{"id":"https://openalex.org/W2474699779","doi":"https://doi.org/10.1021/acs.jproteome.6b00319","title":"Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation","display_name":"Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation","publication_year":2016,"publication_date":"2016-07-12","ids":{"openalex":"https://openalex.org/W2474699779","doi":"https://doi.org/10.1021/acs.jproteome.6b00319","mag":"2474699779","pmid":"https://pubmed.ncbi.nlm.nih.gov/27402189","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6128406"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jproteome.6b00319","doi":"https://doi.org/10.1021/acs.jproteome.6b00319","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.6b00319","pdf_url":null,"source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","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":"Journal of Proteome Research","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6128406","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004888617","display_name":"Nicholas McIlvain Riley","orcid":"https://orcid.org/0000-0002-1536-2966","observed_orcids":["https://orcid.org/0000-0002-1536-2966"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas M. Riley","raw_affiliation_strings":["Department\rof Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","Genome\rCenter of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Genome\rCenter of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056449861","display_name":"Marshall W. Bern","orcid":"https://orcid.org/0000-0003-0342-9390","observed_orcids":["https://orcid.org/0000-0003-0342-9390"]},"institutions":[{"id":"https://openalex.org/I4210127121","display_name":"Protein Metrics (United States)","ror":"https://ror.org/02av9qc14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127121"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marshall Bern","raw_affiliation_strings":["Protein Metrics, Inc., San Carlos, California 94070, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Metrics, Inc., San Carlos, California 94070, United States","institution_ids":["https://openalex.org/I4210127121"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007686133","display_name":"Michael S. Westphall","orcid":"https://orcid.org/0000-0002-7694-3801","observed_orcids":["https://orcid.org/0000-0002-7694-3801"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael S. Westphall","raw_affiliation_strings":["Genome\rCenter of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome\rCenter of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086840789","display_name":"Joshua J. Coon","orcid":"https://orcid.org/0000-0002-0004-8253","observed_orcids":["https://orcid.org/0000-0002-0004-8253"]},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joshua J. Coon","raw_affiliation_strings":["Department\rof Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","Department\rof Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","Genome\rCenter of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department\rof Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Genome\rCenter of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5086840789"],"corresponding_institution_ids":["https://openalex.org/I135310074"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":1.3278,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.76279121,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"15","issue":"8","first_page":"2768","last_page":"2776"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9922000169754028,"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":0.9922000169754028,"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":0.0052999998442828655,"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/noise-equivalent-temperature-difference","display_name":"noise equivalent temperature difference","score":0.7049999833106995},{"id":"https://openalex.org/keywords/peptide-identification","display_name":"peptide identification","score":0.5920000076293945},{"id":"https://openalex.org/keywords/database-search-algorithms","display_name":"database search algorithms","score":0.7829999923706055},{"id":"https://openalex.org/keywords/human-embryonic-stem-cells","display_name":"human embryonic stem cells","score":0.7620000243186951},{"id":"https://openalex.org/keywords/yeast-proteome","display_name":"yeast proteome","score":0.9470000267028809},{"id":"https://openalex.org/keywords/protein-sequence-coverage","display_name":"protein sequence coverage","score":0.6499999761581421}],"concepts":[{"id":"https://openalex.org/C2777109674","wikidata":"https://www.wikidata.org/wiki/Q3710342","display_name":"Electron-transfer dissociation","level":4,"score":0.5810180306434631},{"id":"https://openalex.org/C123669783","wikidata":"https://www.wikidata.org/wiki/Q902898","display_name":"Electron transfer","level":2,"score":0.5041490793228149},{"id":"https://openalex.org/C102931765","wikidata":"https://www.wikidata.org/wiki/Q189673","display_name":"Dissociation (chemistry)","level":2,"score":0.47987380623817444},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4766733944416046},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42223289608955383},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.388899028301239},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.1941392719745636},{"id":"https://openalex.org/C75473681","wikidata":"https://www.wikidata.org/wiki/Q188651","display_name":"Photochemistry","level":1,"score":0.1777670681476593},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.13623178005218506},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.12249094247817993},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08366867899894714}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000838","descriptor_name":"Anions","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002478","descriptor_name":"Cells, Cultured","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jproteome.6b00319","doi":"https://doi.org/10.1021/acs.jproteome.6b00319","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.6b00319","pdf_url":null,"source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","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":"Journal