Cross-species protein identification using amino acid composition, peptide mass fingerprinting, isoelectric point and molecular mass: a theoretical evaluation.

Proteins can be identified by rapid techniques that do not involve Edman degradation sequencing. These approaches entail the matching of amino acid compositions or tryptic peptide masses of proteins against databases, often in conjunction with estimated protein molecular weight and isoelectric point. As genome sequencing projects progress, proteins from poorly molecularly defined organisms will increasingly be identified by cross-species comparison to proteins from well-defined organisms. To investigate the application of rapid techniques for cross-species protein identification, a total of 65 theoretical cross-species comparisons involving 21 proteins (nine human and 12 E. coli) were undertaken. The degree of conservation of amino acid composition, tryptic peptides, protein isoelectric point and mass was established. Protein amino acid composition was well conserved across species boundaries, whilst tryptic peptides were poorly conserved. The molecular weight of proteins was generally well conserved, but protein isoelectric point was not. These results suggest that cross-species protein identification by rapid techniques will be done best by protein amino acid composition and protein molecular weight.