Figure 1.

Proteogenomics Pipeline. MS/MS spectra and a protein sequence database are input for spectral identification by the Inspect program, which produces peptide/spectrum matches. PSM from Inspect are rescored with PepNovo, and filtered to an approximate 5% pvalue. Peptides are mapped onto the genome, with an additional layer of ORF-level filtering. Finally, peptides are compared to existing annotation. If peptide evidence shows an erroneous protein annotation, the correction is submitted to NCBI.