Suppression effects in enzymatic peptide ladder sequencing using ultraviolet-matrix assisted laser desorption/ionization mass spectrometry

The techniques of enzymatic and chemical peptide ladder sequencing, coupled with ultraviolet - matrix assisted laser desorption/ionization - mass spectrometry (UV-MALDI-MS) have been improving continuously in the last five years and have now become important tools for primary structure identification. In this work, signal suppression effects, appearing in UV-MALDI-MS (excitation 337 nm) of ladder peptides, were investigated using the 17-amino acid peptide dynorphin A. We show, with examples of simple "two-peptide" systems and more complex "multi-peptide" systems, that suppression effects do in fact exist. The magnitude of the observed suppression is strongly dependent upon both the nature and the amount of the suppressing peptide. Suppression behavior of individual ladder peptides was investigated on equimolar mixtures of ten ladder peptides. Significant signal suppression was recorded for all ladder peptides, with some of them being approximately 170 times lower in signal intensity than the pure, i.e., unsuppressed peptide at the same concentration. For the investigated system - dynorphin A, 4-hydroxy-alpha-cyanocinnamic acid (4-HCCA) matrix, UV excitation - a correlation between the extent of suppression and an intractable combination of peptide hydrophobicity and the presence of several basic amino acids can be seen.