Practical Effects of Intramolecular Hydrogen Rearrangement in Electron Transfer Dissociation-Based Proteomics

Ion–ion reactions are valuable tools in mass-spectrometry-based peptide and protein sequencing. To boost the generation of sequence-informative fragment ions from low charge-density precursors, supplemental activation methods, via vibrational and photoactivation, have become widely adopted. However,...

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Bibliographic Details
Published in:Journal of the American Society for Mass Spectrometry 2022-01, Vol.33 (1), p.100-110
Main Authors: Peters-Clarke, Trenton M, Riley, Nicholas M, Westphall, Michael S, Coon, Joshua J
Format: Article
Language:English
Subjects:
Cell Line
Chromatography, Liquid
Electrons
Humans
Hydrogen - chemistry
Peptide Fragments - analysis
Peptide Fragments - chemistry
Peptide Fragments - metabolism
Proteins - analysis
Proteins - chemistry
Proteins - metabolism
Proteomics - methods
Tandem Mass Spectrometry
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Summary:Ion–ion reactions are valuable tools in mass-spectrometry-based peptide and protein sequencing. To boost the generation of sequence-informative fragment ions from low charge-density precursors, supplemental activation methods, via vibrational and photoactivation, have become widely adopted. However, long-lived radical peptide cations undergo intramolecular hydrogen atom transfer from c-type ions to z•-type ions. Here we investigate the degree of hydrogen transfer for thousands of unique peptide cations where electron transfer dissociation (ETD) was performed and was followed by beam-type collisional activation (EThcD), resonant collisional activation (ETcaD), or concurrent infrared photoirradiation (AI-ETD). We report on the precursor charge density and the local amino acid environment surrounding bond cleavage to illustrate the effects of intramolecular hydrogen atom transfer for various precursor ions. Over 30% of fragments from EThcD spectra comprise distorted isotopic distributions, whereas over 20% of fragments from ETcaD have distorted distributions and less than 15% of fragments derived from ETD and AI-ETD reveal distorted isotopic distributions. Both ETcaD and EThcD give a relatively high degree of hydrogen migration, especially when D, G, N, S, and T residues were directly C-terminal to the cleavage site. Whereas all postactivation methods boost the number of c- and z•-type fragment ions detected, the collision-based approaches produce higher rates of hydrogen migration, yielding fewer spectral identifications when only c- and z•-type ions are considered. Understanding hydrogen rearrangement between c- and z•-type ions will facilitate better spectral interpretation.
ISSN:1044-0305
1879-1123
DOI:10.1021/jasms.1c00284