{"id":"https://openalex.org/W2805675654","doi":"https://doi.org/10.1021/acs.analchem.8b00929","title":"Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition","display_name":"Comprehensive Tandem-Mass-Spectrometry Coverage of Complex Samples Enabled by Data-Set-Dependent Acquisition","publication_year":2018,"publication_date":"2018-05-30","ids":{"openalex":"https://openalex.org/W2805675654","doi":"https://doi.org/10.1021/acs.analchem.8b00929","mag":"2805675654","pmid":"https://pubmed.ncbi.nlm.nih.gov/29846054"},"language":"en","primary_location":{"id":"doi:10.1021/acs.analchem.8b00929","doi":"https://doi.org/10.1021/acs.analchem.8b00929","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.analchem.8b00929","pdf_url":null,"source":{"id":"https://openalex.org/S191963794","display_name":"Analytical Chemistry","issn_l":"0003-2700","issn":["0003-2700","1520-6882"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Analytical Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","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/A5003508708","display_name":"Corey D. Broeckling","orcid":"https://orcid.org/0000-0002-6158-827X","observed_orcids":["https://orcid.org/0000-0002-6158-827X"]},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Corey D. Broeckling","raw_affiliation_strings":["Proteomics and Metabolomics Facility, Colorado State University, C-121 Microbiology Building 2021 Campus Delivery, Fort Collins, Colorado 80523, United States"],"raw_orcid":"https://orcid.org/0000-0002-6158-827X","affiliations":[{"raw_affiliation_string":"Proteomics and Metabolomics Facility, Colorado State University, C-121 Microbiology Building 2021 Campus Delivery, Fort Collins, Colorado 80523, United States","institution_ids":["https://openalex.org/I92446798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010952055","display_name":"Emmy Hoyes","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210143873","display_name":"Waters (United Kingdom)","ror":"https://ror.org/048wd7x80","country_code":"GB","type":"company","lineage":["https://openalex.org/I180980256","https://openalex.org/I4210143873"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emmy Hoyes","raw_affiliation_strings":["Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K","institution_ids":["https://openalex.org/I4210143873"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072571226","display_name":"Keith Richardson","orcid":"https://orcid.org/0000-0001-5224-0688","observed_orcids":["https://orcid.org/0000-0001-5224-0688"]},"institutions":[{"id":"https://openalex.org/I4210143873","display_name":"Waters (United Kingdom)","ror":"https://ror.org/048wd7x80","country_code":"GB","type":"company","lineage":["https://openalex.org/I180980256","https://openalex.org/I4210143873"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Keith Richardson","raw_affiliation_strings":["Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K","institution_ids":["https://openalex.org/I4210143873"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083690833","display_name":"Jeffery M. Brown","orcid":"https://orcid.org/0000-0001-8569-7174","observed_orcids":["https://orcid.org/0000-0001-8569-7174"]},"institutions":[{"id":"https://openalex.org/I4210143873","display_name":"Waters (United Kingdom)","ror":"https://ror.org/048wd7x80","country_code":"GB","type":"company","lineage":["https://openalex.org/I180980256","https://openalex.org/I4210143873"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jeffery M. Brown","raw_affiliation_strings":["Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K"],"raw_orcid":"https://orcid.org/0000-0001-8569-7174","affiliations":[{"raw_affiliation_string":"Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, U.K","institution_ids":["https://openalex.org/I4210143873"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080250443","display_name":"Jessica E. Prenni","orcid":"https://orcid.org/0000-0002-0337-8450","observed_orcids":["https://orcid.org/0000-0002-0337-8450"]},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jessica E. Prenni","raw_affiliation_strings":["Department of Horticulture, Colorado State University, 210 Shepardson 1173 Campus Delivery, Fort Collins, Colorado 80523, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Horticulture, Colorado State University, 210 Shepardson 1173 Campus Delivery, Fort Collins, Colorado 80523, United States","institution_ids":["https://openalex.org/I92446798"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003508708"],"corresponding_institution_ids":["https://openalex.org/I92446798"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":2.2148,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.88187462,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"90","issue":"13","first_page":"8020","last_page":"8027"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.3977000117301941,"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":0.3977000117301941,"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":0.3725999891757965,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.22280000150203705,"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/tandem-mass-spectrometry","display_name":"tandem mass spectrometry","score":0.8640000224113464},{"id":"https://openalex.org/keywords/data-independent-acquisition","display_name":"data-independent acquisition","score":0.7960000038146973},{"id":"https://openalex.org/keywords/data-dependent-acquisition","display_name":"data-dependent acquisition","score":0.9459999799728394},{"id":"https://openalex.org/keywords/target-prioritization","display_name":"target prioritization","score":0.8700000047683716},{"id":"https://openalex.org/keywords/small-molecule-analysis","display_name":"small molecule analysis","score":0.6759999990463257},{"id":"https://openalex.org/keywords/quadrupole-time-of-flight","display_name":"quadrupole