Histone Coder

Histone Coder maps and quantifies coexisting post-translational modifications (PTMs) on 5–7 kDa polypeptides using middle-down LC/MS/MS to resolve combinatorial histone marks.

Key Features:

• High mass-accuracy MS/MS analysis: Utilizes electron transfer dissociation (ETD) coupled with high mass-accuracy electrospray ionization (ESI) MS/MS to generate fragmentation patterns for PTM localization.
• Chromatographic separation: Integrates a reversed-phase (RP) trap column followed by weak cation exchange-hydrophilic interaction liquid chromatography (LC) to separate hypermodified histone N-terminal tails.
• Comprehensive data extraction and analysis: Extracts, filters, and analyzes MS/MS data with a focus on quantifying cofragmenting isobaric polypeptide species.
• Quantification of combinatorial marks: Quantifies combinatorial PTMs across histones, reporting 256 combinatorial histone marks across H3, H4, and H2A and identifying 713 different combinatorial marks in purified histone H3.
• Application to genetic perturbations: Measures PTM abundance changes such as the seven-fold reduction in H3K27me2/me3 observed in Suz12(-/-) murine embryonic stem cells.

Scientific Applications:

• Epigenetics research: Quantitative analysis of combinatorial histone PTMs to study gene regulation and chromatin dynamics.
• Middle-down proteomics: Analysis of 5–7 kDa histone polypeptides using LC/MS/MS to retain combinatorial modification information.
• Proteomics quantification: Resolution and quantification of cofragmenting isobaric species and combinatorial marks across histones H3, H4, and H2A.
• Functional genomics: Assessment of PTM changes in genetically modified cells, exemplified by Suz12 knockout effects on H3K27 methylation.

Methodology:

Extracts, filters, and analyzes MS/MS spectra to quantify cofragmenting isobaric polypeptide species and relative abundances of combinatorial PTMs.