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PXD016192

PXD016192 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTandem Mass Tag approach utilizing pervanadate BOOST channels delivers deeper quantitative characterization of the tyrosine phosphoproteome
DescriptionDynamic 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:50:52.300.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterXien Yu Chua
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-11-07 08:31:30ID requested
12020-02-24 01:32:12announced
22020-05-27 04:20:36announced2020-05-27: Updated publication reference for PubMed record(s): 32071147.
2020-05-27: Updated publication reference for DOI(s): 10.1074/mcp.TIR119.001865.
32023-11-14 08:50:53announced2023-11-14: Updated project metadata.
Publication List
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]
Keyword List
submitter keyword: superbinder, trigger channel, phosphotyrosine proteomics,Tandem mass tags, pervanadate
Contact List
Arthur Salomon
contact affiliationDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
contact emailart@drsalomon.com
lab head
Xien Yu Chua
contact affiliationBrown University
contact emailxien_yu_chua@brown.edu
dataset submitter
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Dataset FTP location
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PRIDE project URI
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