Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides
Yuxue Liang, Pedatsur Neta, Xiaoyu Yang, Stephen E. Stein
High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with 3 to 6 residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids are estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides.
Journal of the American Society for Mass Spectrometry
, Neta, P.
, Yang, X.
and Stein, S.
Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides, Journal of the American Society for Mass Spectrometry, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=924081
(Accessed May 25, 2022)