PXD044006

PXD044006 is an original dataset announced via ProteomeXchange.

Title	High-throughput drug target discovery by fully automated proteomics sample preparation platform
Description	Drug development is plagued by inefficiency and high costs due to issues such as inadequate drug efficacy and unexpected toxicity. Mass spectrometry (MS)-based proteomics, particularly isobaric quantitative proteomics, offers a solution to unveil resistance mechanisms and unforeseen side effects related to off-targeting pathways. Thermal proteome profiling (TPP) has gained popularity for drug target identification at the proteome scale. However, it involves experiments with multiple temperature points, resulting in numerous samples and considerable variability in large-scale TPP analysis. We propose a high-throughput drug target discovery workflow that integrates single-temperature TPP, a fully automated proteomics sample preparation platform (autoSISPROT), and Data Independent Acquisition (DIA) quantification. The autoSISPROT platform enables the simultaneous processing of 96 samples in less than 2.5 hours, achieving protein digestion, desalting, and optional TMT labeling (requires an additional 1 hour) with 96-channel all-in-tip operations. The results demonstrated excellent sample preparation performance with >94% digestion efficiency, >98% TMT labeling efficiency, and >0.9 of intraand inter-batch Pearson correlation coefficients. By automatically processing 87 samples, we identified both known targets and potential off-targets of 20 kinase inhibitors, affording over a 10-fold improvement in throughput compared to classical TPP. This fully automated workflow offers a high-throughput solution for proteomics sample preparation and drug target/off-target identification.
HostingRepository	PRIDE
AnnounceDate	2024-01-16
AnnouncementXML	Submission_2024-01-16_06:26:44.742.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qiong Wu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-23 01:01:31	ID requested
⏵ 1	2024-01-16 06:26:45	announced

10.1039/D3SC05937E;

submitter keyword: Fully automated， high-throughput drug target discovery

Ruijun Tian
contact affiliation	Department of Chemistry, Southern University of Science and Technology
contact email	tianrj@sustech.edu.cn
lab head
Qiong Wu
contact affiliation	South University of Science and Technology of China
contact email	13390063506@163.com
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/2024/01/PXD044006

PRIDE project URI

• PRIDE
  1. PXD044006
     1. Label: PRIDE project
     2. Name: High-throughput drug target discovery by fully automated proteomics sample preparation platform