I am looking for a successful protein extraction protocol for soils. I have been favouring detergent based methods using Alkaline SDS, TCS precipitation, and solubilization in guanidine buffer, however in my hands I cannot seem to produce a successful 1D gel separation. I have not been using the desalting step by C18 yet as I did not want to loose too many proteins.
Soils are an extremely difficult matrix to extract proteins out of. Our group has been researching this for many years now, and we were able to publish a paper with a good methodology for this. You have to actually block the binding sites within the soil to keep the raw silica from scavenging up your proteins. It is very involved, but the paper explains the "where and why" behind each step. http://www.ncbi.nlm.nih.gov/pubmed/23776032 or http://onlinelibrary.wiley.com/doi/10.1002/pmic.201300003/abstract%3bjsessionid=925FBC4C2A2023E213DD470B588A0BD2.d02t02
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