The identification of large peptide fragments produced from proteins of known sequence: a computerized approach using amino acid composition indexes and its application to thermolysin.

An approach to identify fragments produced from proteins of known sequence, based on their amino acid composition, is described. A BASIC computer program (SEARCH) was used to quantitate the degree of relatedness between an experimentally determined amino acid composition and theoretical test peptide compositions calculated from a protein of known amino acid sequence. This computerized approach provides a rapid and objective identification of autolytic peptide fragments produced from thermolysin. Three different types composition indexes were compared with respect to their value versus the number of sequence differences between experimental and test compositions. The difference index was found to show a linear relationship and the lowest level of variability in this regard. On the basis of this comparison, we conclude that the difference index is the most reliable indicator of peptide fragment identity.