Affinity-mass spectrometry approaches for elucidating structures and interactions of protein–ligand complexes

Abstract

Affi nity-based approaches in combination with mass spectrometry for molecular structure identifi cation in biological complexes such as protein–protein, and protein–carbohydrate complexes have become popular in recent years. Affi nity- mass spectrometry involves immobilization of a biomolecule on a chemically activated support, affi nity binding of ligand(s), dissociation of the complex, and mass spectrometric analysis of the bound fraction. In this chapter the affi nity-mass spectrometric methodologies will be presented for (1) identifi cation of the epitope structures in the Abeta amyloid peptide, (2) identifi cation of oxidative modifi cations in proteins such as nitration of tyrosine, (3) determination of carbohydrate recognition domains, and as (4) development of a biosensor chip-based mass spectrometric system for concomitant quantifi cation and identifi cation of protein– ligand complexes.