PXD056816

PXD056816 is an original dataset announced via ProteomeXchange.

Title	Spike-in Proteome to enhance Data-Independent Acquisition for Thermal Proteome Profiling
Description	Target deconvolution interactions is essential for elucidating the molecular mechanisms, therapeutic efficacy and off-target toxicity of small molecule drugs. Thermal proteome profiling (TPP) is a robust popular method for identifying drug-protein interactions. Nevertheless, classical implementation of TPP using isobaric labelling of peptides is tedious, time-consuming and costly. This prompt the adoption of label-free approach with data-independent acquisition (DIA), but with substantial compromise in protein coverage and precision. To address these shortcomings, we improvise a spike-in proteome strategy for DIA with TPP to counteract the reduction in protein quantity following sample heating. Protein coverage, data completeness and quantification precision are significantly improved as result. Additionally, a calibration algorithm was developed to correct for spike-in effects on fold changes. The integration of DIA-TPP with the Matrix-Augmented Pooling Strategy (MAPS) to increase experiment throughput demonstrates performance comparable to existing TMT-TPP-MAPS. With this spike-in proteome strategy, we also successfully identified the thermal stabilization of CA13 by dorzolamide hydrochloride, as well as GSTZ1 and TDP1 of opicapone that eluded detection without the spike-in proteome.
HostingRepository	PRIDE
AnnounceDate	2025-03-11
AnnouncementXML	Submission_2025-03-11_08:54:20.310.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	qiqi Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-15 08:13:37	ID requested
⏵ 1	2025-03-11 08:54:20	announced

10.1021/ACS.ANALCHEM.4C04837;

submitter keyword: Data-Independent Acquisition, Thermal Proteome Profiling

Chris Soon Heng Tan
contact affiliation	Southern University of Science and Technology
contact email	christan@sustech.edu.cn
lab head
qiqi Wang
contact affiliation	Southern University of Science and Technology
contact email	12131195@mail.sustech.edu.cn
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/2025/03/PXD056816

PRIDE project URI

• PRIDE
  1. PXD056816
     1. Label: PRIDE project
     2. Name: Spike-in Proteome to enhance Data-Independent Acquisition for Thermal Proteome Profiling