PXD016001

PXD016001 is an original dataset announced via ProteomeXchange.

Title	Predictive signatures of 19 antibiotics-induced Escherichia coli proteomes
Description	Identifying the mode of action (MOA) of antibacterial compounds is the fundamental basis for the development of new antibiotics, and the challenge increases with the emerging secondary and indirect effect from antibiotic stress. Although various omics-based system biology approaches of defining antibiotic MOA are currently available, they still need improved throughput, accuracy and comprehensiveness. Using high resolution accurate mass (HR/AM) based proteomics, we present here a comprehensive reference map of proteomic signatures of Escherichia coli under antibiotics challenge. With state-of-the-art label-free approach, we quantified > 1,500 protein groups in response to 19 FDA-approved antibiotics. Applying several machine learning techniques, we derived a panel of 14 proteins that can be used to classify antibiotics into different MOAs with nearly 100% accuracy. Interestingly, these proteins tend to mediate diverse bacterial cellular and metabolic processes. Transcriptomic level profiling correlates well with changes in protein expression in discriminating different antibiotics. Such expression signatures will aid future studies in identifying MOA of unknown compounds and facilitate the discovery of novel antibiotics. In summary, our study offers a practical approach for effective and rapid proteomic profiling, establishes a high quality reference compendium of microbial proteome in response to a wide range of antibiotics exposure, and provides a previously undescribed group of proteins and RNAs that allows rapid antibiotic classification and MOA determination.
HostingRepository	PRIDE
AnnounceDate	2020-07-23
AnnouncementXML	Submission_2020-07-23_05:33:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yanbao Yu
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-24 02:40:07	ID requested
⏵ 1	2020-07-23 05:33:11	announced

Yu Y, O'Rourke A, Lin YH, Singh H, Eguez RV, Beyhan S, Nelson KE, Proteomes. ACS Infect Dis, 6(8):2120-2129(2020) [pubmed]

curator keyword: Biological

submitter keyword: Quantitative Proteomics

Label-free

Suspension Trapping (S-Trap)

Escherichia coli

Antibiotics

Mode of Action (MOA)

Yanbao Yu
contact affiliation	J. Craig Venter Institute, Rockville, MD 20850
contact email	yayu@jcvi.org
lab head
Yanbao Yu
contact affiliation	J. Craig Venter Institute
contact email	yayu@jcvi.org
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/2020/07/PXD016001

PRIDE project URI

• PRIDE
  1. PXD016001
     1. Label: PRIDE project
     2. Name: Predictive signatures of 19 antibiotics-induced Escherichia coli proteomes