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bioRxiv · 10.1101/2022.06.30.498346

Collisional dissociation of 115 deprotonated peptides of 5-28 amino acids--an updated report on fragment ion types, neutral loss species, and the effect of acidic residues

Zuo, M.-Q.·Sun, R.-X.·Dong, M.-Q.
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Abstract

Highly acidic, D/E-rich peptides or proteins are difficult to identify by positive-ion-mode mass spectrometry (MS), and negative-ion-mode MS is an attractive but insufficiently explored alternative. Based on high-resolution and accurate-mass MS analysis of 115 synthetic peptides of 5-28 amino acids, we confirmed that higher-energy collisional dissociation (HCD) of deprotonated peptides induced abundant backbone or side-chain neutral losses (NL), and updated the ranking list of NLs by abundance. The most abundant fragment ion types are y- > x-, z- > c- if the NL ions are included, or c- > y- > z- > b- if not. The most frequent side-chain NLs involve amino acids C, S, T, D, E, N, Q, and R. Although NL of CO2 is common for all peptides, it is markedly enhanced in D/E-containing peptides. Long peptides and D/E-rich peptides are prone to carrying multiple negative charges. HCD spectra produced from multiply deprotonated peptides have a lower fraction of sequencing ions (i.e., a-, b-, c-, x-, y-, z- ions) than those produced from 1- ([M-H]-) and 2- ([M-2H]2-) precursors. Based on the above findings, we predict that under negative-ion HCD, D/E-rich peptides should be difficult to identify and that choosing a protease to generate peptides containing fewer D/E residues will improve identification of highly acidic proteins.

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Zuo, M.-Q., Sun, R.-X., Dong, M.-Q.. 2022-07-01. Collisional dissociation of 115 deprotonated peptides of 5-28 amino acids--an updated report on fragment ion types, neutral loss species, and the effect of acidic residues. https://doi.org/10.1101/2022.06.30.498346

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