind":[122],"methodological":[124,141],"2":[128,135,139],"Chapters":[134],"3.":[137],"presents":[140],"developments":[142],"make":[144],"proteomic":[147,235,286],"capable":[149],"of,":[150],"addition":[152],"identifying":[154],"proteins,":[157,265,267],"accurately":[158],"quantifying":[159],"rates":[160],"synthesis.":[163],"demonstrate":[165],"quantitative":[168],"approach":[170],"can":[171,293],"measure":[172,233],"proteome-wide":[173],"patterns":[174],"at":[178],"time":[179],"scales":[180],"inaccessible":[181],"alternative":[183],"techniques.":[184],"3,":[187],"use":[189,230,280],"study":[192,297],"function":[195],"small":[198],"RNA":[199],"regulator":[200],"CyaR":[201,210,216],"Escherichia":[203],"coli.":[204],"correctly":[206],"identify":[207],"previously":[208],"known":[209],"targets,":[211,217],"validate":[213],"several":[214],"new":[215,255],"expanding":[218],"functional":[220],"roles":[221],"sRNA":[224],"regulator.":[225],"4,":[228],"profile":[236],"quorum":[239],"sensing":[240],"bacterium":[241],"Vibrio":[242],"harveyi":[243],"during":[244],"time-dependent":[246],"transition":[247],"from":[248],"individual-":[249],"group-behaviors.":[251],"My":[252],"reveals":[254],"quorum-sensing-regulated":[256],"diverse":[259],"functions,":[260],"including":[261],"transcription":[262],"factors,":[263],"chemotaxis":[264],"transport":[266],"involved":[270],"iron":[272],"homeostasis.":[273],"Overall,":[274],"describes":[277],"how":[278],"perform":[283],"quantitative,":[284],"demonstrates":[289],"these":[291],"measurements":[292],"be":[294],"used":[295],"broad":[299],"range":[300],"processes.":[303]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}