PXD076372-1

PXD076372 is an original dataset announced via ProteomeXchange.

Title	Methylation in the human proteome: A meta-analysis of publicly available data sets
Description	Lysine and arginine methylation are fundamental post-translational modifications (PTMs) that can regulate biological processes such as chromatin dynamics, transcriptional activity, and cellular signaling, with misregulation implicated in cancer and neurodevelopmental disorders. While advances in mass spectrometry (MS)-based proteomics have enabled proteome-wide mapping of methylation sites, the confident detection and localization of these modifications remains challenging. In this study, we have reanalyzed publicly available human methylation-enriched datasets using a standardized computational pipeline, to generate a high-confidence atlas of human methylation. Our workflow integrates database searching via the Trans-Proteomic Pipeline with a decoy-based statistical method for the independent estimation of false localization rates. This process yielded a high-confidence Human Methylation Atlas of 1,858 sites (87 methyl-lysine, 1,771 methyl-arginine) across 1,068 proteins, classified into Gold, Silver, and Bronze confidence tiers.
HostingRepository	PRIDE
AnnounceDate	2026-06-09
AnnouncementXML	Submission_2026-06-09_03:48:22.599.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shengbo Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	methylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-31 06:28:34	ID requested
⏵ 1	2026-06-09 03:48:23	announced

Dataset with its publication pending

submitter keyword: Human, Reanalysis, Methylation

Juan Antonio Vizcaino
contact affiliation	EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
contact email	juan@ebi.ac.uk
lab head
Shengbo Wang
contact affiliation	EMBL-EBI
contact email	shengbo_wang@ebi.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD076372
     1. Label: PRIDE project
     2. Name: Methylation in the human proteome: A meta-analysis of publicly available data sets