Preferred protonation: Does electrospray ionization mass spectrometry produce gas-phase or liquid-phase structures? The preferred protonation site in p-aminobenzoic acid depends upon the medium, and the structure of its conjugate acid varies with the solvent used during spraying.

Electrospray ionization of tyrosine from a 3:1 (v:v) CH3OH/H2O solution is found to afford an M - H ion which is a 70:30 mixture of phenoxide and carboxylate ions. This corresponds to the gas-phase equilibrium composition and not the liquid-phase proportions. In contrast, the carboxylate is produced as the dominant ion (approximately 95%) from anhydrous CH3CN and CH3CN/H2O mixtures. The addition of small amounts of CH3OH to the solvent, however, convert the M - H ion back into the gas-phase isomeric ratio. The isomeric structure therefore depends on the solvent system from which an ion is sprayed.

Post-translational modifications (PTMs) of core histones work synergistically to fine tune chromatin structure and function, generating a so-called histone code that can be interpreted by a variety of chromatin interacting proteins. We report a novel online two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) platform for high-throughput and sensitive characterization of histone PTMs at the intact protein level. The platform enables unambiguous identification of 708 histone isoforms from a single 2D LC-MS/MS analysis of 7.5 µg purified core histones. The throughput and sensitivity of comprehensive histone modification characterization is dramatically improved compared with more traditional platforms.