biostudies-literatureUnknown23Raj AVariant peptides resulting from single nucleotide polymorphisms (SNPs) can lead to aberrant protein functions and have translational potential for disease diagnosis and personalized therapy. Variant peptides detected by proteogenomics are fraught with high number of false positives, but there is no uniform and comprehensive approach to assess variant quality across analysis pipelines. Despite class-specific FDR along with ad-hoc filters, the problem is far from solved. These protocols are typically manual and tedious, and thus not uniform across labs. We demonstrate that variant peptide rescoring, integrated with intensity, variant event information and search result features, allows better discrimination of correct variant peptides. Implemented into PgxSAVy - a tool for quality control ofComputational and structural biotechnology journal711-722https://www.ebi.ac.uk/biostudies/studies/S-EPMC10825656biostudies-literaturePgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.PMC10825656Dash DAggarwal SSingh PRaj AYadav AKfalsePgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Variant peptides resulting from single nucleotide polymorphisms (SNPs) can lead to aberrant protein functions and have translational potential for disease diagnosis and personalized therapy. Variant peptides detected by proteogenomics are fraught with high number of false positives, but there is no uniform and comprehensive approach to assess variant quality across analysis pipelines. Despite class-specific FDR along with ad-hoc filters, the problem is far from solved. These protocols are typically manual and tedious, and thus not uniform across labs. We demonstrate that variant peptide rescoring, integrated with intensity, variant event information and search result features, allows better discrimination of correct variant peptides. Implemented into PgxSAVy - a tool for quality control of2024-01-01T00:00:00Z2024 Dec2026-06-02T22:46:38.977Z2024-11-21T03:39:07.369ZS-EPMC108256563829247410.1016/j.csbj.2023.12.033