Theoretical possibilities and limitations of protease primary specificity determination by statistical analysis of MALDI mass-spectra of proteolysis products

Abstract

Possibilities and limitations of the method of examination of proteolytic enzymes' primary spec ificity by statistical analysis of MALDI (matrix assisted laser desorption/ionization) mass spectra of products obtained by protein substrate proteolysis, without direct determination of their amino acid sequences, were investigated theoretically. The optimum range given by the measurement errors of the peptides' masses for obtaining a statistical set of the events, and the form of statistical data presentation, were chosen. It was shown that the proposed method can be applied only for proteases with a relatively narrow primary specificity (two or three amino acids). The influence of protein substrate molecular weight and amino acid composition on the efficiency of specifics for a particular protease amino acid, revealed under statistical treatment of the set of proteolysis product masses, was studied on the model of trypsin, chymotrypsin, glutamylendopeptidase, pepsin (pH 1.3).