Gas-phase conformation can have an influence on peptide fragmentation

Full-text article (445 kB)
(subscribers only)

Eur. J. Mass Spectrom. 7, 89 - 99 (2001)

Gas-phase conformation can have an influence on peptide fragmentation

William J. Griffiths^* and Andreas P. Jonsson
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden. E-mail:

ABSTRACT:

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.

Keywords: mass spectrometry, tandem mass spectrometry, electrospray, peptide, fragmentation mechanism

You can now buy this paper on-line in PDF format; it costs only £11.75. Just click on the BUY on-line button. You can pay on-line through a secure server and get access immediately.