Steps for matching a theoretical envelope with an experimental envelope. (a) A mass spectrum contains an experimental envelope with four peaks p1′,p2′,p3′,p4′. One peak p2′ is selected as the base peak. (b) For a given charge state z, the averagine formula of a charge z ion is computed such that the m/z value of its most abundant isotopomer equals that of the base peak, and the theoretical isotopomer distribution is obtained. (c) The theoretical peaks in the theoretical isotopomer distribution are matched to experimental peaks with similar m/z values in the mass spectrum. (d) The theoretical peak intensities, which are initialized as the isotopomer probabilities, are scaled so that the sum of the intensities of the top three peaks (red bold peaks) in the theoretical envelope is the same to that (black bold peaks) of the experimental envelope.