Peptide scrambling during collision-induced dissociation is influenced by N-terminal residue basicity



Chawner, Ross, Holman, Stephen W, Gaskell, Simon J and Eyers, Claire E ORCID: 0000-0002-3223-5926
(2014) Peptide scrambling during collision-induced dissociation is influenced by N-terminal residue basicity. Journal of the American Society of Mass Spectrometry, 25 (11). pp. 1927-1938.

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Abstract

‘Bottom up’ proteomic studies typically use tandem mass spectrometry data to infer peptide ion sequence, enabling identification of the protein whence they derive. The majority of such studies employ collision-induced dissociation (CID) to induce fragmentation of the peptide structure giving diagnostic b-, y-, and a- ions. Recently, rearrangement processes that result in scrambling of the original peptide sequence during CID have been reported for these ions. Such processes have the potential to adversely affect ion accounting (and thus scores from automated search algorithms) in tandem mass spectra, and in extreme cases could lead to false peptide identification. Here, analysis of peptide species produced by Lys-N proteolysis of standard proteins is performed and sequences that exhibit such rearrangement processes identified. The effect of increasing the gas-phase basicity of the N-terminal lysine residue through derivatization to homoarginine toward such sequence scrambling is then assessed. The presence of a highly basic homoarginine (or arginine) residue at the N-terminus is found to disfavor/inhibit sequence scrambling with a coincident increase in the formation of b(n-1)+H2O product ions. Finally, further analysis of a sequence produced by Lys-C proteolysis provides evidence toward a potential mechanism for the apparent inhibition of sequence scrambling during resonance excitation CID.

Item Type: Article
Additional Information: ## TULIP Type: Articles/Papers (Journal) ##
Uncontrolled Keywords: Collision-induced dissociation, b-ion rearrangement, Peptide scrambling
Depositing User: Symplectic Admin
Date Deposited: 10 Aug 2016 07:28
Last Modified: 19 Jan 2023 07:32
DOI: 10.1021/jasms.8b04652
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3002837