PXD024133

PXD024133 is an original dataset announced via ProteomeXchange.

Title	CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries
Description	Molecular profiling of small-molecules offers invaluable insights on compound functionality and allows for hypothesis generation of targets. However, current profiling methods are either limited in the number of measurable parameters or throughput. Here, we developed a multiplexed, unbiased framework that by linking genetic to drug-induced changes in nearly a thousand metabolites allows for high-throughput functional annotation of compound libraries in Escherichia Coli. First, we generated a reference map of metabolic changes from (CRISPR) interference with 352 genes in all major essential biological processes. Next, based on the comparison of essential gene knockdown metabolic profiles with 1342 drug-induced metabolic changes we demonstrated the ability to make de novo predictions of compound functionality and revealed drugs interfering with unconventional antibacterial targets. The same framework that combines dynamic gene silencing with metabolomics we implemented in E. coli can be adapted and applied as a general strategy for comprehensive high-throughput analysis of compound functionality, from bacteria to human cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:30:41.708.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ludovic Gillet
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-11 03:35:27	ID requested
1	2021-12-16 02:05:48	announced
2	2023-05-14 14:21:09	announced	2023-05-14: Updated project metadata.
⏵ 3	2024-10-22 05:30:42	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: EPIC-XS

submitter keyword: proteomics,Escherichia Coli, metabolomics, LC-MS, antibacterial drugs, Limited Proteolysis

Mattia Zampieri
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
contact email	zampieri@imsb.biol.ethz.ch
lab head
Ludovic Gillet
contact affiliation	ETH Zurich
contact email	gillet@imsb.biol.ethz.ch
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/2021/12/PXD024133

PRIDE project URI

• PRIDE
  1. PXD024133
     1. Label: PRIDE project
     2. Name: CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries