Valence Parity to Distinguish c' and z~(centre dot) Ions from Electron Capture Dissociation/Electron Transfer Dissociation of Peptides: Effects of Isomers, Isobars, and Proteolysis Specificity

摘要

Valence parity provides a way to distinguish between N-terminal and C-terminal electron capture dissociation/electron transfer dissociation (ECD/ETD) product ions based on their number of hydrogen plus nitrogen atoms determined by accurate mass measurement and forms a basis for de novo peptide sequencing. The effect of mass accuracy (0.1-1 ppm error) on c'/z~(centre dot) overlap and unique elemental composition overlap is evaluated for a database of c'/z~(centre dot) product ions each based on all possible amino acid combinations and four subset databases containing the same c' ions but with z~(centre dot) ions determined by in silico digestion with trypsin, Glu-C, Lys-C, or chymotrypsin. High mass accuracy reduces both c'/z~(centre dot) overlap and unique elemental composition overlap. Of the four proteases, trypsin offers slightly better discrimination between N- and C-terminal ECD/ETD peptides. Interestingly, unique elemental composition overlap curves for c'/c' and z~(centre dot)/z~(centre dot) peptide ions exhibit discontinuities at certain nominal masses for 0.1-1.0 ppm mass error. Also, as noted in the companion article (Polfer et al. Anal. Chem. 2011, DOI: 10.1021/ac201624t), the number of ECD/ETD product ion amino acid compositions as a function of nominal mass increases exponentially with mass but with a superimposed modulation due to higher prevalence of certain elemental compositions.