PXD010799-1

PXD010799 is an original dataset announced via ProteomeXchange.

Title	TargetSeeker-MS: A Bayesian Inference Approach for Drug Target Discovery using Protein Fractionation Coupled to Mass Spectrometry
Description	Determining the affinity of a drug to its putative targets is critical to the understanding of its mechanism and to assess its clinical usefulness and viability. Energetics-based protein separation (EBPS) techniques, such as thermal shift assay, when coupled to mass spectrometry (MS) have shown great potential to identify the targets of a drug on a proteome scale. Nevertheless, the computational analyses assessing the confidence of drug target predictions made by these methods have remained rudimentary and tightly tied to the protocol under which the data were produced. We propose a novel flexible Bayesian inference approach named TargetSeeker-MS to identify drug targets in datasets produced using different EBPS techniques coupled to MS. We show that TargetSeeker-MS identifies known and novel drug targets in C. elegans and HEK 293 samples treated with benomyl, a fungicide. We also demonstrate that TargetSeeker-MS’ drug target identifications are reproducible in C. elegans samples that were processed using two different EBPS techniques (thermal shift assay and a selective precipitation-based separation). In addition, we validate a novel benomyl target by measuring its altered enzymatic activity upon drug treatment in vitro. TargetSeeker-MS, which is available as a web server, allows for the rapid and confident identification of targets of a drug on a proteome scale, thereby providing a better understanding of its mechanisms to ease the evaluation of its clinical viability.
HostingRepository	PRIDE
AnnounceDate	2026-04-06
AnnouncementXML	Submission_2026-04-05_23:24:08.746.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Moresco
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Caenorhabditis elegans; NCBI TaxID: NEWT:6239;
ModificationList	carbamoylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-16 03:45:18	ID requested
⏵ 1	2026-04-05 23:24:09	announced

Lavall, é, e-Adam M, Pelletier A, Diedrich JK, Pinto AFM, Mart, í, nez-Bartolom, é S, Petrascheck M, Moresco JJ, Yates JR, TargetSeeker-MS: A Bayesian Inference Approach for Drug-Target Discovery Using Protein Fractionation Coupled to Mass Spectrometry. J Am Soc Mass Spectrom, 36(4):664-679(2025) [pubmed]

10.1021/jasms.4c00269;

curator keyword: Biological, Biomedical

submitter keyword: Bioinformatics / Drug target discovery / Mass spectrometry / Proteomics / Thermal shift assay

John R. Yates III
contact affiliation	Professor, Dept. of Molecular Medicine The Scripps Research Institute Phone: (858) 784-8863 10550 North Torrey Pines Road, SR-302, La Jolla, CA 92037
contact email	jyates@scripps.edu
lab head
James Moresco
contact affiliation	The Salk Institute for Biological Studies
contact email	jmoresco@salk.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/2026/04/PXD010799

PRIDE project URI

• PRIDE
  1. PXD010799
     1. Label: PRIDE project
     2. Name: TargetSeeker-MS: A Bayesian Inference Approach for Drug Target Discovery using Protein Fractionation Coupled to Mass Spectrometry