{"id":"https://openalex.org/W2138850382","doi":"https://doi.org/10.1093/bioinformatics/btv105","title":"specL\u2014an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics","display_name":"specL\u2014an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics","publication_year":2015,"publication_date":"2015-02-23","ids":{"openalex":"https://openalex.org/W2138850382","doi":"https://doi.org/10.1093/bioinformatics/btv105","mag":"2138850382","pmid":"https://pubmed.ncbi.nlm.nih.gov/25712692"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv105","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2228/49034437/bioinformatics_31_13_2228.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2228/49034437/bioinformatics_31_13_2228.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002516811","display_name":"Christian Panse","orcid":"https://orcid.org/0000-0003-1975-3064"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Christian Panse","raw_affiliation_strings":["Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113432137","display_name":"Christian Trachsel","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christian Trachsel","raw_affiliation_strings":["Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090561267","display_name":"Jonas Grossmann","orcid":"https://orcid.org/0000-0002-6899-9020"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Jonas Grossmann","raw_affiliation_strings":["Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037036136","display_name":"Ralph Schlapbach","orcid":"https://orcid.org/0000-0002-7488-4262"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ralph Schlapbach","raw_affiliation_strings":["Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5002516811","https://openalex.org/A5090561267"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9886,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.73840988,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"31","issue":"13","first_page":"2228","last_page":"2231"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.977400004863739,"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":0.977400004863739,"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":0.007400000002235174,"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"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.003100000089034438,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.8727685213088989},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7149126529693604},{"id":"https://openalex.org/keywords/data-extraction","display_name":"Data extraction","score":0.6053569316864014},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.47935324907302856},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4449451267719269},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.42519986629486084},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4251651167869568},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42450380325317383},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20478525757789612},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1535750925540924},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.1459450125694275},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12035214900970459}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8727685213088989},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7149126529693604},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.6053569316864014},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.47935324907302856},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4449451267719269},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.42519986629486084},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4251651167869568},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42450380325317383},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20478525757789612},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1535750925540924},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.1459450125694275},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12035214900970459},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv105","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2228/49034437/bioinformatics_31_13_2228.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25712692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25712692","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,"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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:www.zora.uzh.ch:109530","is_oa":false,"landing_page_url":"https://www.zora.uzh.ch/109530","pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Panse, Christian; Trachsel, Christian; Grossmann, Jonas; Schlapbach, Ralph  (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.  Bioinformatics, 31(13):2228-2231.","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/13/2228","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/13/2228","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv105","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/13/2228/49034437/bioinformatics_31_13_2228.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320336859","display_name":"Functional Genomics Center Zurich","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138850382.pdf","grobid_xml":"https://content.openalex.org/works/W2138850382.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1737143051","https://openalex.org/W1963898428","https://openalex.org/W1964328150","https://openalex.org/W1988213262","https://openalex.org/W2018126724","https://openalex.org/W2039058260","https://openalex.org/W2054887015","https://openalex.org/W2065096062","https://openalex.org/W2079843936","https://openalex.org/W2141091417","https://openalex.org/W2342557228","https://openalex.org/W2913983662","https://openalex.org/W4235124130","https://openalex.org/W4399578943","https://openalex.org/W6637957273"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2133055377","https://openalex.org/W2921090651","https://openalex.org/W2287365612"],"abstract_inverted_index":{"MOTIVATION:":[0],"Targeted":[1],"data":[2,35,53,144,188,215],"extraction":[3,145],"methods":[4,30,146],"are":[5,47,64,74,216],"attractive":[6],"ways":[7],"to":[8,103,114,119,133],"obtain":[9],"quantitative":[10],"peptide":[11],"information":[12,59],"from":[13,137],"a":[14,78,110,128,184],"proteomics":[15],"experiment.":[16],"Sequential":[17],"Window":[18],"Acquisition":[19,28],"of":[20,33,97,131,151,205],"all":[21,44],"Theoretical":[22],"Spectra":[23],"(SWATH)":[24],"and":[25,43,61,118,163,190,197],"Data":[26],"Independent":[27],"(DIA)":[29],"increase":[31],"reproducibility":[32],"acquired":[34],"because":[36],"the":[37,67,85,98,149,160,195],"classical":[38],"precursor":[39,60],"selection":[40],"is":[41,101,112,157,192],"omitted":[42],"present":[45,127],"precursors":[46],"fragmented.":[48],"However,":[49],"especially":[50],"for":[51,66,140],"targeted":[52,143],"extraction,":[54],"MS":[55],"coordinates":[56,73],"(retention":[57],"time":[58],"fragment":[62],"masses)":[63],"required":[65],"particular":[68],"entities":[69],"(peptide":[70],"ions).":[71],"These":[72],"usually":[75],"generated":[76],"in":[77,84,90,142,148,159,170,194],"so-called":[79],"discovery":[80],"experiment":[81],"earlier":[82],"on":[83],"project":[86],"if":[87],"not":[88],"available":[89,164,217],"public":[91],"spectral":[92,116,138],"library":[93],"repositories.":[94],"The":[95],"quality":[96],"assay":[99,122,135],"panel":[100],"crucial":[102],"ensure":[104],"appropriate":[105],"downstream":[106],"analysis.":[107],"For":[108],"that,":[109],"method":[111],"needed":[113],"create":[115],"libraries":[117,139],"export":[120],"customizable":[121],"panels.":[123],"RESULTS:":[124],"Here,":[125],"we":[126],"versatile":[129],"set":[130],"functions":[132],"generate":[134],"panels":[136],"use":[141],"(SWATH/DIA)":[147],"area":[150],"proteomics.":[152],"AVAILABILITY":[153],"AND":[154],"IMPLEMENTATION:":[155],"specL":[156],"implemented":[158],"R":[161],"language":[162],"under":[165],"an":[166],"open-source":[167],"license":[168],"(GPL-3)":[169],"Bioconductor":[171],"since":[172],"BioC":[173],"3.0":[174],"(R-3.1)":[175],"http://www.bioconductor.org":[176],"(Trachsel":[177],"et":[178],"al.,":[179],"2015).":[180],"A":[181],"vignette":[182],"with":[183],"complete":[185],"tutorial":[186],"describing":[187],"import/export":[189],"analysis":[191],"included":[193],"package":[196],"can":[198],"also":[199],"be":[200],"found":[201],"as":[202],"supplement":[203],"material":[204],"this":[206],"article.":[207],"CONTACT:":[208],"cp@fgcz.ethz.ch":[209],"or":[210],"jg@fgcz.ethz.ch":[211],"SUPPLEMENTARY":[212],"INFORMATION:":[213],"Supplementary":[214],"at":[218],"Bioinformatics":[219],"online.":[220]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
