PXD029500

PXD029500 is an original dataset announced via ProteomeXchange.

Title	SP3-enabled rapid and high coverage chemoproteomic identification of redox-sensitive cysteines
Description	Cysteine residues undergo various oxidative modifications, acting as key sensors of reactive oxygen species (ROS) and reactive nitrogen species (RNS). Given that ROS and RNS have known roles in many pathophysiological processes, numerous proteome-wide strategies to profile cysteine oxidation state have emerged in the last decade. Recent advancements to traditional redox profiling methods include incorporation of costly isotopic labeling reagents to allow for more quantitative assessment of oxidation states. These methods are typically carried out by using sequential thiol capping and reduction steps in order to label redox-sensitive cysteines, often found in di-cysteine motifs (‘CXXC’ or ‘CXXXC’). Tailored, pricy algorithms are commonly used to analyze redox-profiling datasets, the majority of which cannot accurately quantify site-of-labeling in redox-motifs; moreover, accurate quantification is confounded by excess labeling reagents during sample preparation. Here, we present a low-cost redox-profiling workflow using newly synthesized isotopic reagents compatible with SP3-bead technology, termed SP3-ROx, that allows for high throughput, rapid identification of redox-sensitive cysteines. We optimize cysteine labeling quantification using the FragPipe suite, an open source GUI for MSfragger-based search algorithm. Application of SP3-ROx to naive and activated T cells identifies redox-senstive cysteines, showcasing the utility of this workflow to study biological processes.
HostingRepository	PRIDE
AnnounceDate	2022-03-02
AnnouncementXML	Submission_2022-03-02_02:42:15.124.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Heta Desai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-02 03:55:16	ID requested
⏵ 1	2022-03-02 02:42:15	announced

Dataset with its publication pending

submitter keyword: chmoproteomics, redox, T cells, quantitation, isotopic, mass spectrometry, cysteines

Keriann Backus
contact affiliation	Biological Chemistry Department, David Geffen School of Medicine, UCLA
contact email	kbackus@mednet.ucla.edu
lab head
Heta Desai
contact affiliation	UCLA
contact email	hets@g.ucla.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029500
     1. Label: PRIDE project
     2. Name: SP3-enabled rapid and high coverage chemoproteomic identification of redox-sensitive cysteines