MALDI TOF/TOF-Based Approach for the Identification of d- Amino Acids in Biologically Active Peptides and Proteins

Johannes Koehbach, Christian W. Gruber, Christian Becker, David P. Kreil, Alexander Jilek

Several biologically active peptides contain a D-amino acid in a well-defined position, which is position 2 in all peptide epimers isolated to date from vertebrates and also some from invertebrates. The detection of such D-residues by standard analytical techniques is challenging. In tandem mass spectrometric (MS) analysis, although fragment masses are the same for all stereoisomers, peak intensities are known to depend on chirality. Here, we observe that the effect of a D-amino acid in the second N-terminal position on the fragmentation pattern in matrix assisted laser desorption (MALDI)-time-of-flight (TOF)/TOF spectrometry strongly depends on the peptide sequence. Stereosensitive fragmentation (SF) is correlated to a neighbourhood-effect, but the D-residue also exerts an overall effect influencing distant bonds. In a fingerprint analysis, multiple peaks can thus serve to identify the chirality of a sample in short time and potentially high throughput. Problematic variations between individual spots could be successfully suppressed by co-spotting deuterated analogues of the epimers. By identifying the [D-Leu2] isomer of the predicted peptide GH-2 (gene derived bombininH) in skin secretions of the toad Bombina orientalis, we demonstrated the analytical power of SF-MALDI-TOF/TOF measurements. In conclusion, SF-MALDI-TOF/TOF MS combines high sensitivity, versatility and the ability to complement other methods.