ArticleJournal of the American Society for Mass Spectrometry2019
Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails.
Article in Journal of the American Society for Mass Spectrometry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- Histone modification cross-talk: analytical tools and molecular mechanisms.The Biochemical journal · 2026Review
- Biochemistry and regulation of histone lysine L-lactylation.Nature reviews. Molecular cell biology · 2026Review
- Mass Spectrometry Quantification of Epigenetic Changes: A Scoping Review for Cancer and Beyond.International journal of molecular sciences · 2025Article
- Circular Engineered Sortase for Interrogating Histone H3 in Chromatin.Journal of the American Chemical Society · 2024Article
- Optimized and Robust Workflow for Quantifying the Canonical Histone Ubiquitination Marks H2AK119ub and H2BK120ub by LC-MS/MS.Journal of proteome research · 2024Article
- A circular engineered sortase for interrogating histone H3 in chromatin.bioRxiv : the preprint server for biology · 2024Article
- A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms.Journal of proteome research · 2024Article
- Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins.EMBO reports · 2024Review
- Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation.Nature communications · 2024Article
- An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS.bioRxiv : the preprint server for biology · 2024Article
- Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3.Protein science : a publication of the Protein Society · 2023Article
- Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation.Epigenetics & chromatin · 2023Article
- Uncovering the impacts of alternative splicing on the proteome with current omics techniques.Wiley interdisciplinary reviews. RNA · 2022Review
- An Improved Top-Down Mass Spectrometry Characterization ofJournal of the American Society for Mass Spectrometry · 2021Article
- Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases.Journal of the American Society for Mass Spectrometry · 2021Article
- Lysines Acetylome and Methylome Profiling of H3 and H4 Histones in Trichostatin A-Treated Stem Cells.International journal of molecular sciences · 2021Article
- Trimethylacetic Anhydride-Based Derivatization Facilitates Quantification of Histone Marks at the MS1 Level.Molecular & cellular proteomics : MCP · 2021Article
- The Chemical Biology of Reversible Lysine Post-translational Modifications.Cell chemical biology · 2020Review
- High-Throughput Quantitative Top-Down Proteomics: Histone H4.Journal of the American Society for Mass Spectrometry · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has been critical to the advancement of the field of epigenetics. The most sensitive and accurate workflow is similar to the canonical proteomics analysis workflow (bottom-up MS), where histones are digested into short peptides (4-20 aa) and quantitated in extracted ion chromatograms. However, this limits the ability to detect even very common co-occurrences of modifications on histone proteins, preventing biological interpretation of PTM crosstalk. By digesting with GluC rather than trypsin, it is possible to produce long polypeptides corresponding to intact histone N-terminal tails (50-60 aa), where most modifications reside. This middle-down MS approach is used to study distant PTM co-existence. However, the most sensitive middle-down workflow uses weak cation exchange-hydrophilic interaction chromatography (WCX-HILIC), which is less robust than conventional reversed-phase chromatography. Additionally, since the buffer systems for middle-down and bottom-up proteomics differ substantially, it is cumbersome to toggle back and forth between both experimental setups on the same LC system. Here, we present a new workflow using porous graphitic carbon (PGC) as a stationary phase for histone analysis where bottom-up and middle-down sized histone peptides can be analyzed simultaneously using the same reversed-phase buffer setup. By using this protocol for middle-down sized peptides, we identified 406 uniquely modified intact histone tails and achieved a correlation of 0.85 between PGC and WCX-HILIC LC methods. Together, our method facilitates the analysis of single and combinatorial histone PTMs with much simpler applicability for conventional proteomics labs than the state-of-the-art middle-down MS.
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Registered trials
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