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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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Updated: Mar 24, 2026

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

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Published on: September 15, 2015

Next-generation proteomics faces new challenges in environmental biotechnology.

Jean Armengaud¹

¹CEA, DRF, IBiTec-S, SPI, Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", Bagnols-sur-Cèze F-30200, France.

Current Opinion in Biotechnology

|March 8, 2016

Summary

Next-generation proteomics advances environmental biotechnology by analyzing complex microbial communities and distantly related organisms. New mass spectrometry and bioinformatics tools enable deeper insights into biological systems and novel screening strategies.

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Area of Science:

Environmental biotechnology
Microbial ecology
Proteomics

Background:

Environmental biotechnology requires understanding novel biological systems and molecular mechanisms.
Next-generation proteomics, using advanced mass analyzers, can now profile entire proteomes of microorganisms.

Purpose of the Study:

To explore the challenges and advancements in applying next-generation proteomics to environmental samples.
To highlight the role of new technologies in overcoming limitations in analyzing distantly related organisms and microbial mixtures.

Main Methods:

Utilizing next-generation mass spectrometry for comprehensive proteome analysis.
Employing proteogenomics and homology-based proteomics for data interpretation.
Developing innovative bioinformatics tools for complex biological systems.
Applying novel screening strategies like whole proteome thermal profiling and subpopulation proteomics.

Main Results:

Next-generation proteomics facilitates the characterization of microbial proteomes, even from distantly related organisms.
Proteogenomic and homology-based approaches aid in interpreting proteomic data when genomes are established or draft sequences are available.
Advanced mass spectrometry and bioinformatics tools are expanding the scope of metaproteomics and homology-based proteomics.
New cost-effective screening methods are emerging for environmental sample analysis.

Conclusions:

Next-generation proteomics, coupled with advanced bioinformatics, is revolutionizing environmental biotechnology.
The methodology offers powerful solutions for analyzing complex environmental samples, including microbial mixtures and uncharacterized organisms.
Innovative approaches like thermal profiling and subpopulation proteomics are enhancing the efficiency and depth of biological system characterization.