time-of-flight","score":0.8880000114440918}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.9661920070648193},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.622722864151001},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.5888156890869141},{"id":"https://openalex.org/C2777814067","wikidata":"https://www.wikidata.org/wiki/Q1752317","display_name":"Tandem","level":2,"score":0.5679946541786194},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.49794936180114746},{"id":"https://openalex.org/C71043704","wikidata":"https://www.wikidata.org/wiki/Q17144692","display_name":"Selected reaction monitoring","level":4,"score":0.44551753997802734},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42702287435531616},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.3609999418258667},{"id":"https://openalex.org/C113196181","wikidata":"https://www.wikidata.org/wiki/Q485223","display_name":"Analytical Chemistry (journal)","level":2,"score":0.332282692193985},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.11848506331443787},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0755855143070221},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001467","descriptor_name":"Hordeum","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009132","descriptor_name":"Muscles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019697","descriptor_name":"Onions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.analchem.8b00929","doi":"https://doi.org/10.1021/acs.analchem.8b00929","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.analchem.8b00929","pdf_url":null,"source":{"id":"https://openalex.org/S191963794","display_name":"Analytical Chemistry","issn_l":"0003-2700","issn":["0003-2700","1520-6882"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Analytical Chemistry","raw_type":"journal-article"},{"id":"pmid:29846054","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29846054","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":"Analytical chemistry","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1545513697","https://openalex.org/W1964010911","https://openalex.org/W1969165973","https://openalex.org/W1986887325","https://openalex.org/W1995238211","https://openalex.org/W1995478292","https://openalex.org/W1996787813","https://openalex.org/W2001907843","https://openalex.org/W2007805022","https://openalex.org/W2014859022","https://openalex.org/W2018690353","https://openalex.org/W2026834364","https://openalex.org/W2035809951","https://openalex.org/W2037334311","https://openalex.org/W2073371472","https://openalex.org/W2079843936","https://openalex.org/W2080752012","https://openalex.org/W2083653511","https://openalex.org/W2083684832","https://openalex.org/W2083932946","https://openalex.org/W2168590651","https://openalex.org/W2285468881","https://openalex.org/W2308104112","https://openalex.org/W2514341189","https://openalex.org/W2516826190","https://openalex.org/W2562696661","https://openalex.org/W2593533643","https://openalex.org/W2725788675","https://openalex.org/W2754554672","https://openalex.org/W2781370959","https://openalex.org/W4234115454"],"related_works":["https://openalex.org/W3146134477","https://openalex.org/W4385450504","https://openalex.org/W4387398425","https://openalex.org/W2313734891","https://openalex.org/W204019245","https://openalex.org/W1998295756","https://openalex.org/W2814971886","https://openalex.org/W1803908051","https://openalex.org/W2802749921","https://openalex.org/W3177921569"],"abstract_inverted_index":{"Tandem":[0],"mass":[1,175],"spectrometry":[2],"(MS/MS)":[3],"is":[4,28,34,60,113],"an":[5],"invaluable":[6],"experimental":[7],"tool":[8],"for":[9,183],"providing":[10],"analytical":[11],"data":[12,138,141],"supporting":[13],"the":[14,37,55,80,107,116],"identification":[15],"of":[16,47,57,67,82,95,129,133,148,159,186],"small":[17],"molecules":[18],"and":[19,98,135,140,151,163,190],"peptides":[20],"in":[21,40,45,119],"mass-spectrometry-based":[22],"\"omics\"":[23],"experiments.":[24],"Data-dependent":[25],"MS/MS":[26,58,65,76,90,104,181],"(DDA)":[27],"a":[29,41,92,130,157,171,184,192],"real-time":[30,146],"MS/MS-acquisition":[31,149],"strategy":[32],"that":[33,118],"responsive":[35],"to":[36,62,101],"signals":[38],"detected":[39,69],"given":[42],"sample.":[43],"However,":[44],"analysis":[46],"even":[48],"moderately":[49],"complex":[50,187],"samples":[51,189],"with":[52],"state-of-the-art":[53],"instrumentation,":[54],"speed":[56],"acquisition":[59,142],"insufficient":[61],"offer":[63,74],"comprehensive":[64,103,180],"coverage":[66,182],"all":[68],"molecules.":[70],"Data-independent":[71],"approaches":[72],"(DIA)":[73],"greater":[75],"coverage,":[77],"typically":[78,125],"at":[79],"expense":[81],"selectivity":[83],"or":[84],"sensitivity.":[85],"This":[86,111],"report":[87],"describes":[88],"data-set-dependent":[89],"(DsDA),":[91],"novel":[93],"integration":[94],"MS1-data":[96],"processing":[97,139],"target":[99],"prioritization":[100],"enable":[102],"sampling":[105],"during":[106],"initial":[108],"MS-level":[109],"experiment.":[110],"approach":[112],"guided":[114],"by":[115],"premise":[117],"omics":[120],"experiments,":[121],"individual":[122],"injections":[123],"are":[124],"made":[126],"as":[127],"part":[128],"larger":[131],"set":[132,185],"samples,":[134],"feedback":[136],"between":[137],"can":[143],"allow":[144],"approximately":[145],"optimization":[147],"parameters":[150],"nearly":[152],"complete":[153],"MS/MS-sampling":[154],"coverage.":[155],"Using":[156],"combination":[158],"R,":[160],"Proteowizard,":[161],"XCMS,":[162],"WRENS":[164],"software,":[165],"this":[166],"concept":[167],"was":[168],"implemented":[169],"on":[170,195],"liquid-chromatograph-coupled":[172],"quadrupole":[173],"time-of-flight":[174],"spectrometer.":[176],"The":[177],"results":[178],"illustrate":[179],"small-molecule":[188],"demonstrate":[191],"strong":[193],"improvement":[194],"traditional":[196],"DDA.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2018-06-13T00:00:00"}