Figure 2

LC-MS/MS dataset of E. coli lysate searched against a combined E. coli /non- E. coli target-decoy database. Number of peptides (A) and proteins (B) identified with 5% FDR. Number of peptides (C) and proteins (D) falling into the class of corroborating (c) and non-corroborating (nc) peptide hits. (E) Distribution of E. coli and non-E. coli peptides over peptide score. FDR: number of decoy peptides at or above a score divided by the number of target peptides at or above the same score; local FDR: number of decoy peptides in a score window divided by the number of target peptides in that window. (F) Plot of the FDR and the local FDR over the peptide score. The grey zone marks the score region of those peptides that would be included as correct results according to the FDR but excluded by the local FDR. Score is defined as Mascot score minus the homology value if present or minus the identity value.