{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:16:02Z","timestamp":1761488162084},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In the past few years, mass spectrometry (MS) has emerged as the premier tool for identification and quantification of biological molecules such as peptides and glycans. There are two basic strategies: single-MS, which uses a single round of mass analysis, and MS\/MS (or higher order MSn), which adds one or more additional rounds of mass analysis, interspersed with fragmentation steps. Single-MS offers higher throughput, broader mass coverage and more direct quantitation, but generally much weaker identification. Single-MS, however, does work fairly well for the case of N-glycan identification, which are more constrained than other biological polymers. We previously demonstrated single-MS identification of N-glycans to the level of \u2018cartoons\u2019 (monosaccharide composition and topology) by a system that incorporates an expert's detailed knowledge of the biological sample. In this article, we explore the possibility of ab initio single-MS N-glycan identification, with the goal of extending single-MS, or primarily-single-MS, identification to non-expert users, novel conditions and unstudied tissues.<\/jats:p>\n               <jats:p>Results: We propose and test three cartoon-assignment algorithms that make inferences informed by biological knowledge about glycan synthesis. To test the algorithms, we used 71 single-MS spectra from a variety of tissues and organisms, containing more than 2800 manually annotated peaks. The most successful of the algorithms computes the most richly connected subgraph within a \u2018cartoon graph\u2019. This algorithm uniquely assigns the correct cartoon to more than half of the peaks in 41 out of the 71 spectra.<\/jats:p>\n               <jats:p>Contact: \u00a0goldberg@parc.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn636","type":"journal-article","created":{"date-parts":[[2008,12,11]],"date-time":"2008-12-11T01:13:35Z","timestamp":1228958015000},"page":"365-371","source":"Crossref","is-referenced-by-count":21,"title":["Glycan family analysis for deducing <i>N<\/i>-glycan topology from single MS"],"prefix":"10.1093","volume":"25","author":[{"given":"David","family":"Goldberg","sequence":"first","affiliation":[{"name":"1 Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto CA 94304, USA and 2Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Biochemistry Building, Imperial College, London SW7 2AZ, UK"}]},{"given":"Marshall","family":"Bern","sequence":"additional","affiliation":[{"name":"1 Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto CA 94304, USA and 2Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Biochemistry Building, Imperial College, London SW7 2AZ, UK"}]},{"given":"Simon J.","family":"North","sequence":"additional","affiliation":[{"name":"1 Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto CA 94304, USA and 2Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Biochemistry Building, Imperial College, London SW7 2AZ, UK"}]},{"given":"Stuart M.","family":"Haslam","sequence":"additional","affiliation":[{"name":"1 Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto CA 94304, USA and 2Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Biochemistry Building, Imperial College, London SW7 2AZ, UK"}]},{"given":"Anne","family":"Dell","sequence":"additional","affiliation":[{"name":"1 Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto CA 94304, USA and 2Division of Molecular Biosciences, Faculty of Natural Sciences, South Kensington Campus, Biochemistry Building, Imperial College, London SW7 2AZ, UK"}]}],"member":"286","published-online":{"date-parts":[[2008,12,10]]},"reference":[{"key":"2023013109594103700_B1","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1021\/pr060010k","article-title":"Profiling of glycans in serum for the discovery of potential biomarkers for ovarian cancer","volume":"5","author":"An","year":"2005","journal-title":"J. Proteom. Res."},{"key":"2023013109594103700_B2","volume-title":"Functional and Molecular Glycobiology.","author":"Brooks","year":"2002"},{"key":"2023013109594103700_B3","unstructured":"CFG: The Consortium for Functional Glycomics\n          2008\n          (last accessed on 22 December 2008)\n          Available at www.functionalglycomics.org"},{"key":"2023013109594103700_B4","unstructured":"CFG Profiling Data, The Consortium for Functional Glycomics\n          2008\n          (last accessed on 22 December 2008)\n          Available at www.functionalglycomics.org\/glycomics\/publicdata\/glycoprofiling.jsp"},{"key":"2023013109594103700_B5","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1002\/1615-9861(200102)1:2<340::AID-PROT340>3.0.CO;2-B","article-title":"GlycoMod\u2014a software tool for determining glycosylation compositions from mass spectrometric data.","volume":"1","author":"Cooper","year":"2001","journal-title":"Proteomics"},{"key":"2023013109594103700_B6","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1002\/rcm.779","article-title":"Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra.","volume":"16","author":"Ethier","year":"2002","journal-title":"Rapid Commun. 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