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PXD003033

PXD003033 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMultiplexed, Proteome-wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains
DescriptionCharacterizing a protein’s function often requires a description of the cellular state in its absence. Multiplexing in mass spectrometry-based proteomics has now achieved the ability to globally measure protein expression levels in yeast from 10 cell states simultaneously. We applied this approach to quantify expression differences in wild type and 9 deubiquitylating enzyme (DUB) knockout strains with the goal of creating “information networks” which might provide deeper, mechanistic insights into a protein’s biological role. In total, more than 3,700 proteins were quantified with high reproducibility across three biological replicates (30 samples in all). DUB mutants demonstrated different proteomics profiles, consistent with distinct roles for each family member. These included differences in total ubiquitin levels and specific chain linkages. Moreover, specific expression changes suggested novel functions for several DUB family members. For instance, the ubp3Δ mutant showed large expression changes for members of the cytochrome C oxidase complex, consistent with a role for Ubp3 in mitochondrial regulation. Several DUBs also showed broad expression changes for phosphate transporters as well as other components of the inorganic phosphate signaling pathway, suggesting a role for these DUBs in regulating phosphate metabolism. These data highlight the potential of multiplexed proteome-wide analyses for biological investigation and provide a framework for further study of the DUB family. Our methods are readily applicable to the entire collection of yeast deletion mutants, and may help facilitate systematic analysis of yeast and other organisms.
HostingRepositoryPRIDE
AnnounceDate2017-10-24
AnnouncementXMLSubmission_2017-10-24_05:51:09.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMarta Isasa
SpeciesList scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-10-12 01:51:00ID requested
12016-12-08 02:35:40announced
22017-10-24 05:51:10announcedUpdated project metadata.
Publication List
Isasa M, Rose CM, Elsasser S, Navarrete-Perea J, Paulo JA, Finley DJ, Gygi SP, Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains. J Proteome Res, 14(12):5306-17(2015) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: High throughput proteomics, quantitative proteomics, isobaric labeling, TMT, Orbitrap Fusion, deubiquitinases,UBP3, ubiquitin, COX complex, inorganic phosphate pathway.
Contact List
Steven P. Gygi
contact affiliationCell Biology Department Harvard Medical School
contact emailsteven_gygi@hms.harvard.edu
lab head
Marta Isasa
contact affiliationHarvard Medical School
contact emailmarta_isasa@hms.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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