{"id":"https://openalex.org/W2591664289","doi":null,"title":"Shifting the Paradigm: Peptide-Centric Analysis of Systematically Sampled Mass Spectrometry Data","display_name":"Shifting the Paradigm: Peptide-Centric Analysis of Systematically Sampled Mass Spectrometry Data","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2591664289","mag":"2591664289"},"language":"en","primary_location":{"id":"pmh:oai:digital.lib.washington.edu:1773/38147","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/38147","pdf_url":"http://hdl.handle.net/1773/38147","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1773/38147","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036254727","display_name":"Ying Sonia Ting","orcid":"https://orcid.org/0000-0003-2492-3718","observed_orcids":["https://orcid.org/0000-0003-2492-3718"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ying S. Ting","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-2492-3718","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5036254727"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"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":0.9976000189781189,"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":0.9976000189781189,"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":0.0020000000949949026,"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":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/data-independent-acquisition","display_name":"data-independent acquisition","score":0.9729999899864197},{"id":"https://openalex.org/keywords/pecan","display_name":"Carya illinoinensis","score":0.8920000195503235},{"id":"https://openalex.org/keywords/peptide-detection","display_name":"peptide detection","score":0.800000011920929},{"id":"https://openalex.org/keywords/tandem-mass-spectrometry","display_name":"tandem mass spectrometry","score":0.7749999761581421},{"id":"https://openalex.org/keywords/in-vitro-translation","display_name":"in vitro translation","score":0.4440000057220459},{"id":"https://openalex.org/keywords/acquisition-parameter-optimization","display_name":"acquisition parameter optimization","score":0.5600000023841858},{"id":"https://openalex.org/keywords/ss-31","display_name":"SS-31","score":0.9869999885559082},{"id":"https://openalex.org/keywords/cardioprotection","display_name":"cardioprotection","score":0.5360000133514404},{"id":"https://openalex.org/keywords/mitochondrial-proteome","display_name":"mitochondrial proteome","score":0.9210000038146973},{"id":"https://openalex.org/keywords/proteome-dynamics","display_name":"proteome dynamics","score":0.5979999899864197}],"concepts":[{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.6165920495986938},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.41950350999832153},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4068640470504761},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36764445900917053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36581194400787354},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33865466713905334},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.2788246273994446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15973228216171265},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09230801463127136}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:digital.lib.washington.edu:1773/38147","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/38147","pdf_url":"http://hdl.handle.net/1773/38147","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:2591664289","doi":null,"is_oa":false,"landing_page_url":"https://digital.lib.washington.edu:443/researchworks/handle/1773/38147","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":"pmh:oai:digital.lib.washington.edu:1773/38147","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/38147","pdf_url":"http://hdl.handle.net/1773/38147","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2591664289.pdf","grobid_xml":"https://content.openalex.org/works/W2591664289.grobid-xml"},"referenced_works_count":98,"referenced_works":["https://openalex.org/W41483455","https://openalex.org/W75599496","https://openalex.org/W1498897499","https://openalex.org/W1541396877","https://openalex.org/W1553112665","https://openalex.org/W1568341953","https://openalex.org/W1579119691","https://openalex.org/W1722845210","https://openalex.org/W1803908051","https://openalex.org/W1965709178","https://openalex.org/W1971723295","https://openalex.org/W1971887998","https://openalex.org/W1973296195","https://openalex.org/W1976217821","https://openalex.org/W1980322984","https://openalex.org/W1982411844","https://openalex.org/W1984236407","https://openalex.org/W1986873950","https://openalex.org/W1990299806","https://openalex.org/W1991502938","https://openalex.org/W1993450321","https://openalex.org/W1995478292","https://openalex.org/W1995676104","https://openalex.org/W1997308718","https://openalex.org/W2000262030","https://openalex.org/W2000403772","https://openalex.org/W2012154384","https://openalex.org/W2014859022","https://openalex.org/W2016019423","https://openalex.org/W2018126724","https://openalex.org/W2021653707","https://openalex.org/W2023655541","https://openalex.org/W2024799186","https://openalex.org/W2026433130","https://openalex.org/W2026465178","https://openalex.org/W2028673251","https://openalex.org/W2029016248","https://openalex.org/W2035024343","https://openalex.org/W2036102880","https://openalex.org/W2037200002","https://openalex.org/W2039058260