PXD027949
PXD027949 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | ProMetheus: a database of hmSILAC-validated protein methylation sites |
| Description | Protein arginine (R) methylation is a post-translational modification that has been shown to play a role in various biological processes, such as RNA splicing, DNA repair, immune response, signal transduction and tumor development. Here, we present a dataset of high-quality methylations obtained from several different heavy methyl SILAC (hmSILAC) experiments analyzed with a machine learning model that was trained to recognize hmSILAC doublets and show that this model allows for improved high-confidence identification of methyl-peptides. The results of our analysis of the interactions between R-methylated proteins further support the idea that this modification plays a role in modulating protein:protein interactions and suggest a potential new role of R methylation in immunity and macrophage metabolism. Moreover, we intersect the methyl-site dataset with a phosphosite dataset to investigate the cross-talk between R methylation and phosphorylation. Finally, we explore the application of hmSILAC to identify unconventional methylated residues on both histone and non-histone proteins. |
| HostingRepository | PRIDE |
| AnnounceDate | 2023-11-14 |
| AnnouncementXML | Submission_2023-11-14_08:53:00.083.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Enrico Massignani |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | methylated residue; trimethylated residue; dimethylated residue |
| Instrument | Q Exactive HF |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2021-08-16 06:00:32 | ID requested | |
| 1 | 2022-06-02 18:11:28 | announced | |
| ⏵ 2 | 2023-11-14 08:53:05 | announced | 2023-11-14: Updated project metadata. |
Publication List
| Musiani D, Giambruno R, Massignani E, Ippolito MR, Maniaci M, Jammula S, Manganaro D, Cuomo A, Nicosia L, Pasini D, Bonaldi T, PRMT1 Is Recruited via DNA-PK to Chromatin Where It Sustains the Senescence-Associated Secretory Phenotype in Response to Cisplatin. Cell Rep, 30(4):1208-1222.e9(2020) [pubmed] |
| Spadotto V, Giambruno R, Massignani E, Mihailovich M, Maniaci M, Patuzzo F, Ghini F, Nicassio F, Bonaldi T, PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic Acids Res, 48(1):96-115(2020) [pubmed] |
| Fong JY, Pignata L, Goy PA, Kawabata KC, Lee SC, Koh CM, Musiani D, Massignani E, Kotini AG, Penson A, Wun CM, Shen Y, Schwarz M, Low DH, Rialdi A, Ki M, Wollmann H, Mzoughi S, Gay F, Thompson C, Hart T, Barbash O, Luciani GM, Szewczyk MM, Wouters BJ, Delwel R, Papapetrou EP, Barsyte-Lovejoy D, Arrowsmith CH, Minden MD, Jin J, Melnick A, Bonaldi T, Abdel-Wahab O, Guccione E, Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation. Cancer Cell, 36(2):194-209.e9(2019) [pubmed] |
| Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T, Proteomics profiling of arginine methylation defines PRMT5 substrate specificity. Sci Signal, 12(575):(2019) [pubmed] |
| Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T, Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. Mol Biosyst, 9(9):2231-47(2013) [pubmed] |
Keyword List
| submitter keyword: heavy methyl SILAC, SILAC,Methylation |
Contact List
| Tiziana Bonaldi | |
|---|---|
| contact affiliation | European Institute of Oncology IRCCS, 20139 Milan, Italy |
| contact email | tiziana.bonaldi@ieo.it |
| lab head | |
| Enrico Massignani | |
| contact affiliation | European Institute of Oncology IRCSS, Department of Experimental Oncology, Milan, Italy |
| contact email | enrico.massignani@ieo.it |
| dataset submitter | |
Full Dataset Link List
| 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://ftp.pride.ebi.ac.uk/pride/data/archive/2022/06/PXD027949 |
| PRIDE project URI |
Repository Record List
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