Jeremiah Tipton - Valence Parity to Distinguish c and z● Ions from Electron Capture Dissociation/Electron Transfer Dissociation of Peptides: Effects of Isomers, Isobars, and Proteolysis Specificity

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  Publication Details (including relevant citation   information):

  Mao,Y.; Tipton, J.D.; Blakney, G.T.;   Hendrickson, C.L.; Marshall, A.G. Analytical Chemistry,   Technical Note, In Press, September, 20 (2011)


  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 overlap and unique elemental composition overlap   is evaluated for a database of c′/z product ions each   based on all possible amino acid combinations and four subset   databases containing the same c ions but with   z ions determined by in silico digestion   with trypsin, Glu-C, Lys-C, or chymotrypsin. High mass accuracy   reduces both c′/z 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/z 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.

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