INTRODUCTION

Proteins can exist as large complex structures, with some molecules in the population displaying heterogeneity in their amino acid sequence due to improper assembly, degradation, or post-translational modification. The high molecular mass of proteins combined with their complexity makes it particularly challenging to chemically identify an intact protein product using a single analytical method. It is possible to cleave the test protein into smaller fragments which can be identified with sufficient mass resolution to determine the amino acid sequence of the protein. This process is the basis of the protein identification technique commonly known as peptide mapping. The peptide mapping technique involves a digestion step in which the protein is selectively cleaved at amide bonds between specific amino acid residues to yield a predictable set of peptides. Analytical chromatographic separation, detection, and identification of the peptide mixture reveal information on the amino acid sequence of the protein which can be used to identify the protein. Peptide mapping is a comparative procedure; the results from the test protein are contrasted with the results of the reference standard or material similarly treated to determine the identity of the test protein. This comparative identification confirms that the primary structure of the test protein matches that of the reference protein.