PXD066697-1

PXD066697 is an original dataset announced via ProteomeXchange.

Title	DIA-SPROX E.coli and S.cerevisiae Midpoints
Description	The stability of proteins from rates of oxidation (SPROX) technique is a mass spectrometry-based approach for making protein folding stability measurements on the proteomics scale. The development and application of SPROX, to date, has involved the use of quantitative bottom-up proteomics and data dependent acquisition (DDA) strategies using isobaric mass tags. Use of isobaric mass tags is attractive as it enables the mass spectrometry readout in SPROX to be highly multiplexed. However, use of such isobaric mass tags is restricted to DDA strategies, which can be limited in their proteomic coverage compared to data independent acquisition (DIA) strategies. Reported here is a new “one-pot” SPROX workflow that employs a DIA readout and a label-free quantitation strategy. Analysis of the proteins in an E.coli cell lysate using our DIA-SPROX strategy allowed for calculating transition midpoints with reasonable accuracy. The proteins from a S.cerevisiae cell lysate were also assessed for ligand induced changes in their transition midpoints upon the introduction of cyclosporine A (CsA) to identify protein targets of this well-studied ligand. Using DIA-SPROX, we successfully identified known protein targets of CsA with a low false positive rate using a combination of two different software, Spectronaut and DIA-NN, for DIA data processing. We also find that the proteomic coverage obtained using DIA-SPROX is comparable to the coverage obtained in conventional DDA-SPROX experiments. Significantly, this comparable coverage can be achieved without using a methionine-containing peptide enrichment strategy in DIA-SPROX.
HostingRepository	PRIDE
AnnounceDate	2026-03-04
AnnouncementXML	Submission_2026-03-04_03:51:55.800.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Natalie Labbe
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	methylthiolated residue; acetylated residue; monohydroxylated residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-28 21:04:32	ID requested
⏵ 1	2026-03-04 03:51:56	announced

10.1021/JASMS.5C00316;

submitter keyword: None

Michael C.
contact affiliation	Department of Chemistry, Duke University, Durham, NC, United States
contact email	michael.c.fitzgerald@duke.edu
lab head
Natalie Labbe
contact affiliation	Duke University Department of Chemistry
contact email	natalie.labbe@duke.edu
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/2026/03/PXD066697

PRIDE project URI

• PRIDE
  1. PXD066697
     1. Label: PRIDE project
     2. Name: DIA-SPROX E.coli and S.cerevisiae Midpoints