","https://openalex.org/W2045117578","https://openalex.org/W2047234356","https://openalex.org/W2047275456","https://openalex.org/W2049049175","https://openalex.org/W2052597708","https://openalex.org/W2053943711","https://openalex.org/W2055456981","https://openalex.org/W2060743376","https://openalex.org/W2062143232","https://openalex.org/W2072592470","https://openalex.org/W2073371472","https://openalex.org/W2074045262","https://openalex.org/W2077137713","https://openalex.org/W2078598194","https://openalex.org/W2079843936","https://openalex.org/W2080752012","https://openalex.org/W2081465448","https://openalex.org/W2081787927","https://openalex.org/W2083653511","https://openalex.org/W2087331879","https://openalex.org/W2089273345","https://openalex.org/W2094041121","https://openalex.org/W2096057003","https://openalex.org/W2099218842","https://openalex.org/W2102572519","https://openalex.org/W2104728010","https://openalex.org/W2105167594","https://openalex.org/W2106376891","https://openalex.org/W2108699024","https://openalex.org/W2110017950","https://openalex.org/W2112078820","https://openalex.org/W2115509391","https://openalex.org/W2116582554","https://openalex.org/W2117517043","https://openalex.org/W2117911689","https://openalex.org/W2124907615","https://openalex.org/W2126869418","https://openalex.org/W2127422378","https://openalex.org/W2130706354","https://openalex.org/W2132098985","https://openalex.org/W2133258252","https://openalex.org/W2141091417","https://openalex.org/W2141718522","https://openalex.org/W2142194547","https://openalex.org/W2144154273","https://openalex.org/W2149107649","https://openalex.org/W2149136975","https://openalex.org/W2153258759","https://openalex.org/W2155443196","https://openalex.org/W2163954402","https://openalex.org/W2165711628","https://openalex.org/W2167151063","https://openalex.org/W2172116519","https://openalex.org/W2213916467","https://openalex.org/W2313653278","https://openalex.org/W2396923175","https://openalex.org/W2509588349"],"related_works":["https://openalex.org/W7038468128","https://openalex.org/W2979008464","https://openalex.org/W7154669764","https://openalex.org/W2597462446","https://openalex.org/W7126703479","https://openalex.org/W7043556470","https://openalex.org/W7126619113","https://openalex.org/W2781680534","https://openalex.org/W7202330902","https://openalex.org/W6963993925"],"abstract_inverted_index":{"In":[0],"mass":[1,59],"spectrometry-based":[2],"shotgun":[3],"proteomics,":[4],"data-independent":[5],"acquisition":[6,141,173],"(DIA)":[7],"is":[8],"an":[9,119],"emerging":[10],"technique":[11],"due":[12],"to":[13,49,134,167,201,252],"its":[14],"systematic":[15],"and":[16,34,153,191,225,242],"unbiased":[17],"sampling":[18],"of":[19,53,69,109,131,156,171,178,189,194,217,248,265],"precursor":[20,28,145],"ions.However,":[21],"current":[22],"DIA":[23,42,57,78,99,132,137,179,195,240],"methods":[24,138],"often":[25],"use":[26],"wide":[27],"isolation":[29],"windows,":[30],"resulting":[31],"in":[32,41,56,120,175,214,234],"co-fragmentation":[33],"complex":[35],"mixture":[36],"spectra,":[37],"posing":[38],"various":[39],"challenges":[40],"data":[43,54,79,100,133],"analysis.In":[44],"this":[45],"dissertation,":[46],"I":[47,81,86,185,197,210,221],"aim":[48],"shift":[50],"the":[51,66,73,126,129,169,176,187,203,223,231,235,245,256,262,266],"paradigm":[52],"analysis":[55,71,76,93,193,200],"tandem":[58],"spectrometry":[60],"with":[61,114,181,207,239,255],"peptide-centric":[62,70,92,192,199],"analysis.I":[63,158],"first":[64,211],"describe":[65,82],"analytical":[67,116],"advantages":[68],"over":[72],"conventional":[74],"spectrum-centric":[75],"for":[77,94,98],"analysis.Next,":[80],"a":[83,102,164],"new":[84],"tool":[85],"developed,":[87],"named":[88],"PECAN,":[89],"that":[90],"enables":[91],"robust":[95],"peptide":[96,135],"detection":[97,162],"without":[101],"iv":[103],"prerequisite":[104],"library.I":[105],"demonstrate":[106,186],"rigorous":[107],"validation":[108,113],"PECAN":[110,161,190],"performance,":[111],"including":[112],"synthesized":[115],"standards":[117],"using":[118,160],"vitro":[121],"translation":[122],"system.I":[123],"further":[124],"discuss":[125,159],"impact":[127],"on":[128,261],"selectivity":[130],"detection.All":[136],"balance":[139],"between":[140],"parameters,":[142],"such":[143],"as":[144,163],"selectivity,":[146],"fragmentation":[147],"method,":[148],"ion":[149],"injection":[150],"time/dwell":[151],"time,":[152],"resolving":[154],"power":[155],"MS/MS":[157,241],"quantitative":[165],"metric":[166],"characterize":[168,202],"effects":[170],"these":[172],"parameters":[174],"context":[177],"analysis.Along":[180],"two":[182],"other":[183],"applications,":[184],"versatility":[188],"data.Finally,":[196],"apply":[198],"murine":[204,236],"heart":[205,237],"proteome":[206,227,238,246],"SS-31":[208,232,257,267],"treatment.Here,":[209],"show":[212,244],"improvement":[213],"cardiac":[215,268],"function":[216],"SS-31treated":[218],"old":[219],"mice.Next,":[220],"interrogate":[222],"mitochondrial":[224],"global":[226],"changes":[228],"impacted":[229],"by":[230],"treatment":[233],"PECAN.I":[243],"dynamics":[247],"several":[249],"pathways":[250],"hypothesized":[251],"be":[253],"involved":[254],"mechanisms,":[258],"shedding":[259],"light":[260],"underlying":[263],"mechanisms":[264],"protective":[269],"effects.":[270]},"counts_by_year":[{"year":2018,"cited_by_count":1}],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2017-03-16T00:00:00"}
