PXD036569-2

PXD036569 is an original dataset announced via ProteomeXchange.

Title	SITE-SPECIFIC ACTIVITY-BASED PROTEIN PROFILING USING PHOSPHONATE HANDLES
Description	Most drug molecules target proteins. Identification of the exact drug binding sites on these proteins is essential to understand and predict how drugs affect protein structure and function. To address this challenge, we developed a strategy that uses IMAC-enrichable phosphonate affinity tags, for efficient and selective enrichment of peptides bound to an activity-based probe (ABP), enabling the identification of the exact drug binding site. As a proof of concept, using this approach, termed PhosID–ABPP (Activity-based protein profiling), over 500 unique binding sites were reproducibly identified of an alkynylated Afatinib derivative (PF-06672131). As PhosID–ABPP is compatible with intact cell inhibitor treatment, we investigated the quantitative differences in approachable binding sites in intact cells and in lysates of the same cell line and observed and quantified substantial differences. Moreover, an alternative protease digestion approach was used to capture the previously reported binding site on the epidermal growth factor receptor (EGFR), which turned out to remain elusive when using solely trypsin as protease. Overall, we find that PhosID–ABPP is highly complementary to biotin-based enrichment strategies in activity-based protein profiling studies, with PhosID–ABPP providing the advantage of direct ABP-interaction site identification.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:58:34.766.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wouter van Bergen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-08 06:49:53	ID requested
1	2023-01-10 01:22:04	announced
⏵ 2	2023-11-14 08:58:35	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Chemical proteomics

Activity-based protein profiling

Site-specific

Phosphonate affinity handles

Fe(III)-immobilized metal affinity chromatography.

A.J.R. Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, University Utrecht, Utrecht, The Netherlands
contact email	a.j.r.heck@uu.nl
lab head
Wouter van Bergen
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
contact email	w.vanbergen@uu.nl
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/2023/01/PXD036569

PRIDE project URI

• PRIDE
  1. PXD036569
     1. Label: PRIDE project
     2. Name: SITE-SPECIFIC ACTIVITY-BASED PROTEIN PROFILING USING PHOSPHONATE HANDLES