{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Poudel S"],"funding":["NIA NIH HHS"],"pagination":["410-418"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12469151"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["24(2)"],"pubmed_abstract":["The identification of peptides is a cornerstone of mass spectrometry-based proteomics. Spectral library-based algorithms are well-established methods to enhance the identification efficiency of peptides during database searches in proteomics. However, these algorithms are not specifically tailored for tandem mass tag (TMT)-based proteomics due to the lack of high-quality TMT spectral libraries. Here, we introduce JUMPlib, a computational tool for a TMT-based spectral library search. JUMPlib comprises components for generating spectral libraries, conducting library searches, filtering peptide identifications, and quantifying peptides and proteins. Fragment ion indexing in the libraries increases the search speed and utilizing the experimental retention time of precursor ions improves peptid"],"journal":["Journal of proteome research"],"pubmed_title":["JUMPlib: Integrative Search Tool Combining Fragment Ion Indexing with Comprehensive TMT Spectral Libraries."],"pmcid":["PMC12469151"],"funding_grant_id":["RF1 AG064909","U19 AG069701","RF1 AG068581"],"pubmed_authors":["Poudel S","Shrestha H","Wu L","High AA","Yuan ZF","Fu Y","Wang X","Peng J"],"additional_accession":[]},"is_claimable":false,"name":"JUMPlib: Integrative Search Tool Combining Fragment Ion Indexing with Comprehensive TMT Spectral Libraries.","description":"The identification of peptides is a cornerstone of mass spectrometry-based proteomics. Spectral library-based algorithms are well-established methods to enhance the identification efficiency of peptides during database searches in proteomics. However, these algorithms are not specifically tailored for tandem mass tag (TMT)-based proteomics due to the lack of high-quality TMT spectral libraries. Here, we introduce JUMPlib, a computational tool for a TMT-based spectral library search. JUMPlib comprises components for generating spectral libraries, conducting library searches, filtering peptide identifications, and quantifying peptides and proteins. Fragment ion indexing in the libraries increases the search speed and utilizing the experimental retention time of precursor ions improves peptid","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Feb","modification":"2026-06-03T21:34:44.998Z","creation":"2026-05-02T03:07:43.296Z"},"accession":"S-EPMC12469151","cross_references":{"pubmed":["39715016"],"doi":["10.1021/acs.jproteome.4c00410"]}}