PXD058580-1

PXD058580 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Improved Proteome-wide Succinylome Analysis by Data-Independent Acquisition Using High-Quality Succinyl Spectral Libraries
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.
HostingRepository	MassIVE
AnnounceDate	2024-12-13
AnnouncementXML	Submission_2024-12-13_09:59:37.824.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
Instrument	Orbitrap Eclipse

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-04 10:56:28	ID requested
⏵ 1	2024-12-13 09:59:38	announced

Publication List

no publication

no publication

Keyword List

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

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

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/v07/MSV000096592/