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PXD036569-2

PXD036569 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSITE-SPECIFIC ACTIVITY-BASED PROTEIN PROFILING USING PHOSPHONATE HANDLES
DescriptionMost 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:58:34.766.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterWouter van Bergen
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListcarbamoylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-09-08 06:49:53ID requested
12023-01-10 01:22:04announced
22023-11-14 08:58:35announced2023-11-14: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Chemical proteomics
Activity-based protein profiling
Site-specific
Phosphonate affinity handles
Fe(III)-immobilized metal affinity chromatography.
Contact List
A.J.R. Heck
contact affiliationBiomolecular Mass Spectrometry and Proteomics, University Utrecht, Utrecht, The Netherlands
contact emaila.j.r.heck@uu.nl
lab head
Wouter van Bergen
contact affiliationBiomolecular 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 emailw.vanbergen@uu.nl
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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