ArticleJournal of proteome research2018
EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed, 190 citations in OpenAlex.
- Antagonistic roles of histone H3 lysine methyltransferases dictate tumor immune surveillance.Nature communications · 2026Article
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- The glycine N-methyltransferase amino-terminus regulates folate-dependent feedback inhibition and S-adenosylmethionine homeostasis.The Journal of biological chemistry · 2026Article
- Depletion of CARM1 slows in vivo tumorigenicity and rewires developmental programming in glioma stem-like cells.Cell reports · 2026Article
- MPOInt: An Epigenetics-Driven Workflow for Integrative Multi-Level Proteomics.Journal of proteome research · 2026Article
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- Rapid Histone Post-Translational Modification Analysis Using Alternative Proteases and Tandem Mass Tags.Analytical chemistry · 2026Article
- Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation.The Journal of biological chemistry · 2026Article
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- Histone succinylation directly inhibits Jumonji domain demethylases and stabilizes repressive chromatin states.bioRxiv : the preprint server for biology · 2026Article
- Glucose-dependent spatial and temporal modulation of oligodendrocyte progenitor cell proliferation via ACLY-regulated histone acetylation.Nature neuroscience · 2026Article
- Rapid Histone Post-Translational Modification Analysis Using Alternative Proteases and Tandem Mass Tags.bioRxiv : the preprint server for biology · 2026Article
- The GNMT N-terminus Couples Folate Feedback to Methyl-donor Homeostasis.bioRxiv : the preprint server for biology · 2026Article
- dCas9-metabolic enzyme fusions modulate global and locus-specific gene expression.bioRxiv : the preprint server for biology · 2026Article
- Long-term maintenance of H3K27me3 in postmitotic neurons is dispensable for gene expression regulation.bioRxiv : the preprint server for biology · 2026Article
- TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency.Cell stem cell · 2026Article
- NSD2 upregulation is driven by high-risk HPV E6/E7 and disrupts epithelial differentiation in HPV-associated head and neck cancer.Journal of experimental & clinical cancer research : CR · 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
- Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity.Nature communications · 2025Article
64 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here we present EpiProfile 2.0, an extended version of our 2015 software (v1.0), for accurate quantification of histone peptides based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. EpiProfile 2.0 is now optimized for data-independent acquisition through the use of precursor and fragment extracted ion chromatography to accurately determine the chromatographic profile and to discriminate isobaric forms of peptides. The software uses an intelligent retention time prediction trained on the analyzed samples to enable accurate peak detection. EpiProfile 2.0 supports label-free and isotopic labeling, different organisms, known sequence mutations in diseases, different derivatization strategies, and unusual PTMs (such as acyl-derived modifications). In summary, EpiProfile 2.0 is a universal and accurate platform for the quantification of histone marks via LC-MS/MS. Being the first software of its kind, we anticipate that EpiProfile 2.0 will play a fundamental role in epigenetic studies relevant to biology and translational medicine. EpiProfile is freely available at https://github.com/zfyuan/EpiProfile2.0_Family .
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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.