PXD058995-1

PXD058995 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic Profiling Reveals Functional Microproteins in T Cells
Description	Noncanonical micropeptides, i.e., polypeptides mostly under 10 kDa, are encoded by genomic sequences that have been previously annotated as noncoding but now known as small open reading frames (sORFs). The recent identification of microproteins encoded by sORFs has provided evidence that many sORFs encode functional microproteins that play crucial roles in various biological processes. T cell activation is a critical biological process for adaptive immune response. Understanding key players in this process will allow us to decipher the complex mechanisms as well as develop immunotherapy for treating a wide range of diseases. Although there have been extensive studies on canonical proteins in T cell activation, the microproteins in T cells and their roles have been uncharted water to date. In this study, we combined nascent proteomics and quantitative proteomics to identify 411 novel microproteins in primary human T cells, including 83 nascent microproteins that are defined as newly synthesized polypeptides emerged during the translation of mRNA. We activated the T cell function with either PMA/Ionomycin (distal activation) or CD3/CD28 activating antibodies (proximal activation), and obtained a comprehensive canonical protein and microprotein profiles to pinpoint common and distinct differentially expressed proteins under these two activation conditions. After experimental testing, three microproteins numbered T1, T2 and T3 were found to be functional in regulating T cell activation. Bioinformatic and proteomic analyses suggested that T1 was functional related to immune as negative feedback to T cell activation. Our study not only established an integrated approach to uncover and elucidate novel microproteins but also highlight the significant role of microproteins in regulating T cell activation.
HostingRepository	PRIDE
AnnounceDate	2025-08-04
AnnouncementXML	Submission_2025-08-03_19:09:17.028.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD058995
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Tianyang Zhu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-18 07:49:56	ID requested
⏵ 1	2025-08-03 19:09:17	announced

10.1016/j.mcpro.2025.100914;

Yang Y, Chen C, Li K, Zhang Y, Chen L, Shi J, Mu Q, Xu Y, Zhao Q, Proteogenomics Reveals Microproteins in Activated T Cells. Mol Cell Proteomics, 24(6):100914(2025) [pubmed]

10.6019/PXD058995;

submitter keyword: proteomics,T cell activation, microprotein

Yang Yang
contact affiliation	The Hong Kong Polytechnic University
contact email	yangss.yang@connect.polyu.hk
lab head
Tianyang Zhu
contact affiliation	Hong Kong Polytechnical University
contact email	tianyang.zhu@connect.polyu.hk
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/2025/08/PXD058995

PRIDE project URI

• PRIDE
  1. PXD058995
     1. Label: PRIDE project
     2. Name: Proteogenomic Profiling Reveals Functional Microproteins in T Cells