Discrimination Effects in MALDI-MS of Mixtures of Peptides—Analysis of the Proteome

Abstract

Peptide ion suppression in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) can hinder the detection of site-specific post-translational protein modifications. Within a peptide mixture, the presence or absence of a particular peptide can affect the ion intensities of other peptides in the mixture. These effects have been studied using equimolar solutions of target peptides and observation of the increase or decrease in ion intensity of the peptides upon the removal or addition of individual peptides. Gas-phase basicities and hydrophobicity measures have been used to rationalize this behaviour. ZipTips have been used to remove impurities and reduce the number of peptides present at any moment in a solution, a procedure that results in a significant increase in the total percentage of the amino acid coverage of enzymatically digested proteins. The efficacy of this approach was demonstrated using specifically nitrated lysozyme and specifically nitrated myoglobin.