Figure 3

LC-MS/MS dataset of E. coli lysate searched against a combined E. coli /non- E. coli target-decoy (ACE) database. (A) Distribution of target peptides (green) and decoy peptides (blue) over the peptide score. (B) as in panel (A) but the target peptides below the score cut-off at 5% FDR split into two distributions: those matching to proteins identified by peptides above the score cut-off (green) and those that do not (left behind: grey). (C) Number of peptides (corroborated and non-corroborated) identified as a function of the score cut-off. (D) Number of peptides and proteins identified by Mascot alone (Msc), and with 5% FDR as a function of the way in which the FDR was determined: number of decoy peptides at or above the score cut-off divided by the target peptides at or above the score cut-off (FDR); number of decoy peptides in a score window divided by the number of target peptides in that window (local FDR; Loc); as local FDR but considering separately peptides that corroborate each other in matching the same protein in or above the current score window and those that do not corroborate (CNC local FDR; cnc).