PXD034275

PXD034275 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	In-depth Analysis of the Sirtuin 5-regulated Mouse Brain Acylome using Library-free Data-Independent Acquisitions
Description	Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through combinatory effects of multiple PTMs. Lysine residues are targeted for various PTMs, including malonylation and succinylation. Due to specific challenges of PTM mass spectrometry-based proteomics encountered during data acquisition and processing, novel and innovative workflows have emerged using data-independent acquisition (DIA) to ensure confident PTM identification, precise site localization, and accurate and robust label-free quantification. In this study, we present a powerful approach combining antibody-based enrichment with comprehensive DIA acquisitions and spectral library-free data processing using directDIA (Spectronaut). The identical DIA data can be used to generate spectral libraries and to comprehensively identify and quantify PTMs, reducing the amount of enriched sample needed, and acquisition time, while offering a fully automated workflow. We analyzed brains from wild-type and Sirtuin 5 (SIRT5)-knock out mice, and discovered and quantified 466 malonylated and 2,211 succinylated peptides. SIRT5 regulation remodeled the acylomes, by targeting 171 malonylated and 640 succinylated sites. Affected pathways included carbohydrate and lipid metabolisms, synaptic vesicle cycle, and neurodegenerative diseases. We revealed 46 common SIRT5-regulated malonylation and succinylation sites, suggesting potential PTM crosstalk. This innovative and efficient workflow offers deeper insights into the mouse brain lysine malonylome and succinylome.
HostingRepository	MassIVE
AnnounceDate	2022-12-14
AnnouncementXML	Submission_2022-12-14_15:31:48.484.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joanna Bons
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Succinyl:13C(4); N6-malonyl-L-lysine
Instrument	Orbitrap Eclipse

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-04 20:40:35	ID requested
⏵ 1	2022-12-14 15:31:48	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Acylome, Brain, Data-independent acquisition, Post-translational modifications, Sirtuin

submitter keyword: Acylome, Brain, Data-independent acquisition, Post-translational modifications, Sirtuin

Contact List

Birgit Schilling
contact affiliation	Buck Institute
contact email	bschilling@buckinstitute.org
lab head
Joanna Bons
contact affiliation	Buck Institute for Research on Aging
contact email	jbons@buckinstitute.org
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive.ucsd.edu/MSV000089606/