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 Edm an degradation sequencing. These approaches entail the matching of ami no acid compositions or tryptic peptide masses of proteins against dat abases, often in conjunction with estimated protein molecular weight a nd isoelectric point. As genome sequencing projects progress, proteins from poorly molecularly defined organisms will increasingly be identi fied by cross-species comparison to proteins from well-defined organis ms. To investigate the application of rapid techniques for cross-speci es protein identification, a total of 65 theoretical cross-species com parisons involving 21 proteins (nine human and 12 E. coli) were undert aken. The degree of conservation of amino acid composition, tryptic pe ptides, protein isoelectric point and mass was established. Protein am ino acid composition was well conserved across species boundaries, whi lst tryptic peptides were poorly conserved. The molecular weight of pr oteins 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 compositio n and protein molecular weight. (C) 1997 Academic Press Limited.