PXD017193

PXD017193 is an original dataset announced via ProteomeXchange.

Title	Improved discrimination of asymmetric and symmetric protein arginine dimethylation by optimizing the normalized collision energy in LC-MS proteomics
Description	Here we optimize the HCD Normalized Collision Energy (NCE) in order to generate neutral losses of monomethylamine and dimethylamine which can be lost by symmetric dimethylarginine and asymmetric dimethylarginine, respectively. By testing a range of NCEs across two different methyl enrichment techniques, we identified the optimal NCE as 32 to both generate neutral losses and to improve identifications of dimethyl PSMs. We achieve a 2-to-3 fold increase in the number of unique DMA peptides assigned neutral losses desginating them as ADMA or SDMA. This method will be useful to others interested in analyzing dimethylarginine peptides through mass spectrometry, where ADMA and SDMA have identical masses but differing neutral losses, and differing biological functions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:05:59.040.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Hartel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	asymmetric dimethyl-L-arginine; monomethylated residue; symmetric dimethyl-L-arginine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-20 02:56:41	ID requested
1	2020-05-26 16:36:43	announced
⏵ 2	2024-10-22 05:06:07	announced	2024-10-22: Updated project metadata.

Hartel NG, Liu CZ, Graham NA, Improved Discrimination of Asymmetric and Symmetric Arginine Dimethylation by Optimization of the Normalized Collision Energy in Liquid Chromatography-Mass Spectrometry Proteomics. J Proteome Res, 19(8):3123-3129(2020) [pubmed]

10.1021/acs.jproteome.0c00116;

submitter keyword: arginine, PRMT, Mass Spectrometry, methylation, ADMA, PTM, HCD, neutral loss, Proteomics, SDMA,LCMS

Nicholas A. Graham
contact affiliation	Mork Family Dept of Chem Eng and Mat Sci
contact email	nagraham@usc.edu
lab head
Nicolas Hartel
contact affiliation	USC
contact email	nhartel@usc.edu
dataset submitter

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/2020/05/PXD017193

PRIDE project URI

• PRIDE
  1. PXD017193
     1. Label: PRIDE project
     2. Name: Improved discrimination of asymmetric and symmetric protein arginine dimethylation by optimizing the normalized collision energy in LC-MS proteomics