Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted LC-MS/MS of E. coli CRISPRi library

ABSTRACT: Accumulating metabolites in CRISPRi identified with FI-MS extracts were measured with targeted LC-MS/MS.

INSTRUMENT(S): 6546 Q-TOF LC/MS (Agilent instrument model)

ORGANISM(S): Escherichia Coli (ncbitaxon:562)

SUBMITTER: Prof. Hannes Link

PROVIDER: MSV000098755 | MassIVE | Thu Aug 07 00:58:00 BST 2025

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Targeted LC-MS/MS with non-annotated m/z-features in MetE CRISPRi strain

Project description:A FI-MS screen identified accumulating m/z-features in E. coli metE CRISPRi strain which cannot be annotated as iML1515 metabolites. These m/z-features were measured via targeted LC-MS/MS and strcuture elucidation was performed via SIRIUS.

2025-08-04 | MSV000098714 | MassIVE

A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 dataset

Project description:In this study, we developed a workflow to systematically and selectively induce increases in metabolites by knocking down enzymes with CRISPR interference (CRISPRi). Therefore, we created a sorted CRISPRi library targeting all 1,515 metabolic genes in the most recent genome-scale metabolic model of E. coli (iML1515). In a first step, we screened the metabolome of the CRISPRi library with a fast flow-injection mass spectrometry, which revealed strong and specific accumulation of 36% of the predicted metabolites in the iML1515 model. The accumulating metabolites were unique to certain knockdowns, especially those metabolites associated with the CRISPRi targeted-pathway. Therefore, we followed-up on accumulating metabolites that were directly associated to the CRISPRi target-gene (i.e. all reactants of the respective enzyme) and measured their fragmentation spectra and chromatographic retention times with LC-MS2. This resulted in experimental fragmentation spectra and chromatographic retention times of 111 metabolites.

2024-08-07 | MSV000095536 | MassIVE

A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 12C/13C dataset

Project description:In this study, we developed a workflow to systematically and selectively induce increases in metabolites by knocking down enzymes with CRISPR interference (CRISPRi). Therefore, we created a sorted CRISPRi library targeting all 1,515 metabolic genes in the most recent genome-scale metabolic model of E. coli (iML15159). In a first step, we screened the metabolome of the CRISPRi library with a fast flow-injection mass spectrometry, which revealed strong and specific accumulation of 36% of the predicted metabolites in the iML1515 model. The accumulating metabolites were unique to certain knockdowns, especially those metabolites associated with the CRISPRi targeted-pathway. Therefore, we followed-up on accumulating metabolites that were directly associated to the CRISPRi target-gene (i.e. all reactants of the respective enzyme) and measured their fragmentation spectra and chromatographic retention times with LC-MS2. This resulted in experimental fragmentation spectra and chromatographic retention times of 111 metabolites. Three of these fragmentation spectra were verified by 13C labelling experiments.

2024-08-07 | MSV000095538 | MassIVE

FI-MS analysis of E. coli CRISPRi library

Project description:In this study, we measured the metabolome response of 1,515 CRISPR interference (CRISPRi) E. coli strains targeting all genes in the iML1515 metabolic model with flow-injection mass spectrometry.

2025-08-03 | MSV000098712 | MassIVE

A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - FI-MS dataset

2024-08-07 | MSV000095534 | MassIVE

GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 dataset

2024-08-07 | MSV000095536 | GNPS

GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 12C/13C dataset

Project description:In this study, we developed a workflow to systematically and selectively induce increases in metabolites by knocking down enzymes with CRISPR interference (CRISPRi). Therefore, we created a sorted CRISPRi library targeting all 1,515 metabolic genes in the most recent genome-scale metabolic model of E. coli (iML15159). In a first step, we screened the metabolome of the CRISPRi library with a fast flow-injection mass spectrometry, which revealed strong and specific accumulation of 36% of the predicted metabolites in the iML1515 model. The accumulating metabolites were unique to certain knockdowns, especially those metabolites associated with the CRISPRi targeted-pathway. Therefore, we followed-up on accumulating metabolites that were directly associated to the CRISPRi target-gene (i.e. all reactants of the respective enzyme) and measured their fragmentation spectra and chromatographic retention times with LC-MS2. This resulted in experimental fragmentation spectra and chromatographic retention times of 111 metabolites. Three of these fragmentation spectra were verified by 13C labelling experiments.

2024-08-07 | MSV000095538 | GNPS

GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - FI-MS dataset

2024-08-07 | MSV000095534 | GNPS

Library dependent LC-MS/MS acquisition via mzAPI/Live.

Project description:The use of MS for characterization of small molecules, nucleotides, and proteins in model organisms as well as primary tissues and clinical samples continues to proliferate at a rapid pace. The complexity and dynamic range of target analytes in biological systems hinders comprehensive analysis and simultaneously drives improvements in instrument hardware and software. As a result, state-of-the-art commercial mass spectrometers are equipped with sophisticated embedded control systems that provide robust acquisition methods accessed through intuitive graphical interfaces. Although optimized for speed, these preconfigured scan functions are otherwise closed to end-user customization beyond simple, analytical-centric parameters supplied by the manufacturer. Here, we present an open-source framework (mzAPI/Live) that enables users to generate arbitrarily complex LC-MS(n) acquisition methods via simple Python scripting. As a powerful proof-of-concept, we demonstrate real-time assignment of tandem mass spectra through rapid query of NIST peptide libraries. This represents an unprecedented capability to make acquisition decisions based on knowledge of analyte structures determined during the run itself, thus providing a path toward biology-driven MS data acquisition for the broader community.

| S-EPMC3779148 | biostudies-literature

Correlation Analysis of Expression Profile and Quantitative iTRAQ-LC-MS/MS Proteomics Reveals Resistance Mechanism Against TuMV in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Project description:To better examine the molecular mechanisms behind the virus infection, we conducted a correlation analysis of RNA-Seq and quantitative iTRAQ-LC-MS/MS in TuMV-infected and in healthy Chinese cabbage leaves.

2020-08-07 | GSE151932 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data