We present a novel approach to quantify isomeric peptides from histones H3 and H4. Tryptic digestion of histones typically produces isomeric peptides that cannot be resolved by reverse-phase chromatography, and give rise to mixed MS/MS spectra containing several common fragment ions. Here, we describe a new approach that combines a high resolution LC-MS/MS analysis with a novel bioinformatics tool to deconvolute composite spectra derived from a mixture of acetylated isomers and determine site-specific acetylation stoichiometry. This method improves existing techniques enabling the study of histone acetylation dynamics and its role in chromatin biology.
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