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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

Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level.

Martin Keller¹, Robert Hettich

¹Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, MS-6026, Oak Ridge, TN 37831, USA. kellerm@ornl.gov

Microbiology and Molecular Biology Reviews : MMBR

|March 5, 2009

Summary

Environmental proteomics, enabled by increased sequencing, analyzes proteins in complex environments. This review covers sample prep, key technologies like 2D-PAGE and LC-MS, and future bioinformatics integration.

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Area of Science:

Environmental proteomics
Metagenomics
Proteomics

Background:

Advancements in sequencing technology have spurred the growth of metagenomic projects.
Metagenomics provides the foundation for applying environmental proteomics.
Environmental proteomics analyzes the complete set of proteins in environmental samples.

Purpose of the Study:

To review the current state of environmental proteomics.
To detail sample preparation methods.
To discuss major technologies and findings in the field.

Main Methods:

Two-dimensional electrophoresis (2D-PAGE) based environmental proteomics.
Liquid chromatography-mass spectrometry (LC-MS) based environmental proteomics.
Bioinformatic integration with mass spectrometry.

Main Results:

Highlights key publications and significant scientific discoveries in environmental proteomics.
Discusses the integration of experimental mass spectrometry with bioinformatics.
Identifies critical improvements in sample handling and data analysis.

Conclusions:

Environmental proteomics is a rapidly advancing field with significant potential.
Improved sample handling and bioinformatics integration are crucial for future progress.
The synergy between metagenomics and proteomics offers new insights into environmental systems.