PXD061498 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site |
| Description | While a number of efficient chemical proteomics methods are available for determining protein targets of pharmaceutical drugs, each approach exhibits its own “blind spot” and development of complementary techniques is needed. Here, we introduce the Above-Filter Digestion Proteomics (AFDIP) approach based on the monitoring of the rate of trypsin digestion. Digestion rate is decreased at the site of ligand binding to its target protein, while other sites may simultaneously experience an increase the digestion rate. Molecular dynamics (MD) simulations revealed that this increase may be due to allosteric structural changes related to backbone flexibility. We showcase the utility of AFDIP for deconvoluting the targets of versatile drugs and metabolites. Like other techniques, AFDIP allows for a two-dimensional analysis, with the second dimension based on drug concentration. AFDIP exhibits structural resolution, identifying drug target binding sites within ≤10 Å, and 1for larger proteins often ≤5 Å of the crystallography-determined binding sites. Compared to earlier introduced limited proteolysis approaches, AFDIP provides easier sample preparation, deeper proteome analysis and broader sequence coverage. AFDIP is expected to find its place among the most efficient chemical proteomics methods currently available. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-03-17 |
| AnnouncementXML | Submission_2026-03-17_02:18:42.580.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Bohdana Sokolova |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | iodoacetamide derivatized residue |
| Instrument | Orbitrap Fusion Lumos |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-03-05 03:42:38 | ID requested | |
| ⏵ 1 | 2026-03-17 02:18:43 | announced | |
Publication List
| 10.1021/acs.jproteome.5c00927; |
| Sokolova B, Gharibi H, Jafari M, Lyu H, Lovera S, Gaetani M, Saei AA, Zubarev RA, Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site. J Proteome Res, 25(3):1556-1570(2026) [pubmed] |
Keyword List
| submitter keyword: proteomics, drug target,LC-MSMS |
Contact List
| Roman Zubarev |
|---|
| contact affiliation | Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden |
| contact email | roman.zubarev@ki.se |
| lab head | |
| Bohdana Sokolova |
|---|
| contact affiliation | Karolinska Institutet |
| contact email | bohdana.sokolova@ki.se |
| dataset submitter | |
Full Dataset Link List
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/2026/03/PXD061498 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD061498
- Label: PRIDE project
- Name: Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site
