Mass Spectrometric Methods for Peptide Sequencing: Applications to Immunology and Protein Acylation

The earliest applications of tandem quadrupole mass spectrometry to sequence analysis of an unknown peptide [1] and a protein [2] required nanomoles of sample. Today, peptides in complex mixtures can be sequenced routinely on a Finnigan triple quadrupole instrument at the 10 femtomole level [3]. Microsequence analysis by the classical Edman degradation approach requires at least 10–100 times this amount of material, making mass spectrometry the most sensitive method in the world for this purpose. It is also the method of choice for characterizing posttranslational modifications. In this chapter, we discuss the mass spectrometric approach for sequencing naturally processed peptides bound to class I major histocompatibility complex molecules (MHC), and the methods used for the identification of an acylation site found in adenylate cyclase toxin.