{"doi":"10.1021/jasms.1c00288","title":"GlycoDeNovo2: An Improved MS/MS-Based <i>De Novo</i> Glycan Topology Reconstruction Algorithm","abstract":"Glycan structure identification is essential to understanding the roles of glycans in various biological processes. Previously, we developed GlycoDeNovo, a de novo 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 p-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","year":2022,"id":264887,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.957,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":923005,"name":"Juan Wei","orcid":"0000-0002-8621-6253","position":1,"is_corresponding":false},{"id":282448,"name":"Ting Yang","orcid":"0000-0001-7201-4231","position":2,"is_corresponding":false},{"id":516385,"name":"Cheng Lin","orcid":"0000-0003-3653-9633","position":3,"is_corresponding":false},{"id":391253,"name":"Catherine E. Costello","orcid":"0000-0003-1594-5122","position":4,"is_corresponding":false},{"id":805224,"name":"Pengyu Hong","orcid":"0000-0002-3177-2754","position":5,"is_corresponding":false},{"id":923415,"name":"Zizhang Chen","orcid":null,"position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":null,"created_at":"2026-07-19T00:26:41.845195Z","pmid":"35157458","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}