{"id":"https://openalex.org/W4282966867","doi":"https://doi.org/10.1158/1538-7445.am2022-6340","title":"Abstract 6340: Deep, unbiased and peptide-centric plasma proteomics with differential analysis of proteoforms enabling proteogenomic studies of NSCLC at scale","display_name":"Abstract 6340: Deep, unbiased and peptide-centric plasma proteomics with differential analysis of proteoforms enabling proteogenomic studies of NSCLC at scale","publication_year":2022,"publication_date":"2022-06-15","ids":{"openalex":"https://openalex.org/W4282966867","doi":"https://doi.org/10.1158/1538-7445.am2022-6340"},"language":"en","primary_location":{"id":"doi:10.1158/1538-7445.am2022-6340","doi":"https://doi.org/10.1158/1538-7445.am2022-6340","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2022-6340","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","indexed_in":["crossref"],"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/A5060468814","display_name":"Margaret K. R. Donovan","orcid":"https://orcid.org/0000-0001-5240-4216","observed_orcids":["https://orcid.org/0000-0001-5240-4216"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Margaret Donovan","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079262737","display_name":"Henry Darchon Huang","orcid":"https://orcid.org/0000-0003-3281-2663","observed_orcids":["https://orcid.org/0000-0003-3281-2663"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Henry Huang","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"John Blume","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"John Blume","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022616302","display_name":"Marwin Ko","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marwin Ko","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003755911","display_name":"Ryan W. Benz","orcid":"https://orcid.org/0000-0002-8924-6116","observed_orcids":["https://orcid.org/0000-0002-8924-6116"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ryan Benz","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025310563","display_name":"Theodore L. Platt","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Theodore Platt","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Juan Cuevas","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Juan Cuevas","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108224144","display_name":"Serafim Batzoglou","orcid":"https://orcid.org/0009-0009-1513-8452","observed_orcids":["https://orcid.org/0009-0009-1513-8452"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Serafim Batzoglou","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000721597","display_name":"Asim S. Siddiqui","orcid":"https://orcid.org/0000-0002-0359-2334","observed_orcids":["https://orcid.org/0000-0002-0359-2334"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Asim Siddiqui","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053752264","display_name":"Omid Cameron Farokhzad","orcid":"https://orcid.org/0000-0003-2009-270X","observed_orcids":["https://orcid.org/0000-0003-2009-270X","https://orcid.org/0000-0001-7787-6658","https://orcid.org/0000-0003-4575-4394"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Omid Farokhzad","raw_affiliation_strings":["1Seer, Inc., Redwood City, CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Seer, Inc., Redwood City, CA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":"82","issue":"12_Supplement","first_page":"6340","last_page":"6340"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9990000128746033,"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":0.9990000128746033,"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":0.0003000000142492354,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":9.999999747378752e-05,"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/plasma-proteomics","display_name":"plasma proteomics","score":0.9520000219345093},{"id":"https://openalex.org/keywords/proteoforms","display_name":"proteoforms","score":0.9599999785423279},{"id":"https://openalex.org/keywords/proteogenomics","display_name":"proteogenomics","score":0.8429999947547913},{"id":"https://openalex.org/keywords/non-small-cell-lung-cancer","display_name":"non-small cell lung cancer","score":0.9779999852180481},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"alternative splicing","score":0.7950000166893005},{"id":"https://openalex.org/keywords/protein-isoforms","display_name":"protein isoforms","score":0.906000018119812},{"id":"https://openalex.org/keywords/allelic-variation","display_name":"allelic variation","score":0.9409999847412109},{"id":"https://openalex.org/keywords/early-stage-cancer-detection","display_name":"early-stage cancer detection","score":0.6060000061988831},{"id":"https://openalex.org/keywords/plasma-biomarkers","display_name":"plasma