Author Guidelines for 8

Table 1. Cleavage rule Digesting Reagent C Armillaria B AspN B Thermolysin B Clostripain A LysC A Pancreatic Elastase A Digesting Reagent C CNBr_Cys { Chymotrypsin A if Trypsin A V8 Ammonium Acetate A V8 Phosphate Buffer A Hydroxylamine A Mild Acid Hydrolysis A We present a stochastic model of proteolytic digestion of a proteome, assuming the distribution of parent protein lengths in the proteome, the relative abundances of the 20 amino acids in the proteome, and the digestion “rules” of the enzyme used in the digestion. We derived a closed form expression for the fragment mass distribution for a large class of enzymes including the widely used Trypsin. The expression uses the distribution of lengths in a mixture of proteins taken from a proteome, as well as the relative abundances of the 20 amino acids in the proteome. The agreement between theory and the in silico digest is excellent.