of Proteome Research","raw_type":"journal-article"},{"id":"pmid:27402189","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27402189","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":"Journal of proteome research","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5079851","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6128406","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6128406","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6128406","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"J Proteome Res","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:5079851","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6128406","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2009733722","display_name":null,"funder_award_id":"DGE-1256259","funder_id":"https://openalex.org/F4320337368","funder_display_name":"Division of Graduate Education"},{"id":"https://openalex.org/G2430835952","display_name":"Negative Electron Transfer Dissociation for Phospho-Histidine Analysis","funder_award_id":"R01GM114122","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7412017687","display_name":"Activated-Ion Negative Electron Transfer Dissociation For High-Throughput Glycoproteomics","funder_award_id":"R21GM118341","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000880556","display_name":"Structure, Function and Regulation of the Proteome","funder_award_id":"R35GM118110","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320312526","display_name":"Thermo Fisher Scientific","ror":"https://ror.org/012wakq07"},{"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/F4320337368","display_name":"Division of Graduate Education","ror":"https://ror.org/00whkrf32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W86688592","https://openalex.org/W1874835939","https://openalex.org/W1892358288","https://openalex.org/W1974091449","https://openalex.org/W1974877017","https://openalex.org/W1976147793","https://openalex.org/W1979589544","https://openalex.org/W1981595275","https://openalex.org/W1985625499","https://openalex.org/W1987182008","https://openalex.org/W2002170438","https://openalex.org/W2004515150","https://openalex.org/W2007207485","https://openalex.org/W2013916945","https://openalex.org/W2026448476","https://openalex.org/W2026465178","https://openalex.org/W2033998822","https://openalex.org/W2047275456","https://openalex.org/W2049232888","https://openalex.org/W2049386164","https://openalex.org/W2050357198","https://openalex.org/W2051627828","https://openalex.org/W2058521653","https://openalex.org/W2060047073","https://openalex.org/W2065094145","https://openalex.org/W2065501622","https://openalex.org/W2067708744","https://openalex.org/W2085971372","https://openalex.org/W2090803329","https://openalex.org/W2093208477","https://openalex.org/W2096217402","https://openalex.org/W2100768052","https://openalex.org/W2106538021","https://openalex.org/W2110438218","https://openalex.org/W2111306975","https://openalex.org/W2112446570","https://openalex.org/W2116910875","https://openalex.org/W2140980918","https://openalex.org/W2147698768","https://openalex.org/W2155443196","https://openalex.org/W2313579901","https://openalex.org/W2338828725","https://openalex.org/W2419323450"],"related_works":["https://openalex.org/W7101038180","https://openalex.org/W1892358288","https://openalex.org/W86688592","https://openalex.org/W1951350816","https://openalex.org/W7096238307","https://openalex.org/W2049386164","https://openalex.org/W2085971372","https://openalex.org/W2049232888","https://openalex.org/W2117502453","https://openalex.org/W2313579901"],"abstract_inverted_index":{"Negative":[0],"electron-transfer":[1],"dissociation":[2],"(NETD)":[3],"has":[4],"emerged":[5],"as":[6,116,118],"a":[7],"premier":[8],"tool":[9],"for":[10,103],"peptide":[11,127,162,164],"anion":[12],"analysis,":[13],"offering":[14],"access":[15],"to":[16,46,73],"acidic":[17],"post-translational":[18],"modifications":[19],"and":[20,81,120,130,163,168],"regions":[21],"of":[22,77,91,111,145],"the":[23,70,75,109,146],"proteome":[24,159,193],"that":[25,178],"are":[26,44],"intractable":[27],"with":[28,38,184],"traditional":[29],"positive-mode":[30],"approaches.":[31,197],"Whole-proteome":[32],"scale":[33],"characterization":[34,194],"is":[35],"now":[36],"possible":[37],"NETD,":[39],"but":[40],"proper":[41],"informatic":[42],"tools":[43],"needed":[45],"capitalize":[47],"on":[48],"advances":[49,186],"in":[50,133,182,187,195],"instrumentation.":[51],"Currently":[52],"only":[53],"one":[54],"database":[55],"search":[56,67],"algorithm":[57,102],"(OMSSA)":[58],"can":[59,190],"process":[60],"NETD":[61,66,105,135],"data.":[62],"Here":[63],"we":[64,82,107,150,176],"implement":[65],"capabilities":[68],"into":[69],"Byonic":[71],"platform":[72],"improve":[74,192],"sensitivity":[76],"negative-mode":[78,143,157,196],"data":[79,188],"analyses,":[80,136],"benchmark":[83],"these":[84],"improvements":[85],"using":[86],"90":[87],"min":[88],"LC-MS/MS":[89],"analyses":[90],"tryptic":[92],"peptides":[93],"from":[94,141],"human":[95,147],"embryonic":[96],"stem":[97],"cells.":[98],"With":[99],"this":[100],"new":[101,179],"searching":[104],"data,":[106,160],"improved":[108],"number":[110],"successfully":[112],"identified":[113,121],"spectra":[114],"by":[115],"much":[117],"80%":[119],"8665":[122],"unique":[123],"peptides,":[124],"24":[125],"639":[126],"spectral":[128,165],"matches,":[129],"1338":[131],"proteins":[132],"activated-ion":[134],"more":[137],"than":[138],"doubling":[139],"identifications":[140,167],"previous":[142],"characterizations":[144],"proteome.":[148],"Furthermore,":[149],"reanalyzed":[151],"our":[152],"recently":[153],"published":[154],"large-scale,":[155],"multienzyme":[156],"yeast":[158],"improving":[161],"match":[166],"considerably":[169],"increasing":[170],"protein":[171],"sequence":[172],"coverage.":[173],"In":[174],"all,":[175],"show":[177],"informatics":[180],"tools,":[181],"combination":[183],"recent":[185],"acquisition,":[189],"significantly":[191]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":7}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-07-22T00:00:00"}
