MassIVE MSV000096592

Partial Public PXD058580

Improved Proteome-wide Succinylome Analysis by Data-Independent Acquisition Using High-Quality Succinyl Spectral Libraries

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Description

Protein post-translational modifications (PTMs) are crucial and dynamic modulators of protein functions, interactions, and localizations as well as biological pathways and cellular signaling. Lysine succinylation analysis remains challenging, but sophisticated workflows combining succinylated peptide enrichments and quantitative mass spectrometry approaches have revolutionized proteome-wide succinylome analysis. The implementation of data-independent acquisition (DIA)-mass spectrometry has greatly advanced the detection of low abundance succinylated peptides, succinylome coverage, identification reproducibility, and quantification accuracy. However, the complexity of DIA data requires dedicated data processing algorithms and tools, that typically rely on spectral libraries. These reference libraries can be generated from experimental data-dependent acquisition (DDA) acquisitions of representative study samples submitted to DDA database search engines for confident succinylated peptide identification and precise PTM site localization. Here, we describe how to build DDA PTM spectral libraries using various software tools, specifically Spectronaut (Biognosys), SpectroMine (Biognosys), and MSFragger (Nesvizhskii Lab). The generated libraries were imported into Skyline for the previously published DIA succinylome analysis of Sirtuin-5 knocked-out vs wild-type mouse brains in order to accurately quantify and visualize PTM-containing peptides. [doi:10.25345/C53N20S1J] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Spectral library ; Succinylation ; Data-dependent acquisition (DDA) ; Post-translational modifications ; Data-independent acquisition (DIA) ; Quantitative proteomics ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Birgit Schilling, Buck Institute, USA
Submitting User: JoannaBons
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Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.