Dataset Information

Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Brain, Liver, Cell Culture

SUBMITTER: Marta Isasa

LAB HEAD: Steven P. Gygi

PROVIDER: PXD004628 | Pride | 2016-10-10

REPOSITORIES: Pride

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Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes.

Rose Christopher M CM Isasa Marta M Ordureau Alban A Prado Miguel A MA Beausoleil Sean A SA Jedrychowski Mark P MP Finley Daniel J DJ Harper J Wade JW Gygi Steven P SP

Cell systems 20160922 4

System-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 into 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 quant ...[more]

PMID: 27667366

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