Metaproteomics is the analysis of the proteins, including enzymes, produced by the microbial community present in a sample. Since enzymes are the catalyst molecules that directly mediate metabolic and other cellular processes, detection of a specific protein biomarker is an indicator of activity.
Because the enzyme (e.g. sulfite reductase) is the molecule in the microorganism that directly catalyzes a specific biochemical reaction, detection of the corresponding protein biomarker in the sample is a direct indicator of activity such as sulfate reduction.
Combined with metagenomics results, shotgun proteomics (discovery, global proteomics) can be performed to identify proteins present in an environmental sample. The detection of a specific biomarker peptide indicates that the corresponding gene is expressed, the enzyme is being produced, and the pathway is active.
For known protein/peptide targets, targeted proteomics rather than shotgun proteomics can be performed to quantify those specific biomarkers. Results reported as fmoles/mL.
Target specific biomarker peptides from known enzymes directly responsible microbial processes linked to MIC.
HOW TO USE PROTEOMICS:
Proteomics is an emerging molecular microbiological method (MMM). Consider proteomics analysis when demonstrating a specific microbial activity is a critical, additional line of evidence supporting other MMM such as QuantArray®-MIC or Next Generation Sequencing (NGS).
Use Proteomics to help answer…
- What proteins are being produced?
- Which biochemical pathways are active?
- Is a specific protein/enzyme involved in MIC being produced?
- Are proteins involved in sulfur metabolism being produced?
- Proteins involved in nitrate metabolism present after treatment?
- What is the abundance of a target protein?