Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies
Characterization of geomicrobial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities and the role they play in regulating atmospheric CO2 levels and the Earth’s climate. A significant challenge in studying soil microbial proteins is their initial dissociation from the complex mixture of particles found in natural soil. Due to bias of the most robust cells, the removal of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in-situ lysis of bacterial cells leads to the expulsion of proteins to the soil surface, which can lead to potentially high levels of adsorption due to the physicochemical properties of both the protein and the soil. We investigated various compounds for their ability to block protein adsorption soil sites prior to in-situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding lysed Escherichia coli proteins to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil textures; use of an optimized desorption buffer further increases the number of identifications.
- Research Organization:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 1114894
- Report Number(s):
- PNNL-SA-92783; 47418; 44717; KP1601010
- Journal Information:
- Proteomics, 13(18-19):2776-2785, Journal Name: Proteomics, 13(18-19):2776-2785
- Country of Publication:
- United States
- Language:
- English
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