PXD015208-2

PXD015208 is an original dataset announced via ProteomeXchange.

Title	Middle-down proteomics reveals RNA binding proteins harbor dense sites of methylation and phosphorylation
Description	Arginine (Arg)-rich RNA-binding proteins play an integral role in RNA metabolism. Post-translational modifications (PTMs) within Arg-rich domains, such as phosphorylation and methylation, regulate multiple steps in RNA metabolism. However, the identification of PTMs within Arg-rich domains with complete trypsin digestion is extremely challenging due to the high density of Arg residues within these proteins. Here, we leveraged a middle-down proteomic approach coupled with electron transfer dissociation (ETD) mass spectrometry to map previously unknown sites of phosphorylation and methylation within the Arg-rich domains of U1-70K and structurally similar RNA binding proteins. From nuclear extracts of HEK293 cells, we achieved coverage of 29,114 residues and identified 681 PTMs currently unannotated in database repositories. Remarkably, the Arg-rich domains in RNA binding proteins are densely modified by methylation and phosphorylation compared with the remainder of the proteome, with methylation and phosphorylation often jointly occurring in Arg-rich peptides within RSRS motifs. Although they share a common motif, phosphorylation and methylation may oppose one another. Collectively, these findings suggest that the level of PTMs within Arg-rich domains may be among the highest in the proteome, and a possible unexplored regulator of RNA metabolism. These data also serve as a resource to facilitate future mechanistic studies of these PTMs in RNA binding protein structure and function.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:58:28.392.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eric Dammer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; phosphorylated residue; dimethylated residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-29 03:36:52	ID requested
1	2020-01-31 02:32:31	announced
⏵ 2	2024-10-22 04:58:29	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.9b00633;

Kundinger SR, Bishof I, Dammer EB, Duong DM, Seyfried NT, Middle-Down Proteomics Reveals Dense Sites of Methylation and Phosphorylation in Arginine-Rich RNA-Binding Proteins. J Proteome Res, 19(4):1574-1591(2020) [pubmed]

submitter keyword: middle-down, RS protein,ETD, decision tree, basic-acidic domains

Nicholas T. Seyfried
contact affiliation	Emory University School of Medicine Departments of Biochemistry and Neurology
contact email	nseyfri@emory.edu
lab head
Eric Dammer
contact affiliation	Emory University
contact email	edammer@emory.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015208
     1. Label: PRIDE project
     2. Name: Middle-down proteomics reveals RNA binding proteins harbor dense sites of methylation and phosphorylation