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Related Experiment Video

Updated: May 3, 2026

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Published on: September 15, 2015

Quantitative metaproteomics: functional insights into microbial communities.

Chongle Pan¹, Jillian F Banfield

¹Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.

Methods in Molecular Biology (Clifton, N.J.)

|February 12, 2014

Summary

This summary is machine-generated.

Quantitative metaproteomics precisely measures microbial community protein abundances. This study details three methods—label-free, (15)N metabolic, and isobaric chemical labeling—for analyzing microbial ecosystems.

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Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions

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Published on: October 20, 2020

Area of Science:

Microbiology
Proteomics
Bioinformatics

Background:

Quantitative metaproteomics offers insights into microbial community functions.
Understanding protein expression changes is crucial for studying microbial ecosystems.

Purpose of the Study:

To present and evaluate three quantitative metaproteomics strategies.
To demonstrate the application of these strategies in a model microbial community.

Main Methods:

Shotgun proteomics workflow.
Two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS).
Database searching against metagenomic protein databases.
Label-free, (15)N metabolic labeling, and isobaric chemical labeling techniques.

Main Results:

Successful establishment of quantitative metaproteomics using three distinct labeling strategies.
Demonstration of the workflow in a complex microbial community from acid mine drainage.
Accurate determination of relative protein abundances within the microbial community.

Conclusions:

The described quantitative metaproteomics strategies are effective for analyzing microbial communities.
This approach provides a comprehensive view of metabolic activities and protein expression changes.
The methods are applicable to various environmental conditions and perturbations.