{"paper":{"title":"Running PeptideProphet Separately on Replicates Improves Peptide Identification Results","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.GN","stat.AP"],"primary_cat":"q-bio.QM","authors_text":"Chao Yang, Weichuan Yu, Zengyou He","submitted_at":"2012-11-27T02:42:15Z","abstract_excerpt":"Limited spectrum coverage is a problem in shotgun proteomics. Replicates are generated to improve the spectrum coverage. When integrating peptide identification results obtained from replicates, the state-of-the-art algorithm PeptideProphet combines Peptide-Spectrum Matches (PSMs) before building the statistical model to calculate peptide probabilities.\n  In this paper, we find the connection between merging results of replicates and Bagging, which is a standard routine to improve the power of statistical methods. Following Bagging's philosophy, we propose to run PeptideProphet separately on e"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1211.6198","kind":"arxiv","version":3},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}