{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T22:46:58Z","timestamp":1786142818910,"version":"3.56.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,19]],"date-time":"2019-08-19T00:00:00Z","timestamp":1566172800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000289","name":"CRUK","doi-asserted-by":"publisher","award":["C33325\/A23619"],"award-info":[{"award-number":["C33325\/A23619"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy\/light pair are assigned. In such cases, having a pair of MS\/MS spectra that differ due to an isotopic label can assist in identifying the relevant m\/z values that support the correct peptide annotation or can be used for de novo sequencing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS\/MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra. The result is a tool to visually compare two spectra, and downloadable peaks lists that can be used to support de novo sequencing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>HiLight-PTM is released using shinyapps.io by RStudio, and can be accessed from any internet browser at https:\/\/harrywhitwell.shinyapps.io\/hilight-ptm\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz654","type":"journal-article","created":{"date-parts":[[2019,8,17]],"date-time":"2019-08-17T11:33:28Z","timestamp":1566041608000},"page":"938-939","source":"Crossref","is-referenced-by-count":2,"title":["HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs"],"prefix":"10.1093","volume":"36","author":[{"given":"Harry J","family":"Whitwell","sequence":"first","affiliation":[{"name":"Department of Chemical Engineering, Imperial College London , London, SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr","given":"Peter","family":"DiMaggio","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering, Imperial College London , London, SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,19]]},"reference":[{"key":"2023013110085181100_btz654-B1","doi-asserted-by":"crossref","first-page":"3175","DOI":"10.1002\/pmic.201500108","article-title":"Quantitative proteomics using SILAC: principles, applications, and developments","volume":"15","author":"Chen","year":"2015","journal-title":"Proteomics"},{"key":"2023013110085181100_btz654-B2","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1021\/pr101065j","article-title":"Andromeda: a peptide search engine integrated into the MaxQuant environment","volume":"10","author":"Cox","year":"2011","journal-title":"J. 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Chromat"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz654\/29718181\/btz654.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/3\/938\/48981977\/bioinformatics_36_3_938.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/3\/938\/48981977\/bioinformatics_36_3_938.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:26:45Z","timestamp":1675189605000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/3\/938\/5551339"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,8,19]]},"references-count":6,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2020,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz654","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,2,1]]},"published":{"date-parts":[[2019,8,19]]}}}