MassIVE MSV000089606

Partial Public PXD034275

In-depth Analysis of the Sirtuin 5-regulated Mouse Brain Acylome using Library-free Data-Independent Acquisitions

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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. [doi:10.25345/C5MC8RK90] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Acylome ; Brain ; Data-independent acquisition ; Post-translational modifications ; Sirtuin

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Principal Investigators:
(in alphabetical order) 		Birgit Schilling, Buck Institute, USA
Submitting User: JoannaBons
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