PXD007965-2

PXD007965 is an original dataset announced via ProteomeXchange.

Title	Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification
Description	Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. Recently, we reported on the establishment, by ABPP, of the serine hydrolase interaction landscape of the experimental drug BIA 10-2474, thereby providing a potential explanation for the adverse side effects observed with this compound. ABPP allows mapping of protein interaction landscapes of inhibitors in cells, tissues and animal models. Here, we describe a protocol for identifying the in vivo selectivity profile of covalent inhibitors using ABPP with label-free quantitative proteomics as exemplified by experimental data on the diacylglycerol lipase inhibitor DH376 in mouse brain, liver, kidney and testes. The protocol has been optimized using label-free quantification methods to have high proteome coverage and to allow the simultaneous comparison of multiple biological samples. The stages of the protocol include tissue lysis, probe incubation, enrichment, sample preparation, liquid chromatography-mass spectrometry measurement, processing and data analysis. The results include evidence of target engagement in a native proteome and the identification of potential off-targets for the inhibitor under investigation. The entire protocol takes at least four days (depending on the number of samples).
HostingRepository	PRIDE
AnnounceDate	2018-02-23
AnnouncementXML	Submission_2018-03-27_23:44:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Bogdan Florea
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-13 05:33:53	ID requested
1	2018-02-22 19:27:46	announced
⏵ 2	2018-03-27 23:44:59	announced	Updated publication reference for PubMed record(s): 29565900.

van Rooden EJ, Florea BI, Deng H, Baggelaar MP, van Esbroeck ACM, Zhou J, Overkleeft HS, van der Stelt M, Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification. Nat Protoc, 13(4):752-767(2018) [pubmed]

curator keyword: Technical

submitter keyword: Activity-based protein profiling

covalent inhibitors

chemical proteomics

label-free quantification

target engagement

Mario van der Stelt
contact affiliation	Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, Netherlands.
contact email	m.van.der.stelt@chem.leidenuniv.nl
lab head
Bogdan Florea
contact affiliation	Leiden Institute for Chemistry
contact email	b.florea@chem.leidenuniv.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/2018/02/PXD007965

PRIDE project URI

• PRIDE
  1. PXD007965
     1. Label: PRIDE project
     2. Name: Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification