PXD061795

PXD061795 is an original dataset announced via ProteomeXchange.

Title	SICyLIA-cTMT enables dissecting redox proteome dynamics with high accuracy and depth at micrograms scale (PART1 = murine kidney cells upon hydrogen peroxide treatment)
Description	Cysteine oxidative modifications are fundamental signaling events that regulate cellular functions under both physiological and pathological conditions. However, our understanding of these modifications is limited by their low abundance and the technical challenges associated with studying their dynamics in a comprehensive and unbiased manner. Here, we developed the SICyLIA-TMT workflow, which uses light and heavy iodoacetamide (IAA) to sequentially label reduced and reversibly oxidized cysteine residues within the same sample. By applying tandem mass tags (TMTs) to differentially label peptides of each experimental conditions, our strategy allows simultaneous analysis of both oxidative modification dynamics and protein levels across multiple experimental conditions from only micrograms of starting material. Furthermore, to enhance the detection of low-abundance, cysteine residues carrying oxidative modifications, we dedicated a TMT channel as carrier for heavy IAA-labelled peptides (SICyLIA-cTMT). This strategy remarkably increased the quantification of reversibly oxidized cysteine residues and enabled precise stoichiometry calculations. Last, combining SICyLIA-TMT with the latest generation of MS instruments, Orbitrap Astral, we halved the measuring time in the mass spectrometer without impacting the depth of the redox proteome. We showed the applicability of SICyLIA-TMT to both cells in culture and full organs under stress condition. Hence, SICyLIA-cTMT is a versatile method that achieves unparalleled quantification accuracy and depth of the redox proteome while significantly reducing MS analysis time, making a significant step change in the study of oxidative signaling.
HostingRepository	PRIDE
AnnounceDate	2025-10-01
AnnouncementXML	Submission_2025-10-01_02:56:29.777.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD061795
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sergio Lilla
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-13 08:05:16	ID requested
⏵ 1	2025-10-01 02:56:30	announced

10.6019/PXD061795;

submitter keyword: Redox proteomics

Mass spectrometry

Oxidative signaling

Fibroblasts

Cancer

Obesity

Redox stress.

Sara Rossana Zanivan
contact affiliation	CRUK Scotland Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom
contact email	s.zanivan@crukscotlandinstitute.ac.uk
lab head
Sergio Lilla
contact affiliation	Proteomics
contact email	s.lilla@beatson.gla.ac.uk
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2025/10/PXD061795

PRIDE project URI

• PRIDE
  1. PXD061795
     1. Label: PRIDE project
     2. Name: SICyLIA-cTMT enables dissecting redox proteome dynamics with high accuracy and depth at micrograms scale (PART1 = murine kidney cells upon hydrogen peroxide treatment)