PXD052370-1
PXD052370 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity |
| Description | The emerging popularity of single-cell sequencing technologies has revealed unexpected heterogeneity of chromatin states and gene expression in seemingly homogeneous cell populations. Similarly, single-cell proteomics has proven capable of quantifying heterogeneity of proteomes amongst single cells, yet, due to their low stoichiometry, it remains limited in investigating the heterogeneity of protein post-translational modifications (PTMs). Here, we present a robust mass spectrometry-based method for the unbiased analysis of hPTMs at single-cell level, in order to investigate the complex relationship between the regulation of epigenetic marks and cell identity. We show that our method can identify both single and combinatorial hPTMs (68 peptidoforms in total), which includes nearly all of the most studied hPTMs. Our single-cell method achieves technical reproducibility comparable to traditional bulk histone experiments, and distinguishes between technical noise and biological cell-to-cell variation of hPTM abundances. As a proof of concept, we treated cells with sodium butyrate, a histone deacetylase inhibitor, and demonstrate that our method can i) distinguish between treated and non-treated cells , ii) identify sub-populations of cells that respond differently to treatment, and iii) reveal how hPTM regulation differs in the context of drug treatment using covariation analysis. Overall, these experiments establish the applicability of our method to investigate chromatin heterogeneity at the single-cell level, which has important implications for understanding complex disease states like cancer and aging. This innovative method provides new opportunities for analyzing the histone code by utilizing cellular heterogeneity to uncover regulatory principles. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-10-07 |
| AnnouncementXML | Submission_2025-10-07_07:07:50.239.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Malvina |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Oxidation; Propionyl |
| Instrument | timsTOF Ultra |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-05-18 19:18:47 | ID requested | |
| ⏵ 1 | 2025-10-07 07:07:50 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: single cell, histones, post-translational modification, chromatin |
Contact List
| Simone Sidoli | |
|---|---|
| contact affiliation | Albert Einstein College of Medicine |
| contact email | simone.sidoli@einsteinmed.edu |
| lab head | |
| Malvina | |
| contact affiliation | Papanastasiou |
| contact email | malpap@broadinstitute.org |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v07/MSV000094801/ |
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