{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["An Z"],"funding":["Strategic Priority Research Program of the Chinese Academy of Sciences"],"pagination":["391-405"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC6356076"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["18(2)"],"pubmed_abstract":["The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification o"],"journal":["Molecular & cellular proteomics : MCP"],"pubmed_title":["PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome."],"pmcid":["PMC6356076"],"funding_grant_id":["XDB13010600"],"pubmed_authors":["Qian X","Gong F","Tan M","An Z","Zhai L","Fu Y","Ying W"],"additional_accession":[]},"is_claimable":false,"name":"PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome.","description":"The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification o","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 Feb","modification":"2026-05-07T14:01:36.858Z","creation":"2025-04-06T13:25:16.05Z"},"accession":"S-EPMC6356076","cross_references":{"pubmed":["30420486"],"doi":["10.1074/mcp.ra118.000812","10.1074/mcp.RA118.000812"]}}