PXD004628

PXD004628 is an original dataset announced via ProteomeXchange.

Title	Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes
Description	Systems-wide quantitative analysis of ubiquitylomes has proven to be a valuable tool for elucidating targets and mechanisms of the ubiquitin-driven signaling systems, as well as gaining insights in neurodegenerative diseases and cancer. Current mass spectrometry methods for ubiquitylome detection require large amounts of starting material and rely on stochastic data collection to increase replicate analyses. We describe a method compatible with cell line and tissue samples for large-scale quantification of 5,000-9,000 ubiquitylation forms across ten samples simultaneously. Using this method we reveal site-specific ubiquitylation in mammalian brain and liver tissues, as well as in cancer cells undergoing proteasome inhibition. To demonstrate the power of the approach for signal-dependent ubiquitylation, we examined protein and ubiquitylation dynamics for mitochondria undergoing PARKIN and PINK1-dependent mitophagy. This analysis revealed the largest collection of PARKIN and PINK1-dependent ubiquitylation targets to date in a single experiment, and also revealed a subset of proteins recruited to the mitochondria during mitophagy.
HostingRepository	PRIDE
AnnounceDate	2016-10-10
AnnouncementXML	Submission_2016-10-10_01:01:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marta Isasa
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitination signature tetrapeptidyl lysine
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-21 03:09:59	ID requested
⏵ 1	2016-10-10 01:01:16	announced

Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP, Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. Cell Syst, 3(4):395-403.e4(2016) [pubmed]

submitter keyword: Ubiquitin, 10-plex TMT, Orbitrap Fusion Lumos Tribrid Mass Spectrometer, mouse, bortezomib, mithocondria

Steven P. Gygi
contact affiliation	Cell Biology Department Harvard Medical School
contact email	steven_gygi@HMS.HARVARD.EDU
lab head
Marta Isasa
contact affiliation	Harvard Medical School
contact email	marta_isasa@hms.harvard.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/2016/10/PXD004628

PRIDE project URI

• PRIDE
  1. PXD004628
     1. Label: PRIDE project
     2. Name: Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes