{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Chen Z"],"funding":["NSF","National Center for Research Resources","NCRR NIH HHS","National Institute of General Medical Sciences","NIH HHS","NIGMS NIH HHS"],"pagination":["436-445"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9149727"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["33(3)"],"pubmed_abstract":["Glycan structure identification is essential to understanding the roles of glycans in various biological processes. Previously, we developed GlycoDeNovo, a <i>de novo</i> algorithm for reconstructing glycan topologies from tandem mass spectra (MS/MS). In this work, we introduce GlycoDeNovo2 that contains two major improvements to GlycoDeNovo. First, we use the precursor mass measured for a peak that likely corresponds to a glycan to determine its potential compositions, which are used to constrain the search space, enable parallel computation, and hence speed up topology reconstruction. Second, we developed a procedure to calculate the empirical <i>p</i>-value of a reconstructed topology candidate. Experimental results are provided to demonstrate the effectiveness of GlycoDeNovo2."],"journal":["Journal of the American Society for Mass Spectrometry"],"pubmed_title":["GlycoDeNovo2: An Improved MS/MS-Based <i>De Novo</i> Glycan Topology Reconstruction Algorithm."],"pmcid":["PMC9149727"],"funding_grant_id":["NIH R24 GM134210","R24 GM134210","S10 RR025082","S10 OD021728","NIH R01 GM132675","R01 GM132675","NIH S10 RR025082","NSF OAC 1920147"],"pubmed_authors":["Lin C","Chen Z","Costello CE","Wei J","Hong P","Tang Y"],"additional_accession":[]},"is_claimable":false,"name":"GlycoDeNovo2: An Improved MS/MS-Based <i>De Novo</i> Glycan Topology Reconstruction Algorithm.","description":"Glycan structure identification is essential to understanding the roles of glycans in various biological processes. Previously, we developed GlycoDeNovo, a <i>de novo</i> algorithm for reconstructing glycan topologies from tandem mass spectra (MS/MS). In this work, we introduce GlycoDeNovo2 that contains two major improvements to GlycoDeNovo. First, we use the precursor mass measured for a peak that likely corresponds to a glycan to determine its potential compositions, which are used to constrain the search space, enable parallel computation, and hence speed up topology reconstruction. Second, we developed a procedure to calculate the empirical <i>p</i>-value of a reconstructed topology candidate. Experimental results are provided to demonstrate the effectiveness of GlycoDeNovo2.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Mar","modification":"2025-04-05T14:19:55.16Z","creation":"2025-04-05T14:19:55.16Z"},"accession":"S-EPMC9149727","cross_references":{"pubmed":["35157458"],"doi":["10.1021/jasms.1c00288"]}}