Gas phase conformation can have an influence on peptide fragmentation.

In the post-genomic era, mass spectrometry is destined to fulfil a central role in biomedical research, and it is in the area of protein identification that mass spectrometry is now most rapidly expanding. An important identification method is to subject a protein to proteolysis and determine the resulting peptide masses and/or primary structure. From such determinations proteins can be identified. Tandem mass spectrometry (MS/MS) is used to determine primary structure and, for high-throughput identification, computer-based automated strategies are a prerequisite. Computer programs are available for such identifications, where simulated MS/MS spectra of amino acid sequences within a database are generated and compared to experimental spectra. Such algorithms take into account empirical rules for peptide fragmentation, rather than specific gas-phase ion chemistry. For example, fragmentation of each peptide bond is usually considered to be equally facile. In reality, this is not the case. Gas-phase ion chemistry bears an important role in determining the abundance of fragment ions in MS/MS spectra. In this communication, the gas-phase ion chemistry responsible for the facile cleavage between Gln and Gly residues is investigated, particularly in relation to Proline Rich Protein-1.