PXD064146-1

PXD064146 is an original dataset announced via ProteomeXchange.

Title	A Detergent-Free Grinding Sample Preparation Method Dramatically Enhances PELSA for Mapping Integral Membrane Protein-Ligand Interaction
Description	The conventional use of detergent-containing buffers for integral membrane protein (IMP) extraction may disrupt native protein conformations, potentially compromising the performance of ligand target identification. As a result, there is a lack of reliable, unbiased, detergent-free proteomic methods that enable the identification of ligand binding IMPs. In this study, we developed DFG-PELSA (Detergent-Free Grinding sample preparation method coupled with Peptide-centric Local Stability Assay), an innovative workflow that integrates mechanical grinding, extensive trypsinization, and DIA mass spectrometry for the proteome-wide identification of ligand binding proteins and binding regions with enhanced ability to identify IMP target proteins. Our method successfully recovered over 1,000 transmembrane proteins from HeLa cells while maintaining their native conformations. This method successfully mapped the interaction and binding regions of AMP-PNP with IMPs such as SERCA2 and ABCB6. DFG-PELSA also revealed the target and off-target mechanisms of tyrosine kinase inhibitors (TKIs), providing valuable insights for drug discovery and optimization. Additionally, DFG-PELSA identified stability shifts induced by cardiotonic steroids binding to the transmembrane region of ATP1A1, demonstrating its effectiveness in studying challenging IMP targets. These applications highlight DFG-PELSA's unique capability in studying ligand-membrane protein interactions, offering a useful platform for structure-based drug discovery and target validation.
HostingRepository	PRIDE
AnnounceDate	2025-10-15
AnnouncementXML	Submission_2025-10-15_06:16:22.776.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ting Yu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-21 05:30:56	ID requested
⏵ 1	2025-10-15 06:16:23	announced

Dataset with its publication pending

submitter keyword: Sample Preparation

Membrane Protein

Protein-Ligand Interaction

Mingliang Ye
contact affiliation	State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
contact email	mingliang@dicp.ac.cn
lab head
Ting Yu
contact affiliation	Dalian Institute of Chemical Physics, CAS
contact email	yuting@dicp.ac.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD064146
     1. Label: PRIDE project
     2. Name: A Detergent-Free Grinding Sample Preparation Method Dramatically Enhances PELSA for Mapping Integral Membrane Protein-Ligand Interaction