Assessment of the effect of noise removal on the identification performance illustrated by the receiver operating characteristic (ROC). The identification rate is robust against different levels of peak noise filters up to 10%. We decided to use a conservative noise removal level of 2%. Recall (true positives) reflects the number of correctly identified peptides based on SEQUEST search, whereas 1 specificity corresponds to all ProMEX peptide identifications which did not match to the SEQUEST identifications. As a comparison, results from using the Euclidean distance are also included which proved to be inferior to the dot product.