Number of proteins identified with 5% FDR in an analysis of human serum as a function of the way in which the FDR was determined (key as in Figure 2D). 646 proteins were identified in addition by the current FDR approach taking proteins with one and more peptides together when compared to our CNC local FDR approach (FN+FP). Under these conditions also 222 decoy proteins are identified (D) indicating that more than 1 out of 3 additional proteins (FP) are identified on false grounds and thus would devaluate the final protein list. Our method identifies 22 additional proteins with two or more peptides. Correct proteins (FN) are missed as a result of a stringent FDR estimation and would profit from an independent protein list created from peptide identifications using a higher local FDR.