Fig. 2.

Lower cutoff for FDR control in the reduced database generates additional identifications (Jurkat). A Scatter plot comparing for each spectrum its PSM score from the full (x-axis) or reduced database (y-axis) searches. A color code indicates the type of match (“target,” “decoy,” or “no match”) in the two searches. Score cutoffs obtained by TDC at 1% FDR are shown as red and blue lines for the full and reduced database, respectively. The upper-right insert zooms in on PSMs accepted at 1% FDR only in the reduced database, due to the lower score cutoff at 1% FDR (arrow pointing to the dashed circle). B Number of reallocations whose score in the reduced database was equal to or lower or higher than the score in the full database. C PSM scores for reallocations to target matches in the reduced database, grouped by the type of match in the full database. The number of reallocations passing the reduced database cutoff at 1% FDR is shown in blue (“nb valid reallocations”) and of those passing the full database cutoff at 1% FDR—additional valid identifications exclusively generated by reallocation, independent of the lower cutoff—in red (“nb valid pure reallocations”). D Number of additional spectra (left) and number of spectra identifying additional peptides (right) exclusively identified in the reduced database search due to (i) lower score cutoff at 1% FDR in the reduced database compared to the full database—i.e., PSMs only passing the cutoff from the reduced database search, including identical PSMs in both searches (black) and reallocations from target (gray), decoy (orange), or no match (magenta) in the full database to target matches in the reduced database; (ii) pure reallocation—i.e., additional identifications exclusively due to reallocation. The Venn diagram illustrates the corresponding non-redundant number of additional peptides (i.e., not identified in the full database search) identified by these spectra