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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Related Experiment Video

Updated: Sep 30, 2025

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

Published on: December 20, 2010

Photoaffinity Capture Compounds to Profile the Magic Spot Nucleotide Interactomes.

Thomas M Haas¹, Benoît-Joseph Laventie², Simon Lagies¹

¹Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg im Breisgau, Germany.

Angewandte Chemie (International Ed. in English)

|March 16, 2022

Summary

Magic Spot Nucleotides (MSN) regulate bacterial stringent responses for survival. This study identified new MSN targets and found pppGpp inhibits ApaH, a key enzyme in bacterial stress adaptation.

Keywords:

Alarmones Magic Spot Nucleotides Photoaffinity Proteomics Stringent Response ppGpp

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Last Updated: Sep 30, 2025

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

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Published on: December 20, 2010

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Published on: December 9, 2016

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

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Published on: October 14, 2022

Area of Science:

Microbiology
Chemical Biology
Biochemistry

Background:

The stringent response is a critical bacterial survival mechanism during stress.
Understanding this response is vital for developing new antibiotics.
Magic Spot Nucleotides (MSN) are key regulators of the stringent response.

Purpose of the Study:

To delineate the Magic Spot Nucleotide (MSN) interactome in *Escherichia coli* and *Salmonella typhimurium*.
To identify novel MSN targets using chemical proteomics.
To investigate the interaction between MSNs and the ApaH enzyme.

Main Methods:

Utilized trifunctional photoaffinity capture compounds to probe MSN interactions.
Developed MSN probes with diverse phosphorylation patterns (pppGpp, ppGpp, pGpp).
Employed chemical proteomics to analyze cytosolic and membrane fractions.

Main Results:

Identified novel putative MSN receptors in both *E. coli* and *S. typhimurium*.
Discovered that pppGpp potently inhibits the non-Nudix hydrolase ApaH.
Demonstrated that ApaH converts pppGpp to pGpp.

Conclusions:

The study provides a comprehensive MSN interactome map for key bacterial species.
New insights into the regulation of bacterial stress response and potential antibiotic targets.
The developed MSN probes are valuable tools for future interactome studies across bacterial species.