ASSIGNMENT OF PROTEIN DISULFIDES BY A COMPUTER METHOD USING MASS-SPECTROMETRIC DATA

We designed a computer program for the assignment of protein disulphid es using mass spectrometric data. All the theoretical linear peptides containing from one to three cysteines are generated on the basis of t he protein sequence. Their combination ways are determined in order to create all the possible disulphide-bridged fragments containing from two to six cysteines and to calculate their molecular weight. One, two and three S-S bridges per linked fragment mere considered, taking int o account the possibility that the fragments contain unabridged residu es, The mass data obtained from the spectral analysis of peptide mixtu res of the digested protein are then associated to the fitting structu res of disulphide-bridged peptides, giving rise to the primary output, This output can then be screened by using information on the specific ity of the proteolytic agent(s) used and/or any further mass data prov ided by Edman degradation and/or carboxypeptidase treatment of the pep tide mixtures. The need for such a computer aid is discussed and examp les of application are given.