{"id":13827,"date":"2018-06-28T08:35:44","date_gmt":"2018-06-28T12:35:44","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/?p=13827"},"modified":"2026-01-07T15:14:34","modified_gmt":"2026-01-07T20:14:34","slug":"new-software-developed-for-glycosaminoglycan-analysis","status":"publish","type":"post","link":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/2018\/06\/28\/new-software-developed-for-glycosaminoglycan-analysis\/","title":{"rendered":"New Software Developed for Glycosaminoglycan Analysis"},"content":{"rendered":"<p style=\"text-align: justify;\">The <a href=\"https:\/\/www.bumc.bu.edu\/biochemcellbio\/profiles\/joseph-zaia\/\">Zaia laboratory&#8217;s<\/a> recent study:\u00a0\u201c<a href=\"http:\/\/www.mcponline.org\/content\/early\/2018\/04\/03\/mcp.RA118.000590.abstract\">Software for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra<\/a>\u201d has been selected to\u00a0appear in a special virtual issue of ASBMB journal content on <a href=\"http:\/\/www.jbc.org\/site\/vi\/\">Omics of lipids, glycans and polar metabolites<\/a>. This paper was selected from\u00a0hundreds of papers and\u00a0best represents the exciting advances made in studying these systems over the last three years.<a href=\"https:\/\/www.bumc.bu.edu\/biochemcellbio\/2018\/06\/28\/new-software-developed-for-glycosaminoglycan-analysis\/zaia-2\/\" rel=\"attachment wp-att-13826\"><img loading=\"lazy\" src=\"\/biochemcellbio\/files\/2018\/06\/Zaia-285x300.png\" alt=\"Zaia\" width=\"285\" height=\"300\" class=\"alignright size-medium wp-image-13826\" srcset=\"https:\/\/www.bumc.bu.edu\/biochemcellbio\/files\/2018\/06\/Zaia-285x300.png 285w, https:\/\/www.bumc.bu.edu\/biochemcellbio\/files\/2018\/06\/Zaia.png 585w\" sizes=\"(max-width: 285px) 100vw, 285px\" \/><\/a><\/p>\n<p style=\"text-align: justify;\">Glycosaminoglycans (GAGs) covalently linked to proteoglycans are characterized by repeating disaccharide units and variable sulfation patterns along the chain. The <a href=\"https:\/\/www.bumc.bu.edu\/biochemcellbio\/profiles\/joseph-zaia\/\">Zaia laboratory<\/a>\u00a0and others have demonstrated the usefulness of tandem mass spectrometry (MS2) for assigning the structures of GAG saccharides; however, manual interpretation of tandem mass spectra is time-consuming, so computational methods must be employed. The Zaia group\u00a0developed <a href=\"https:\/\/github.com\/jdhogan\/gagfinder\/releases\">GAGfinder<\/a>, the first tandem mass spectrum peak finding algorithm developed specifically for GAGs. GAGfinder is a targeted, brute force approach to spectrum analysis that utilizes precursor composition information to generate all theoretical fragments. GAGfinder also performs peak isotope composition annotation, which is typically a subsequent step for averagine-based methods.<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The Zaia laboratory&#8217;s recent study:\u00a0\u201cSoftware for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra\u201d has been selected [&hellip;]<\/p>\n","protected":false},"author":1191,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[4656,104,101,100],"tags":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/posts\/13827"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/users\/1191"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/comments?post=13827"}],"version-history":[{"count":5,"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/posts\/13827\/revisions"}],"predecessor-version":[{"id":13833,"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/posts\/13827\/revisions\/13833"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/media?parent=13827"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/categories?post=13827"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/biochemcellbio\/wp-json\/wp\/v2\/tags?post=13827"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}