PXD017754

PXD017754 is an original dataset announced via ProteomeXchange.

Title	Proteomic Analysis of Ubiquitin Chain Types in Murine Cells and Tissues
Description	Mass spectrometry-based proteomics has become an integral approach for characterising ubiquitin chain-linkage compositions and architectures. In this study, we optimised sample preparation and chromatographic separation of Ubiquitin peptides for Absolute Quantification by Parallel Reaction Monitoring (Ub-AQUA-PRM). Using this refined Ub-AQUA-PRM assay, we were able to quantify all ubiquitin chain types in 10-minute LC-MS/MS runs. We used this method to determine the ubiquitin chain-linkage composition in murine bone marrow-derived macrophages (BMDMs) and different mouse tissues. We could show tissue-specific differences in ubiquitin levels in murine tissues, with polyubiquitin chain types contributing a small proportion to the total pool of ubiquitin. Interestingly, we observed enrichment of atypical ubiquitin chain types (K29 and K33) in heart and muscle. Ubiquitin chain topology profiling using tandem ubiquitin binding entities, directed at K29/K33 ubiquitin chains (TRABID), and mass spectrometry analysis identified several mitochondrial proteins as putatively associated with these atypical ubiquitin chain types. Our approach enabled high-throughput screening of ubiquitin chain-linkage composition in different murine tissues and highlighted a possible role for atypical ubiquitylation in contractile tissues. Our results contribute to our understanding of in vivo ubiquitin chain-linkage composition in murine tissues.
HostingRepository	PRIDE
AnnounceDate	2020-09-28
AnnouncementXML	Submission_2020-09-27_23:15:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthias Trost
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	ubiquitinylated lysine
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-26 23:05:14	ID requested
⏵ 1	2020-09-27 23:15:11	announced

Heunis T, Lamoliatte F, Mar, í, n-Rubio JL, Dannoura A, Trost M, Technical report: Targeted proteomic analysis reveals enrichment of atypical ubiquitin chains in contractile murine tissues. J Proteomics, 229():103963(2020) [pubmed]

submitter keyword: Parallel reaction monitoring, Absolute quantification, Ubiquitin chain-linkage composition, Murine tissues

Matthias Trost
contact affiliation	Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
contact email	matthias.trost@ncl.ac.uk
lab head
Matthias Trost
contact affiliation	Newcastle University
contact email	matthias.trost@ncl.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017754
     1. Label: PRIDE project
     2. Name: Proteomic Analysis of Ubiquitin Chain Types in Murine Cells and Tissues