Data analysis in proteomics is complex and with the extra challenges involved in 
the interpretation of data from N-terminomics experiments, this can be 
daunting.Therefore, we have devised a rational pipeline of steps to approach 
N-terminomics data analysis in a statistically based and valid manner. We have 
automated these steps in CLIPPER, an add-on to the Trans-Proteomic 
Pipeline(TPP). Applying CLIPPER to the analysis of N- terminomics data generated 
by terminal amine isotopic labeling of substrates (TAILS) enables high 
confidence peptide to protein assignment, protein N-terminal characterization 
and annotation, and for protease analysis readily allows protease substrate 
discovery with high confidence.