biomarkers","score":0.5400000214576721}],"concepts":[{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.7039381861686707},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6485022306442261},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6090878248214722},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5492343306541443},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.49259692430496216},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3661728501319885},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3224949240684509},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31224238872528076},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.2937517762184143}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/1538-7445.am2022-6340","doi":"https://doi.org/10.1158/1538-7445.am2022-6340","is_oa":false,"landing_page_url":"https://doi.org/10.1158/1538-7445.am2022-6340","pdf_url":null,"source":{"id":"https://openalex.org/S168522863","display_name":"Cancer Research","issn_l":"0008-5472","issn":["0008-5472","1538-7445"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320273","host_organization_name":"American Association for Cancer Research","host_organization_lineage":["https://openalex.org/P4310320273"],"host_organization_lineage_names":["American Association for Cancer Research"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cancer Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8371999859809875,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3177758304","https://openalex.org/W4283161167","https://openalex.org/W4361300671","https://openalex.org/W3083412892","https://openalex.org/W2531258896","https://openalex.org/W1503289150","https://openalex.org/W7033317632","https://openalex.org/W4360612265","https://openalex.org/W2182676712","https://openalex.org/W2732144023"],"abstract_inverted_index":{"Abstract":[0],"Introduction:":[1],"Comprehensive":[2],"assessment":[3],"of":[4,10,22,33,74,81,109,150,176,181,236,284,289,296],"the":[5,23,34,72,107,121,184,206,297],"proteome":[6,231],"remains":[7],"elusive":[8],"because":[9],"proteoforms":[11,28,285],"arising":[12,99,112],"from":[13,100,113,205],"alternative":[14,101],"splicing,":[15,103],"allelic":[16,114],"variation,":[17],"and":[18,49,59,85,118,162,218,228,239,277],"protein":[19,25,42,97,133,192,196,221,237],"modifications.":[20],"Characterization":[21],"variable":[24],"forms,":[26],"or":[27],"will":[29],"expand":[30],"our":[31],"understanding":[32],"molecular":[35],"mechanisms":[36],"underlying":[37,191],"diseases,":[38],"however":[39],"requires":[40],"unbiased":[41,50,227,276],"coverage":[43],"at":[44,153,244,291],"sufficient":[45,247],"scale.":[46],"Scalable,":[47],"deep":[48,229],"proteomics":[51,280],"studies":[52,288],"have":[53],"been":[54],"impractical":[55],"due":[56],"to":[57,93,131,248],"cumbersome":[58],"lengthy":[60],"workflows":[61],"required":[62],"for":[63,215,300],"complex":[64],"samples,":[65],"like":[66],"blood":[67],"plasma.":[68],"Here,":[69],"we":[70,146,198],"demonstrate":[71],"power":[73],"Proteograph":[75,126,224],"in":[76,168,173,242],"a":[77,174,245],"proof-of-concept":[78],"proteogenomic":[79,287],"analysis":[80,283],"80":[82],"healthy":[83],"controls":[84,169],"61":[86],"early-stage":[87],"non-small-cell":[88],"lung":[89],"cancer":[90],"(NSCLC)":[91],"samples":[92,124],"dissect":[94],"differences":[95,140],"between":[96],"isoforms":[98],"gene":[102],"as":[104,106],"well":[105],"identification":[108,235],"novel":[110],"peptides":[111,129,136,151,240],"variation.":[115],"Materials,":[116],"Methods":[117],"Results:":[119],"Processing":[120],"141":[122],"plasma":[123,160,166,230,279],"with":[125,137,281],"yielded":[127],"21,959":[128],"corresponding":[130],"2,499":[132],"groups.":[134],"Using":[135],"significant":[138],"abundance":[139,167,185],"(p":[141],"<":[142],"0.05;":[143],"Benjamini-Hochberg":[144],"corrected),":[145],"extracted":[147],"proteins":[148],"comprised":[149],"where":[152],"least":[154],"one":[155],"peptide":[156],"had":[157],"significantly":[158,164],"higher":[159],"abundance,":[161],"another":[163],"lower":[165],"vs.":[170],"cancer,":[171],"resulting":[172],"set":[175],"putative":[177],"proteoforms.":[178],"For":[179],"three":[180],"these":[182],"proteins,":[183],"variation":[186],"is":[187],"possibly":[188],"explained":[189],"by":[190],"isoforms.":[193],"To":[194],"identify":[195],"variants,":[197],"performed":[199],"exome":[200],"sequencing":[201],"on":[202],"29":[203],"individuals":[204],"NSCLC":[207,290],"study,":[208],"created":[209],"personalized":[210],"mass":[211],"spectrometry":[212],"search":[213],"libraries":[214],"each":[216],"individual,":[217],"identified":[219],"464":[220],"variants.":[222],"Conclusions:":[223],"can":[225],"generate":[226],"profiles":[232],"that":[233],"enable":[234,249],"variants":[238],"present":[241],"plasma,":[243],"scale":[246,292],"population-scale":[250],"proteomic":[251],"studies.":[252],"Citation":[253],"Format:":[254],"Margaret":[255],"Donovan,":[256],"Henry":[257],"Huang,":[258],"John":[259],"Blume,":[260],"Marwin":[261],"Ko,":[262],"Ryan":[263],"Benz,":[264],"Theodore":[265],"Platt,":[266],"Juan":[267],"Cuevas,":[268],"Serafim":[269],"Batzoglou,":[270],"Asim":[271],"Siddiqui,":[272],"Omid":[273],"Farokhzad.":[274],"Deep,":[275],"peptide-centric":[278],"differential":[282],"enabling":[286],"[abstract].":[293],"In:":[294],"Proceedings":[295],"American":[298],"Association":[299],"Cancer":[301,312],"Research":[302],"Annual":[303],"Meeting":[304],"2022;":[305],"2022":[306],"Apr":[307],"8-13.":[308],"Philadelphia":[309],"(PA):":[310],"AACR;":[311],"Res":[313],"2022;82(12_Suppl):Abstract":[314],"nr":[315],"6340.":[316]},"counts_by_year":[],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2022-06-17T00:00:00"}