You can please refer to the links below to obtain certain interesting informations:-

1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413887/

2. http://pubs.acs.org/doi/abs/10.1021/pr100787q?journalCode=jprobs

3. http://www.nature.com/ismej/journal/v1/n3/full/ismej200739a.html

4. https://books.google.co.in/books?id=Sa5v5d2Kb50C&pg=PA268&lpg=PA268&dq=extraction+of+proteins+from+soil+matrix&source=bl&ots=wMfDN1aFN-&sig=FV5Lmir64_h_xBnJ26l7ekyU2d0&hl=en&sa=X&ved=0CEQQ6AEwBWoVChMIjf3njeqAyAIVjxmOCh1ytQXd#v=onepage&q=extraction%20of%20proteins%20from%20soil%20matrix&f=false

Did you try running the soil sample through an ion-exchange resin, micropore filters, ultrafiltration?

You might try using (NH4)2SO4 to precipitate the protein. But first you must determine the % (NH4)2SO4 that will precipitate your protein then carry out gel filtration to partially purify the protein

It is better to dilute the soil solution to many folds for further extraction and identification of your protein.

Soil is rich source of biomolecules as well as microorganisms....a gram of soil may  contains up to billions of microorganisms normally they do have proteins........

If you go for sterilization u may loose or denature the desired protein since u treat with temp...

My advice is go for the dilution and try to identify the desired protein by determining molecular weight using SDS PAGE so then ppt the protein by ammonium sulphate,Dialyse and gor  the Chromatographic technique for further purification...

Regards

Mohan Kumar S

I really do appreciate the suggestions I've received so far. Thank you all.

I have all the papers suggested by Sandip (except the book chapters) and I did a trial experiment based on one of the methods suggested by the authors of those papers. An amount of the compost sample was homogenized and boiled for 10 mins in a Tris-HCl buffer containing 5% SDS followed by precipitation with 25% TCA overnight. The precipitate was a dark mass, which i think is due to interaction with humic substances. I tried to partially recover some soluble proteins from the precipitate by homogenization with PBS. When I probe the PBS solution with protein detection reagents (BCA assay reagents), the characteristic purple color that will confirm the presence of protein in the solution did not develop. However, when I repeated the same step using 5% SDS, some proteins were detected in the solution using the same BCA assay reagents.

Going forward, am going to try some other methods and profile the proteins using SDS-PAGE and immunochemical assay.

I thought about micropore filters, those with 0.45 microns pore size did not work. Maybe some other sizes will work. 

It is quite difficult to completely remove the humic acid component from soils. The most successful method of soil protein identification and analysis (numerically speaking)  has been the method adapted from Chourey et al. 2010 and used in a multiomic study of the antartic soils . http://www.nature.com/nature/journal/v521/n7551/abs/nature14238.html. The humic substances should not cause too much inhibition of signal on Mass spec,  otherwise , you can run the samples on a gel first and then sequence them.  We are currently conducting some research on soil protein extraction . The paper should be due out in the next few months . We have not even  attempted to measure protein concentrations in the soil , because there does not seem to be any accurate or even semi accurate method available.  There are many  things in the soil that will react with protein assays. In the case of BCA , it has been shown that it  proportionally binds to humic acids . There are also other factors to take into acccount such as the pH of the soil since the BCA reaction takes place under alkaline conditions and then there may be the presence of other Cu+ ions in your soil sample ?  This piece of research ( https://www.researchgate.net/publication/223785340_Critical_evaluation_of_methods_for_determining_total_protein_in_soil_solution    ,) states that  there are no commercially available kits that make any sensible measurements of soil protein. The best solution I can think of is to take a known quantity of protein and add humic acid to it in the same proportion that it exists in your soil. you can make trial measurements with this and then apply that factor to your analysis of real soils. If you do come across new methods of soil protein measurement please let me know as it would make a welcome addition to my research.

Article Critical evaluation of methods for determining total protein...

We had no problem detecting the protein with BCA agent with the method in our paper  http://www.nature.com/nature/journal/v521/n7551/abs/nature14238.html, so I'm not sure I would blame the humics if you see the coloration. Humics behaved like peptides and it's extremely difficult to remove them. One solution could be to quickly centrifuge to get a cell pellets before the protein extraction (you will miss some extracellular proteins but your MS/MS spectra will be cleaner). Another interesting paper on that topic: Proteomics. 2013 Oct;13(18-19):2776-85. doi: 10.1002/pmic.201300003. Epub 2013 Aug 16.

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Good luck!