{"id":"https://openalex.org/W2969862994","doi":"https://doi.org/10.1093/bioinformatics/btz654","title":"HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs","display_name":"HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs","publication_year":2019,"publication_date":"2019-08-17","ids":{"openalex":"https://openalex.org/W2969862994","doi":"https://doi.org/10.1093/bioinformatics/btz654","mag":"2969862994","pmid":"https://pubmed.ncbi.nlm.nih.gov/31424526"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/938/48981977/bioinformatics_36_3_938.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/938/48981977/bioinformatics_36_3_938.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074432363","display_name":"Harry J. Whitwell","orcid":"https://orcid.org/0000-0001-8987-4158"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Harry J Whitwell","raw_affiliation_strings":["Department of Chemical Engineering, Imperial College London , London, SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Imperial College London , London, SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001333221","display_name":"Peter A. DiMaggio","orcid":"https://orcid.org/0000-0003-1996-0813"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter DiMaggio","raw_affiliation_strings":["Department of Chemical Engineering, Imperial College London , London, SW7 2AZ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Imperial College London , London, SW7 2AZ, UK","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5074432363"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.06916649,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"36","issue":"3","first_page":"938","last_page":"939"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9775000214576721,"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":0.9775000214576721,"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":0.004600000102072954,"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":0.002199999988079071,"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/matching","display_name":"Matching (statistics)","score":0.7617772221565247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.57021564245224},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4808843433856964},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.47851836681365967},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.46746185421943665},{"id":"https://openalex.org/keywords/spectral-line","display_name":"Spectral line","score":0.41591739654541016},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3883187472820282},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3700508773326874},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33872151374816895},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32066527009010315},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22410470247268677},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.205542653799057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1823940873146057},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1629524827003479},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15611833333969116},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.13959327340126038},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11413916945457458}],"concepts":[{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.7617772221565247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.57021564245224},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4808843433856964},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.47851836681365967},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.46746185421943665},{"id":"https://openalex.org/C4839761","wikidata":"https://www.wikidata.org/wiki/Q212111","display_name":"Spectral line","level":2,"score":0.41591739654541016},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3883187472820282},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3700508773326874},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33872151374816895},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32066527009010315},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22410470247268677},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.205542653799057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1823940873146057},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1629524827003479},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15611833333969116},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.13959327340126038},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11413916945457458},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/938/48981977/bioinformatics_36_3_938.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31424526","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31424526","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:pubmedcentral.nih.gov:9883675","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9883675","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,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/72961","is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/72961","pdf_url":null,"source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"939","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz654","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz654","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/938/48981977/bioinformatics_36_3_938.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1579470452","display_name":null,"funder_award_id":"C33325/A23619","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G1911616144","display_name":null,"funder_award_id":"23619","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2969862994.pdf","grobid_xml":"https://content.openalex.org/works/W2969862994.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2010501769","https://openalex.org/W2036321220","https://openalex.org/W2107892065","https://openalex.org/W2118349439","https://openalex.org/W2148987861","https://openalex.org/W2219698846"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2251519152"],"abstract_inverted_index":{"MOTIVATION:":[0],"Database":[1],"searching":[2],"of":[3,31,102],"isotopically":[4],"labelled":[5],"PTMs":[6],"can":[7,41,56,132,151],"be":[8,57,133,152],"problematic":[9],"and":[10,74,85,106,127,150],"we":[11],"frequently":[12],"find":[13],"that":[14,34,49,70,131],"only":[15],"one,":[16],"or":[17,55],"neither":[18],"in":[19,43],"a":[20,29,120],"heavy/light":[21],"pair":[22,30],"are":[23,164],"assigned.":[24],"In":[25],"such":[26],"cases,":[27],"having":[28],"MS/MS":[32,90],"spectra":[33],"differ":[35],"due":[36],"to":[37,122,135],"an":[38,67],"isotopic":[39],"label":[40],"assist":[42],"identifying":[44],"the":[45,51,78,93,97,100,114],"relevant":[46],"m/z":[47],"values":[48],"support":[50,136],"correct":[52],"peptide":[53],"annotation":[54],"used":[58,134],"for":[59],"de":[60,137],"novo":[61,138],"sequencing.":[62,139],"RESULTS:":[63],"We":[64],"have":[65],"developed":[66],"online":[68],"application":[69,94],"identifies":[71],"matching":[72],"peaks":[73,75,129],"differing":[76],"by":[77,148],"appropriate":[79],"mass":[80,101],"shift":[81],"(difference":[82],"between":[83,88,113],"heavy":[84],"light":[86],"PTM)":[87],"two":[89,115,125],"spectra.":[91,116],"Furthermore,":[92],"predicts,":[95],"from":[96,154],"exact-match":[98],"peaks,":[99],"their":[103],"complementary":[104],"ions":[105],"highlights":[107],"these":[108],"as":[109],"high":[110],"confidence":[111],"matches":[112],"The":[117],"result":[118],"is":[119,144],"tool":[121],"visually":[123],"compare":[124],"spectra,":[126],"downloadable":[128],"lists":[130],"AVAILABILITY":[140],"AND":[141],"IMPLEMENTATION:":[142],"HiLight-PTM":[143],"released":[145],"using":[146],"shinyapps.io":[147],"RStudio,":[149],"accessed":[153],"any":[155],"internet":[156],"browser":[157],"at":[158,166],"https://harrywhitwell.shinyapps.io/hilight-ptm/.":[159],"SUPPLEMENTARY":[160],"INFORMATION:":[161],"Supplementary":[162],"data":[163],"available":[165],"Bioinformatics":[167],"online.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-08-13T07:04:57.449891","created_date":"2025-10-10T00:00:00"}
