Identifying Sites of Posttranslational Modifications in Proteins Via HPLC Peptide Mapping

Abstract

The intent of this chapter is to provide realistic procedures for identifying sites of posttranslational modifications in proteins. Particular emphasis will be directed toward identifying degradative covalent changes, such as deamidation and oxidation, that are thought to be associated with protein “aging” and to influence protein stability. The first issue that arises is how one goes about detecting the more than 100 different posttranslational modifications that have already been identified in proteins (1, 2). In light of this diversity, those techniques are most useful that can detect any, or at least most, possible modifications. Although a technique like isoelectric focusing can detect modifications, such as phosphorylation and deamidation, that result in altering the net charge, this technique would be less likely to detect sulfoxide formation. The two techniques that come closest to being able to rapidly detect most possible modifications are comparative HPLC peptide mapping and mass spectrometry, which can be used to determine accurate masses on both the intact protein and its HPLC-separated peptides. Since electrospray mass spectrometry (ESMS) can routinely determine the mass of a 50 kDa protein within 0.01% (3), any modification that altered the mass of this protein by more than ±5 atomic mass units (amu) could be detected. Hence, assuming that the mass of the nonmodified protein is known, ESMS of the intact protein should succeed in rapidly detecting phosphorylation (+80) and oxidation (+16), but would, for instance, fail to detect deamidation (+1).