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PXD027949

PXD027949 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProMetheus: a database of hmSILAC-validated protein methylation sites
DescriptionProtein 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:53:00.083.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterEnrico Massignani
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmethylated residue; trimethylated residue; dimethylated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-08-16 06:00:32ID requested
12022-06-02 18:11:28announced
22023-11-14 08:53:05announced2023-11-14: 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 affiliationEuropean Institute of Oncology IRCCS, 20139 Milan, Italy
contact emailtiziana.bonaldi@ieo.it
lab head
Enrico Massignani
contact affiliationEuropean Institute of Oncology IRCSS, Department of Experimental Oncology, Milan, Italy
contact emailenrico.massignani@ieo.it
dataset submitter
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Dataset FTP location
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