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Eur. J. Mass Spectrom. DOI: 10.1255/ejms.582

Methylating peptides to prevent adduct ion formation also directs cleavage in collision-induced dissociation mass spectrometry

Clement Poon, Harvey Kaplan and Paul M. Mayer*
Chemistry Department, University of Ottawa, 10 Marie Curie, Ottawa, Canada K1N 6N5

ABSTRACT:
We investigated the effect of N-terminal amino group and carboxyl group methylation on peptide analysis by electrospray mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS/MS). Permethylation of the N-terminal amino group and the carboxyl groups can reduce metal ion adducts but did not enhance sensitivity in electrospray as previously observed for MALDI. N-terminal trimethylated peptides exhibit different CID tandem mass spectra than their unmodified analogues, the results supporting the mobile proton hypothesis of peptide fragmentation. A permanent positive charge at the N-terminus leads to competition between permanent-charge directed processes and loss of the N-terminal trimethyl amino group. Carboxyl methylation has no effect on fragmentation behaviour other than to shift the mass of fragments containing methylated carboxyl groups. Comparison of regular and tandem mass spectra of different methylated peptides allowed probing the location of incomplete methylation, the proton displaced by alkali metal ions and the purity of a mass-selected methylated peptide ion.

Keywords: peptides, salt interference, metal ion adducts, methylation, charge localization, fragmentations

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