Mass Spectrometry of Peptides

The structure of a protein largely determines its biological activity, so knowledge of that structure is necessary for a full understanding of how a protein functions normally in health, and why it functions abnormally in disease.

Electrospray Ionization Mass Spectrometry (ESI-MS) is a technique that can be used to determine protein structure. The fragmentation of a protein during ESI-MS can give clues as to its structure. Our goal is to understand how and why fragmentation happens, so that theses clues can be properly interpreted into structural information. Fragmentation during mass spectrometry can occur in a collision cell or in the mass spectrometer source. These may occur through either positive ions or negative ions. Different fragment polarities can provide complimentary structural information. We use small proteins (peptides) to investigate the effect of amino acid side chains, as well as collision energy, on fragmentation. Understanding how and why fragmentation happens will aid in the determination of protein structure from fragmentation patterns in mass spectrometry.

A proposed fragmentation scheme for the dipeptide Ala-Ser in the negative ion mode is shown below.

fragmentation scheme