Fig. 11
The confidence of endogenous tryptic peptides and proteins identified by X!TANDEM from human plasma on ice and incubated at room temperature. The X!TANDEM algorithm was used to assign the probability of type I error to peptides and thus the cumulative probability of type I error of proteins with 3 or more independent peptide correlations. Panels a scatter plot of peptide Log10 p-value versus Log10 precursor intensity; b sorted peptide p-values versus observations; c Peptide p-value quantile plot; d cumulative protein p-value per protein accession {Black Gene Symbol p-value, Red, FDR (false discovery rate) computed by the method of Benjamini and Hochberg [37]}