Fig. 2.

Error relation between peptide spectrum matches and protein identifications. Impact of dataset and database size on discrepancy between false discovery rate of peptide spectrum matches and protein identifications. Protein database entries are represented as colored circles. true/false peptide spectrum matches (PSM) are depicted as green/red discs. True protein identifications (PID) are supported by at least one correct peptide spectrum match and tagged with a checkmark. The larger the data set or database size, the more pronounced the discrepancy of false discovery rates (FDR) at the level of peptide spectrum matches (PSM) and protein identifications (PID). For large datasets the apparent proteome coverage can deviate significantly from the coverage of true positive (tP) protein identifications.