Assessing the impact of nonspecific cleavage, missed cleavages, and ragged ends on the reproducibility of ErbB2 peptides. The %CV for all ErbB2 peptides detected in each of the four enzyme conditions tested based on (a) number of missed cleavages, (b) specificity of cleavage, and (c) ragged ends. Peptides with at least one nonspecific cleavage or ragged end were considered nonspecific or ragged end peptides. Grey lines indicate the median value for each condition.