Figure 1

Schematic of the Spectrum to Peptide matching pipeline. Forward and reversed (REV-CBS) databases were searched with local implementation of the OMSSA MS/MS search engine. Threshold Expect values for matching peptides were estimated from the false discovery rate (FDR). Best Accepted peptide-spectrum matches (PSM) selection was done by ranking for each MS/MS spectrum the output of each individual peptide database by E-value and selection of the top hit identified peptide sequence.Insert: Detection of a single amino acid polymorphism (SAP). A wildcard character (x) is introduced at each position of a single proteome matching peptide, followed by a pattern search in the complementary proteome. In the given example using the ATCC 1015 single proteome matching peptide as a template, a single equivalent peptide, derived from An18g03570 is retrieved from the complementary proteome. An18g03570 is 99% identical to ATCC 1015 protein 56782.