{"id":"https://openalex.org/W2551893145","doi":"https://doi.org/10.1039/9781782626732-00200","title":"Data Analysis for Data Independent Acquisition","display_name":"Data Analysis for Data Independent Acquisition","publication_year":2016,"publication_date":"2016-11-15","ids":{"openalex":"https://openalex.org/W2551893145","doi":"https://doi.org/10.1039/9781782626732-00200","mag":"2551893145"},"language":"en","primary_location":{"id":"doi:10.1039/9781782626732-00200","is_oa":false,"landing_page_url":"https://doi.org/10.1039/9781782626732-00200","pdf_url":null,"source":{"id":"https://openalex.org/S4306463862","display_name":"Royal Society of Chemistry eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320556","host_organization_name":"Royal Society of Chemistry","host_organization_lineage":["https://openalex.org/P4310320556"],"host_organization_lineage_names":["Royal Society of Chemistry"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteome Informatics","raw_type":"book-chapter"},"type":"book-chapter","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/A5103208256","display_name":"Pedro Navarro","orcid":"https://orcid.org/0000-0002-9052-1824"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pedro Navarro","raw_affiliation_strings":["Institute for Immunology, University Medical Centre of the Johannes Gutenberg University Mainz \u2008 55131 Mainz \u2008 Germany \u2008 pnavarro@uni-mainz.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Immunology, University Medical Centre of the Johannes Gutenberg University Mainz \u2008 55131 Mainz \u2008 Germany \u2008 pnavarro@uni-mainz.de","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071497644","display_name":"Marco Trevis\u00e1n-Herraz","orcid":"https://orcid.org/0000-0002-7129-0602"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marco Trevisan-Herraz","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares \u2008 28029 Madrid \u2008 Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares \u2008 28029 Madrid \u2008 Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058994478","display_name":"Hannes R\u00f6st","orcid":"https://orcid.org/0000-0003-0990-7488"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hannes L. R\u00f6st","raw_affiliation_strings":["Department of Genetics, Stanford University \u2008 Stanford \u2008 CA 94305 \u2008 USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University \u2008 Stanford \u2008 CA 94305 \u2008 USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1643002,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"200","last_page":"228"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998999834060669,"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":0.9970999956130981,"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/data-acquisition","display_name":"Data acquisition","score":0.587246298789978},{"id":"https://openalex.org/keywords/analyte","display_name":"Analyte","score":0.5263094902038574},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5232580900192261},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.4736843407154083},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.45076096057891846},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.4495186507701874},{"id":"https://openalex.org/keywords/shotgun-proteomics","display_name":"Shotgun proteomics","score":0.44546568393707275},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4389199912548065},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42915764451026917},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2705940902233124},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.23719874024391174}],"concepts":[{"id":"https://openalex.org/C163985040","wikidata":"https://www.wikidata.org/wiki/Q1172399","display_name":"Data acquisition","level":2,"score":0.587246298789978},{"id":"https://openalex.org/C10390740","wikidata":"https://www.wikidata.org/wiki/Q2282401","display_name":"Analyte","level":2,"score":0.5263094902038574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5232580900192261},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.4736843407154083},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.45076096057891846},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.4495186507701874},{"id":"https://openalex.org/C68289359","wikidata":"https://www.wikidata.org/wiki/Q7502514","display_name":"Shotgun proteomics","level":4,"score":0.44546568393707275},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4389199912548065},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42915764451026917},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2705940902233124},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.23719874024391174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1039/9781782626732-00200","is_oa":false,"landing_page_url":"https://doi.org/10.1039/9781782626732-00200","pdf_url":null,"source":{"id":"https://openalex.org/S4306463862","display_name":"Royal Society of Chemistry eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320556","host_organization_name":"Royal Society of Chemistry","host_organization_lineage":["https://openalex.org/P4310320556"],"host_organization_lineage_names":["Royal Society of Chemistry"],"type":"ebook platform"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteome Informatics","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1581865243","https://openalex.org/W1803908051","https://openalex.org/W1963898428","https://openalex.org/W1964895626","https://openalex.org/W1965807926","https://openalex.org/W1976217821","https://openalex.org/W1977812518","https://openalex.org/W1981098361","https://openalex.org/W1981536086","https://openalex.org/W1986887325","https://openalex.org/W1988766191","https://openalex.org/W1989833877","https://openalex.org/W1993652628","https://openalex.org/W1995478292","https://openalex.org/W1998295756","https://openalex.org/W2012750155","https://openalex.org/W2013589890","https://openalex.org/W2014859022","https://openalex.org/W2018126724","https://openalex.org/W2023096047","https://openalex.org/W2039058260","https://openalex.org/W2045117578","https://openalex.org/W2051663641","https://openalex.org/W2052597708","https://openalex.org/W2053662574","https://openalex.org/W2053943711","https://openalex.org/W2054492185","https://openalex.org/W2055202150","https://openalex.org/W2060378908","https://openalex.org/W2062143232","https://openalex.org/W2062859898","https://openalex.org/W2065096062","https://openalex.org/W2066138347","https://openalex.org/W2068481474","https://openalex.org/W2073371472","https://openalex.org/W2074161895","https://openalex.org/W2079843936","https://openalex.org/W2082392199","https://openalex.org/W2083653511","https://openalex.org/W2087331879","https://openalex.org/W2096057003","https://openalex.org/W2102572519","https://openalex.org/W2105167594","https://openalex.org/W2105891806","https://openalex.org/W2107710616","https://openalex.org/W2110057023","https://openalex.org/W2112078820","https://openalex.org/W2113381588","https://openalex.org/W2116582554","https://openalex.org/W2117365920","https://openalex.org/W2129528062","https://openalex.org/W2139803981","https://openalex.org/W2141091417","https://openalex.org/W2143340505","https://openalex.org/W2153258759","https://openalex.org/W2154388126","https://openalex.org/W2155901917","https://openalex.org/W2199791113","https://openalex.org/W2313102331","https://openalex.org/W2315120599"],"related_works":["https://openalex.org/W2951814114","https://openalex.org/W2317633934","https://openalex.org/W2411658885","https://openalex.org/W3125403609","https://openalex.org/W2071075116","https://openalex.org/W111275185","https://openalex.org/W2035809951","https://openalex.org/W2105581585","https://openalex.org/W4289534419","https://openalex.org/W4297476651"],"abstract_inverted_index":{"Mass":[0],"spectrometry-based":[1],"proteomics":[2],"using":[3],"soft":[4],"ionization":[5],"techniques":[6],"has":[7,110],"been":[8,61,111],"used":[9,36],"successfully":[10],"to":[11,51,156],"identify":[12],"large":[13,26],"numbers":[14],"of":[15,28,43,89,101,108,124,147,164],"proteins":[16],"from":[17,95],"complex":[18],"biological":[19],"samples.":[20,53],"However,":[21,99],"reproducible":[22,67],"quantification":[23],"across":[24],"a":[25,162],"number":[27,88],"samples":[29],"is":[30],"still":[31],"highly":[32],"challenging":[33],"with":[34,161],"commonly":[35],"\u201cshotgun":[37],"proteomics\u201d":[38],"which":[39],"uses":[40],"stochastic":[41],"sampling":[42],"the":[44,87,96,102,120,145,148,159,165],"peptide":[45,75],"analytes":[46,76],"(data":[47],"dependent":[48],"acquisition;":[49],"DDA)":[50],"analyze":[52],"Recently,":[54],"data":[55,112,131],"independent":[56],"acquisition":[57,97],"(DIA)":[58],"methods":[59],"have":[60],"investigated":[62],"for":[63,66,105],"their":[64,130],"potential":[65],"protein":[68],"quantification,":[69],"since":[70],"they":[71],"deterministically":[72],"sample":[73],"all":[74],"in":[77,153,168],"every":[78],"single":[79],"run.":[80],"This":[81],"increases":[82],"reproducibility":[83],"and":[84,92],"sensitivity,":[85],"reduces":[86],"missing":[90],"values":[91],"removes":[93],"stochasticity":[94],"process.":[98],"one":[100],"major":[103],"challenges":[104,167],"wider":[106],"adoption":[107],"DIA":[109,154],"analysis.":[113],"In":[114],"this":[115,169],"chapter":[116,160],"we":[117,141],"will":[118,142],"introduce":[119],"five":[121],"most":[122],"well-known":[123],"these":[125],"techniques,":[126],"as":[127,129,136],"well":[128],"analysis":[132],"methods,":[133],"classified":[134],"either":[135],"targeted":[137],"or":[138],"untargeted;":[139],"then,":[140],"discuss":[143],"briefly":[144],"meaning":[146],"false":[149],"discovery":[150],"rate":[151],"(FDR)":[152],"experiments,":[155],"finally":[157],"close":[158],"review":[163],"current":[166],"subject.":[170]},"counts_by_year":[],"updated_date":"2026-07-23T05:56:39.545243","created_date":"2025-10-10T00:00:00"}
