{"doi":"10.1101/2022.10.19.512904","title":"MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features","abstract":"Abstract Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, for rescoring peptide-to-spectrum matches using additional features incorporating deep learning-based predictions of peptide properties, such as LC retention time, ion mobility, and MS/MS spectra. We demonstrate the utility of MSBooster, in tandem with MSFragger and Percolator, in several different workflows, including nonspecific searches (immunopeptidomics), direct identification of peptides from data independent acquisition data, single-cell proteomics, and data generated on an ion mobility separation-enabled timsTOF MS platform. MSBooster is fast, robust, and fully integrated into the widely used FragPipe computational platform.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":296568,"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":28,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9508,"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":230152,"name":"Fengchao Yu","orcid":"0000-0002-7695-3698","position":1,"is_corresponding":false},{"id":230154,"name":"Guo Ci Teo","orcid":"0000-0003-3212-4051","position":2,"is_corresponding":false},{"id":804316,"name":"Vadim Demichev","orcid":"0000-0002-2424-9412","position":3,"is_corresponding":false},{"id":28498,"name":"Markus Ralser","orcid":"0000-0001-9535-7413","position":4,"is_corresponding":false},{"id":51780,"name":"Alexey I. Nesvizhskii","orcid":"0000-0002-2806-7819","position":5,"is_corresponding":false},{"id":983404,"name":"Kevin Yang","orcid":"0000-0002-8569-4579","position":0,"is_corresponding":true}],"reference_count":76,"raw_metadata":null,"created_at":"2026-07-19T00:31:16.555318Z","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":[]}