ArticleJournal of proteome research2015
Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry.
Article in Journal of proteome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
37 citing papers in PubMed, 70 citations in OpenAlex.
- Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone-specific acetylation changes.Cell reports · 2026Article
- Proteomic Analysis of Histone Sequence Variants and Post-translationally Modified Forms.Advances in experimental medicine and biology · 2026Review
- Mass Spectrometry Quantification of Epigenetic Changes: A Scoping Review for Cancer and Beyond.International journal of molecular sciences · 2025Article
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- An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications.Journal of the American Society for Mass Spectrometry · 2023Article
- Identification of Cofragmented Combinatorial Peptide Isomers by Two-Dimensional Partial Covariance Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2023Article
- Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions.Mycology · 2023Review
- Proteomic characterization of post-translational modifications in drug discovery.Acta pharmacologica Sinica · 2022Review
- Histone Acid Extraction and High Throughput Mass Spectrometry to Profile Histone Modifications in Arabidopsis thaliana.Current protocols · 2022Article
- Mass spectrometry-based characterization of histones in clinical samples: applications, progress, and challenges.The FEBS journal · 2022Review
- Article
- Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.Cell host & microbe · 2021Article
- PTMViz: a tool for analyzing and visualizing histone post translational modification data.BMC bioinformatics · 2021Article
- Gut microbiome variation modulates the effects of dietary fiber on host metabolism.Microbiome · 2021Article
- Biological and catalytic functions of sirtuin 6 as targets for small-molecule modulators.The Journal of biological chemistry · 2020Review
- Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails.Journal of the American Society for Mass Spectrometry · 2019Article
- On top of biosynthetic gene clusters: How epigenetic machinery influences secondary metabolism in fungi.Biotechnology advances · 2019Review
- Comparison of data-acquisition methods for the identification and quantification of histone post-translational modifications on a Q Exactive HF hybrid quadrupole Orbitrap mass spectrometer.Rapid communications in mass spectrometry : RCM · 2019Article
- Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model.Nature microbiology · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Histone post-translational modifications (PTMs) are important regulators of chromatin structure and gene expression. Quantitative analysis of histone PTMs by mass spectrometry remains extremely challenging due to the complex and combinatorial nature of histone PTMs. The most commonly used mass spectrometry-based method for high-throughput histone PTM analysis is data-dependent acquisition (DDA). However, stochastic precursor selection and dependence on MS1 ions for quantification impede comprehensive interrogation of histone PTM states using DDA methods. To overcome these limitations, we utilized a data-independent acquisition (DIA) workflow that provides superior run-to-run consistency and postacquisition flexibility in comparison to DDA methods. In addition, we developed a novel DIA-based methodology to quantify isobaric, co-eluting histone peptides that lack unique MS2 transitions. Our method enabled deconvolution and quantification of histone PTMs that are otherwise refractory to quantitation, including the heavily acetylated tail of histone H4. Using this workflow, we investigated the effects of the histone deacetylase inhibitor SAHA (suberoylanilide hydroxamic acid) on the global histone PTM state of human breast cancer MCF7 cells. A total of 62 unique histone PTMs were quantified, revealing novel SAHA-induced changes in acetylation and methylation of histones H3 and H4.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.