Why b, y's? Sodiation-induced tryptic peptide-like fragmentation of non-tryptic peptides

Tryptic peptides are the analytes of choice for mass spectrometric analysis of protein and peptide as they display a favorable fragmentation pattern due to the presence of a C-terminal basic amino acid residue. Clean y fragment ion series is most commonly observed for these species. In contrast, non-tryptic peptides with undefined locations of basic amino acid residues give rise to a mixture of b and y fragment ions, often preventing unambiguous assignment of fragment ion types, which in turn impedes the interpretation of the product ion spectra. Here we report that the fragmentation pattern of multiply charged rion-tryptic peptides can be modulated by fragmenting the monosodiated multiply charged species instead of the multiply protonated species. Even when b fragment ions dominate the product ion spectrum of the protonated species clue to the presence of a charge sequestering basic residue at the N-terminus, mainly singly charged sodium cationized y fragment ions [y(n) + Na](+) are observed upon fragmentation of the cationized species, i.e., tryptic peptide-like fragmentation of non-tryptic peptides is achieved. Several examples of this fragmentation pattern are described, thus strongly suggesting that sodium cation may be complexed near or at the C-terminus even in the presence of other acidic residues within the peptide. This effect is especially pronounced in the case of the doubly charged non-tryptic peptides. This controlled modulation of the fragmentation behavior of non-tryptic peptides is shown to be advantageous for the de novo sequencing of non-tryptic bioactive peptides as it facilitates the differentiation between b and y ions. (C) 2007 Elsevier B.V. All rights reserved.