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Journal of The American Society for Mass Spectrometry

, Volume 25, Issue 11, pp 1927–1938

First Online: 19 August 2014Received: 17 April 2014Revised: 14 July 2014Accepted: 16 July 2014

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 bn-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.

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Abstractᅟ

Key wordsCollision-induced dissociation b-ion rearrangement Peptide scrambling Lys-C Lys-N  Download fulltext PDF



Autor: Ross Chawner - Stephen W. Holman - Simon J. Gaskell - Claire E. Eyers

Fuente: https://link.springer.com/



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