PXD016192

PXD016192 is an original dataset announced via ProteomeXchange.

Title	Tandem Mass Tag approach utilizing pervanadate BOOST channels delivers deeper quantitative characterization of the tyrosine phosphoproteome
Description	Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers’ ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, a novel method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of trigger channels – cells treated with the promiscuous tyrosine phosphatase inhibitor pervanadate (PV) – selectively increased the relative abundance of pTyr-containing peptides. After PV facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered sensitive quantitation of each peptide for the experimental samples while the quantitation from PV trigger channels was ignored. This method yielded up to 6.3-fold boost in quantification depth of statistically significant data derived from contrived ratios, compared to TMT without trigger channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The trigger channel strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly boost the levels of those modifications across the proteome are available.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:52.300.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xien Yu Chua
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-07 08:31:30	ID requested
1	2020-02-24 01:32:12	announced
2	2020-05-27 04:20:36	announced	2020-05-27: Updated publication reference for PubMed record(s): 32071147. 2020-05-27: Updated publication reference for DOI(s): 10.1074/mcp.TIR119.001865.
⏵ 3	2023-11-14 08:50:53	announced	2023-11-14: Updated project metadata.

Chua XY, Mensah T, Aballo T, Mackintosh SG, Edmondson RD, Salomon AR, Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome. Mol Cell Proteomics, 19(4):730-743(2020) [pubmed]

submitter keyword: superbinder, trigger channel, phosphotyrosine proteomics,Tandem mass tags, pervanadate

Arthur Salomon
contact affiliation	Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
contact email	art@drsalomon.com
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/2020/03/PXD016192

PRIDE project URI

• PRIDE
  1. PXD016192
     1. Label: PRIDE project
     2. Name: Tandem Mass Tag approach utilizing pervanadate BOOST channels delivers deeper quantitative characterization of the tyrosine phosphoproteome