PXD043895

PXD043895 is an original dataset announced via ProteomeXchange.

Title	CysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry
Description	Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function, urging the need for accurate cysteine oxidation quantification to decode protein redox regulation. Here, we present a novel approach called CysQuant that enables simultaneous quantification of cysteine oxidation degrees and protein abundancies. Reduced and reversibly oxidized cysteines are differentially labeled with light and heavy iodoacetamide isotopologues and analyzed using data-dependent acquisition (DDA) or data-independent acquisition (DIA) mass spectrometry. Using in silico predicted spectral libraries, plexDIA quantified on average 18% oxidized in the model plant Arabidopsis thaliana, though revealed a subset of highly oxidized cysteines part of disulfide bridges in AlphaFold2 predicted protein structures. Studying protein redox regulation of plant seedlings in response to excessive light, CysQuant successfully identified the well-established increased reduction of Calvin-Benson cycle enzymes, in addition to discovery of other, yet uncharacterized redox-sensitive disulfides in plastidial enzymes. CysQuant is widely applicable to diverse mass spectrometry platforms studying the cysteine modification status.
HostingRepository	PRIDE
AnnounceDate	2023-07-21
AnnouncementXML	Submission_2023-07-21_00:24:57.366.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	PatrickWillems
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-19 02:13:58	ID requested
⏵ 1	2023-07-21 00:24:57	announced

Dataset with its publication pending

submitter keyword: Cysteine oxidation, redox, data-independent acquisition, plexDIA

KrisGevaert
contact affiliation	Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium. Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium.
contact email	Kris.Gevaert@Ugent.be
lab head
PatrickWillems
contact affiliation	PSB-VIB
contact email	pawil@psb.ugent.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD043895
     1. Label: PRIDE project
     2. Name: CysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry