{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T01:20:42Z","timestamp":1769217642504,"version":"3.49.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2018,8,7]],"date-time":"2018-08-07T00:00:00Z","timestamp":1533600000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004774","name":"New England Biolabs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004774","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Joint Council Office Visiting Investigator Programme"},{"name":"Biomedical Research Council Strategic Positioning Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Many eukaryotic proteins are modified by N-glycans. Liquid chromatography (ultra-performance \u2013UPLC and high-performance\u2013HPLC) coupled with mass spectrometry (MS) is conventionally used to characterize N-glycan structures. Software can automatically assign glycan structures by matching their observed retention times and masses with standardized values in reference databases. However, more precise confirmation of N-glycan structures can be derived using exoglycosidases, enzymes that remove specific monosaccharides from glycans. Exoglycosidase removal of monosaccharides results in signature peak shifts, in both UPLC and MS1, yielding an effective way to verify N-glycan structure with high detail (down to the position and isomeric linkage of each monosaccharide). Because manual interpretation of exoglycosidase data is complex and time consuming, we developed GlycanAnalyzer, a web application that pattern matches N-glycan peak shifts following exoglycosidase digestion and automates structure assignments. GlycanAnalyzer significantly improves assignment accuracy over other auto-assignment methods on tests with a monoclonal antibody and four glycan standards (100% versus 82% for the next best software). By automating data interpretation, GlycanAnalyzer enables the easier use of exoglycosidases to precisely define N-glycan structure.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/glycananalyzer.neb.com. Datasets available online.<\/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\/bty681","type":"journal-article","created":{"date-parts":[[2018,8,6]],"date-time":"2018-08-06T12:03:57Z","timestamp":1533557037000},"page":"688-690","source":"Crossref","is-referenced-by-count":19,"title":["GlycanAnalyzer: software for automated interpretation of <i>N<\/i>-glycan profiles after exoglycosidase digestions"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3994-5522","authenticated-orcid":false,"given":"Ian","family":"Walsh","sequence":"first","affiliation":[{"name":"Bioprocessing Technology Institute Agency for Science, Technology and Research (A*STAR), Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry","family":"Nguyen-Khuong","sequence":"additional","affiliation":[{"name":"Bioprocessing Technology Institute Agency for Science, Technology and Research (A*STAR), Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katherine","family":"Wongtrakul-Kish","sequence":"additional","affiliation":[{"name":"Bioprocessing Technology Institute Agency for Science, Technology and Research (A*STAR), Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shi Jie","family":"Tay","sequence":"additional","affiliation":[{"name":"Bioprocessing Technology Institute Agency for Science, Technology and Research (A*STAR), Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Chew","sequence":"additional","affiliation":[{"name":"Bioprocessing Technology Institute Agency for Science, Technology and Research (A*STAR), Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tasha","family":"Jos\u00e9","sequence":"additional","affiliation":[{"name":"New England Biolabs, 240 County Road, Ipswich, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher H","family":"Taron","sequence":"additional","affiliation":[{"name":"New England Biolabs, 240 County Road, Ipswich, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pauline M","family":"Rudd","sequence":"additional","affiliation":[{"name":"Bioprocessing Technology Institute Agency for Science, Technology and Research (A*STAR), Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,7]]},"reference":[{"key":"2023051511011041500_bty681-B1","doi-asserted-by":"crossref","first-page":"D1237","DOI":"10.1093\/nar\/gkv1041","article-title":"GlyTouCan 1.0 \u2013 The international glycan structure repository","volume":"44","author":"Aoki-Kinoshita","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023051511011041500_bty681-B2","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1039\/b907931a","article-title":"The repertoire of glycan determinants in the human glycome","volume":"5","author":"Cummings","year":"2009","journal-title":"Mol. BioSyst"},{"key":"2023051511011041500_bty681-B3","doi-asserted-by":"crossref","first-page":"1235681","DOI":"10.1126\/science.1235681","article-title":"Emerging principles for the therapeutic exploitation of glycosylation","volume":"343","author":"Dalziel","year":"2014","journal-title":"Science"},{"key":"2023051511011041500_bty681-B4","doi-asserted-by":"crossref","first-page":"2220","DOI":"10.1093\/bioinformatics\/btv129","article-title":"GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data","volume":"31","author":"Duffy","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051511011041500_bty681-B5","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1093\/bioinformatics\/btu425","article-title":"GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination","volume":"30","author":"Gotz","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051511011041500_bty681-B6","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/glycob\/cww005","article-title":"Symbol nomenclature for glycans (SNFG)","volume":"26","author":"Haltiwanger","year":"2016","journal-title":"Glycobiology"},{"key":"2023051511011041500_bty681-B7","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1038\/nchembio.437","article-title":"A systematic approach to protein glycosylation analysis: a path through the maze","volume":"6","author":"Mari\u00f1o","year":"2010","journal-title":"Nat. Chem. Biol"},{"key":"2023051511011041500_bty681-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ab.2007.12.012","article-title":"HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software","volume":"376","author":"Royle","year":"2008","journal-title":"Anal. Biochem"},{"key":"2023051511011041500_bty681-B9","article-title":"GlycoStore: a database of retention properties for glycan analysis","volume":"1","author":"Zhao","year":"2018","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/4\/688\/50320252\/bioinformatics_35_4_688.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/4\/688\/50320252\/bioinformatics_35_4_688.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T11:02:47Z","timestamp":1684148567000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/4\/688\/5067854"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,7]]},"references-count":9,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2019,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty681","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,2,15]]},"published":{"date-parts":[[2018,8,7]]}}}