PXD025853

PXD025853 is an original dataset announced via ProteomeXchange.

Title	Mice primary T cell phosphotyrosine proteomics enabled by BOOST
Description	Signal propagation mediating numerous cellular processed in T cells is orchestrated by tyrosine phosphorylation with a high degree of regulation1, 2. Because aberrant tyrosine phosphorylation can result in many diseases3, a method to systematically quantify this dynamic process can be helpful in understanding the mechanistic underpinnings of T cell functions. However, accurate quantitation of tyrosine phosphorylation is challenging due to its low abundance4. Mass spectrometry(MS) based phosphotyrosine proteomics has emerged to be an attractive solution for wide scale profiling of the tyrosine phosphoproteome5, 6. Many advances have been made in this field to improve the enrichment efficiency of phosphotyrosine(pTyr)-containing peptides to improve the coverage depth7-11. Separately, computational methods of Fourier transform-(FT)MS such as an Orbitrap analyzer have also made significantly progress in the quantitation of TMT samples. For example, the phase-constrained spectrum deconvolution method (ΦSDM) have been shown to substantially improve the spectral quality and speed of FT-MS instruments12. ΦSDM deconvolves FT spectra into frequency distributions to allow more efficient extraction of the harmonic components of the oscillating ions12. As a result, higher mass resolution and accuracy can be achieved with shorter transient times12. We recently developed the BOOST approach by coupling PV boost channel in a multiplexed TMT approach to significantly increase the quantitative depth of the tyrosine phosphoproteome13. While it has been shown to work in Jurkat cell line, it has not been demonstrated to work in scarce mice primary T cells. Here, we demonstrate the first phosphotyrosine proteomics performed in mice primary T cells using BOOST that enabled the identification of more than 6000 pTyr peptides using only 1 mg of protein. We further demonstrated the importance of ΦSDM, in which when disabled, enabled significantly deeper quantitation depth in low-abundance samples. Using samples with contrived ratios, disabling ΦSDM improved the precision of low-abundance peptides and allowed the quantitation of up to 2-fold more increase in statistically significant ratios.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:22:40.389.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xien Yu Chua
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-06 23:41:56	ID requested
1	2021-06-03 20:26:13	announced
⏵ 2	2024-10-22 05:22:40	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: T cell, BOOST, phosphotyrosine proteomics, TMT,Mice

Arthur Salomon
contact affiliation	Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
contact email	arthur_salomon@brown.edu
lab head
Xien Yu Chua
contact affiliation	Brown University
contact email	xien_yu_chua@brown.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/2021/06/PXD025853

PRIDE project URI

• PRIDE
  1. PXD025853
     1. Label: PRIDE project
     2. Name: Mice primary T cell phosphotyrosine proteomics enabled by BOOST