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PXD013453-2

PXD013453 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleR2-P2 rapid-robotic phosphoproteomics enables multidimensional cell signaling studies
DescriptionRecent developments in mass spectrometry-based proteomics have enabled systems-level studies of cellular signaling, where >10,000 phosphosites can be routinely identified and quantified. Yet, current analyses are limited in throughput, reproducibility, and robustness, hampering experiments that involve multiple perturbations, such as those needed to map kinase-substrate relationships, capture pathway crosstalks, and network inference analysis. To address these challenges and fully exploit the potential of phosphoproteomics, we introduce rapid-robotic-phosphoproteomics (R2-P2), an end-to-end automated method that processes samples in a 96-well format, from a protein extract to mass spectrometry-ready phosphopeptides. R2-P2 uses magnetic particles for both protein sample cleanup and phosphopeptide enrichment. R2-P2 is more flexible, high-throughput, rapid, and robust than classical protocols. To showcase the method, we have applied it, in combination with data-independent acquisition mass spectrometry, to study signaling dynamics in the mitogen-activated protein kinase (MAPK) pathway in the yeast model Saccharomyces cerevisiae. Our results reveal broad and specific signaling events along the mating, the high-osmolarity glycerol, and the invasive growth branches of the MAPK pathway, with robust phosphorylation of downstream regulatory proteins and transcription factors. Our method greatly facilitates large-scale signaling studies involving hundreds of perturbations and will open the door to systems-level studies aiming to capture the complexity of signaling.
HostingRepositoryPRIDE
AnnounceDate2019-12-12
AnnouncementXMLSubmission_2022-01-07_05:19:08.087.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMario Leutert
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListphosphorylated residue
InstrumentOrbitrap Fusion Lumos; Q Exactive; Q Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-04-11 00:05:31ID requested
12019-12-12 07:54:00announced
22022-01-07 05:19:08announced2022-01-07: Updated publication reference for DOI(s): 1015252/msb.20199021.
32023-11-14 07:43:33announced2023-11-14: Updated project metadata.
Publication List
1015252/msb.20199021;
Keyword List
curator keyword: Biological
submitter keyword: phosphoproteomics / signaling / MAPK / mass spectrometry / SP3 / DIA/ R2-P2
Contact List
Judit Villén
contact affiliationDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA
contact emailjvillen@uw.edu
lab head
Mario Leutert
contact affiliationDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA
contact emailmarioleutert@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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