PXD064541-1

PXD064541 is an original dataset announced via ProteomeXchange.

Title	Peptide-centric local stability assay (PELSA) for sensitive identification of ligand targeting proteins and binding sites at proteome scale
Description	Recently, a robust ligand modification-free method, termed as peptide-centric local stability assay (PELSA), was developed to identify the protein targets and binding regions of diverse ligands at proteomics scale. This method has unprecedented sensitivity and can be broadly applicable to ligands including drugs, metabolites, metal ions, antibodies etc. However, conduction of PELSA experiment and the extraction of key information on ligand-protein interaction, including the binding protein, binding site, and binding affinity, is not a trivial task. To address this, we introduce a protocol for the conducting of PELSA experiment and the processing of PELSA dataset, including raw data processing and result visualization. Key points, such as selection of ligand concentration, timing of trypsinization, and quality control between different replicates, are also discussed. Finally, we demonstrate how the protocol provided are appropriate for screening the targeting proteins of staurosporine, for screening the targeting proteins of 5-methyltetrahydrofolate, as well as for the dose-dependent PELSA analysis of inhibitors targeting HSP90 family. It takes 2 days to complete the PELSA protocol (additional 8 d to prepare cells), 1 d for sample preparation, 1 d for LC-MS/MS analysis and data processing.
HostingRepository	iProX
AnnounceDate	2025-05-30
AnnouncementXML	Submission_2025-06-03_00:24:47.290.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiayang Yan
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-03 00:24:26	ID requested
⏵ 1	2025-06-03 00:24:47	announced

Dataset with its publication pending

submitter keyword: Target protein identification, peptide local stability

Mingliang Ye
contact affiliation	Dalian Institute of Chemical Physics. Chinese Academy of Sciences
contact email	mingliang@dicp.ac.cn
lab head
Jiayang Yan
contact affiliation	Dalian Institute of Chemical Physics. Chinese Academy of Sciences
contact email	yanjiayang@dicp.ac.cn
dataset submitter

iProX dataset URI