PXD054862-1

PXD054862 is an original dataset announced via ProteomeXchange.

Title	Comprehensive profiling of degrader-protein interactions
Description	Targeted protein degradation and induced proximity both refer to advanced strategies that leverage the recruitment of target proteins to another protein to facilitate their modification, regulation or degradation. As the biological complexity of molecular glues and degraders has become increasingly apparent, there is a growing need for advances in unbiased methodology to unveil hidden chemical targets. Here we establish a high throughput affinity purification mass spectrometry workflow in cell lysates for the unbiased identification of molecular glue interactomes. We map the targets of 20 molecular glues across two orthogonal cell lines identifying 270 proteins as chemically recruited to CRBN and demonstrate the power of enrichment methods for identifying novel protein targets that are often overlooked using global whole cell screening methods. We not only drastically increase the breadth of zinc finger transcription factors that are targetable, but more importantly identify many novel non-zinc finger proteins as targets of IMiD molecular glues. We use alignments with structures obtained from the Alphafold2 database as a method to estimate confidence in experimental hits and we experimentally validate several targets to show direct interaction and subsequent ubiquitylation. Our study provides a comprehensive inventory of targets chemically recruited to CRBN and delivers a robust and scalable workflow for identifying new drug-induced protein interactions in cell lysates.
HostingRepository	PRIDE
AnnounceDate	2025-07-21
AnnouncementXML	Submission_2025-07-21_11:40:33.471.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eric Fischer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-14 02:39:41	ID requested
⏵ 1	2025-07-21 11:40:33	announced

Dataset with its publication pending

submitter keyword: proteomics, cereblon, targeted protein degradation, molecular glue, PROTAC, degrader, ubiquitin,IMiD, E3 ligase

Eric Fischer
contact affiliation	Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
contact email	eric_fischer@dfci.harvard.edu
lab head
Eric Fischer
contact affiliation	Dana-Farber Cancer Institute
contact email	eric_fischer@dfci.harvard.edu
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/2025/07/PXD054862

PRIDE project URI

• PRIDE
  1. PXD054862
     1. Label: PRIDE project
     2. Name: Comprehensive profiling of degrader-protein interactions