biostudies-literatureLeDuc RDHHS | NIH | National Institute of General Medical SciencesNIDA NIH HHSHHS | NIH | National Institute on Drug AbusePaul G. Allen Family FoundationNIGMS NIH HHS796-805https://www.ebi.ac.uk/biostudies/studies/S-EPMC6442365biostudies-literatureUnknown18(4)Within the last several years, top-down proteomics has emerged as a high throughput technique for protein and proteoform identification. This technique has the potential to identify and characterize thousands of proteoforms within a single study, but the absence of accurate false discovery rate (FDR) estimation could hinder the adoption and consistency of top-down proteomics in the future. In automated identification and characterization of proteoforms, FDR calculation strongly depends on the context of the search. The context includes MS data quality, the database being interrogated, the search engine, and the parameters of the search. Particular to top-down proteomics-there are four molecular levels of study: proteoform spectral match (PrSM), protein, isoform, and proteoform. Here, a conMolecular & cellular proteomics : MCPAccurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics.PMC644236511715P41GM108569P30 DA018310P41 GM108569P30DA018310Fellers RTEarly BPGreer JBThomas PMKelleher NLShams DPLeDuc RDfalseAccurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics.Within the last several years, top-down proteomics has emerged as a high throughput technique for protein and proteoform identification. This technique has the potential to identify and characterize thousands of proteoforms within a single study, but the absence of accurate false discovery rate (FDR) estimation could hinder the adoption and consistency of top-down proteomics in the future. In automated identification and characterization of proteoforms, FDR calculation strongly depends on the context of the search. The context includes MS data quality, the database being interrogated, the search engine, and the parameters of the search. Particular to top-down proteomics-there are four molecular levels of study: proteoform spectral match (PrSM), protein, isoform, and proteoform. Here, a con2019-01-01T00:00:00Z2019 Apr2026-04-30T10:29:50.07Z2025-04-04T09:44:41.883ZS-EPMC64423653064707310.1074/mcp.ra118.00099310.1074/mcp.RA118.000993