PXD041271

PXD041271 is an original dataset announced via ProteomeXchange.

Title	Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics
Description	Phosphotyrosine (pY) enrichment is critical for expanding fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY can handle up to 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic and tyrosine-specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:34.502.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD041271
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexis Chang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-01 15:50:34	ID requested
1	2023-05-05 15:39:19	announced
⏵ 2	2023-11-14 08:45:35	announced	2023-11-14: Updated project metadata.

10.6019/PXD041271;

Chang A, Leutert M, Rodriguez-Mias RA, Vill, é, n J, Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. J Proteome Res, 22(6):1868-1880(2023) [pubmed]

submitter keyword: HeLa, LC-MSMS, KingFisher, Orbitrap Eclipse, Orbitrap Exploris 480, Phosphotyrosine enrichment

Judit Villen
contact affiliation	Villen Lab, Department of Genome Sciences, University of Washington. Seattle, WA, USA.
contact email	jvillen@uw.edu
lab head
Alexis Chang
contact affiliation	University of Washington
contact email	alexisn1@uw.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/2023/05/PXD041271

PRIDE project URI

• PRIDE
  1. PXD041271
     1. Label: PRIDE project
     2. Name: Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics