The gut microbiota is a dynamic community that is pivotal for human health and fitness. Dysbiosis of the gut microbiota can cause a series of problems. By doing metaproteomic analysis, researchers can look at gut microbiota from a new angle. Since brought up in 2004, metaproteomics, a subject that focuses on all the genes and proteins identified from complex communities, has undergone tremendous progress in the past decade. Back in the early stages, metaproteomic research is proceeded mainly by the methods of 2D-gel electrophoresis and followed by were for mass spectrometry analysis of single proteins one after another manually, which are time-consuming, laborious and relatively low throughput. And now, more advanced technologies have been put into use in metaproteomic research and offer the ability to resolve genotype-phenotype linkages from gut microbiota samples. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) can detect tens of thousands of proteins from microbial populations within a single sample, and amino acid sequences and relative abundance information of detected peptides are also determined, which allows for the characterization of expressed protein functions within communities and specific matches to be made to microbial lineages, with potential subspecies resolution.
Figure 1. Applications of metaproteomics in the study of the gut microbiota (Xiao 2017)
CD Genomics, as a preeminent corporation that has many years of experience in proteomics, provides leading gut metaproteomics LC-MS/MS services, the workflow generally falls into the following steps:
Protein Extraction
Sample preparation (protein extraction) is a key step in proteomics research, with the quality of the sample weighing heavily on the subsequent steps. We provide delicate protein extraction techniques according to the state of the raw material and research purpose, to guarantee an outcome with high fidelity and reliability.
Protein Purification
The purification of proteins is another critical step to ensure sample quality for LC-MS/MS detection. We provide various solutions such as FASP digestion and SDS-PAGE, all towards a solitary goal – the accuracy and fidelity of testing results.
Tryptic Digestion
Tryptic digestion breaks down proteins into peptides for LC-MS/MS detection, we offer solutions including FASP digestion and in-gel digestion.
LC-MS/MS
Our LC-MS/MS instrument can produce tens of thousands of high-resolution spectra per hour, which enables in-depth analysis of the gut metaproteome and uncovers various information including protein abundance, functions, and even genotype-phenotype linkages coupled with genomic technologies.
Figure 2. Overview of a metaproteomics workflow based on LC-MS/MS (Ryan 2013)
Data Analysis
Combined with optimized algorithms and powerful computing platforms, we can process the huge amount of data produced by LC-MS/MS, and offer a comprehensive pack from peak lists to protein database searching, and metaproteomics analysis and visualization. Analysis projects include but are not limited to:
- Spectra filtering
- Database search algorithms
- de novo sequencing
- Fetching meta-information
- Group redundant protein identification
- Statistical test
- Correlation analysis
- Clustering
- Principal component analysis
- Taxonomy profiles
- Functional profiles
- Pathway analysis
We dedicate to providing the highest level of service in gut microbiota research. To find out more about LC-MS/MS services, please feel free to contact us.
References
1. Xiao M; et al. Metaproteomic strategies and applications for gut microbial research. Applied Microbiology and Biotechnology. 2017, 101.
2. Ryan S; et al. Sample Handling and Mass Spectrometry for Microbial Metaproteomic Analyses. Methods in Enzymology. 2013, 531.
*For Research Use Only. Not for use in diagnostic procedures.