{"doi":"10.1101/2022.02.11.480137","title":"Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data","abstract":"Abstract We present LC-MS 2 Struct, a machine learning framework for structural annotation of small molecule data arising from liquid chromatography-tandem mass spectrometry (LC-MS 2 ) measurements. LC-MS 2 Struct jointly predicts the annotations for a set of mass spectrometry features in a sample, using a novel structured prediction model trained to optimally combine the output of state-of-the-art MS 2 scorers and observed retention orders. We evaluate our method on a dataset covering all publicly available reversed phase LC-MS 2 data in the MassBank reference database, including 4327 molecules measured using 18 different LC conditions from 16 contributors, greatly expanding the chemical analytical space covered in previous multi-MS 2 scorer evaluations. LC-MS 2 Struct obtains significantly higher annotation accuracy than earlier methods and improves the annotation accuracy of state-of-the-art MS 2 scorers by up to 106%. The use of stereochemistry-aware molecular fingerprints improves prediction performance, which highlights limitations in existing approaches and has strong implications for future computational LC-MS 2 developments.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":299856,"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":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9442,"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":35995,"name":"Emma L. Schymanski","orcid":"0000-0001-6868-8145","position":1,"is_corresponding":false},{"id":108308,"name":"Juho Rousu","orcid":"0000-0002-0705-4314","position":2,"is_corresponding":false},{"id":883730,"name":"Eric Bach","orcid":"0000-0001-6200-5462","position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":null,"created_at":"2026-07-19T00:31:49.412501Z","pmid":null,"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":[]}