as discussed above, I would say that 2D-DIGE is by far the best method to do these kind of analysis. 

I recently came across a nice review about proteomic tools for environmental microbiology. It is a good overview and the methods should be applicable for your research as well.

http://www.ncbi.nlm.nih.gov/pubmed/23894077

Thanks all for your suggestions. 

We thought Quantitative proteomics might give us the individual differentially regulated proteins, but due to the experiment cost it may not be feasible at this time point and same goes for 2D-DIGE as well. I could certainly use 2D electrophoresis.

I would recommend mass spectrometry-based proteomics discovery methods if you have decent equipment available. After the initial discovery phase, you might try selective reaction monitoring - if the (triple quad) equipment is available

You can use a new methodology based on gel-free approach (i.e. LC-MS-MS). It is less labor than 2D, but the cost is twice higher. In fact, this approach used a liquid chromatography separation coupled with a MS detector. You can obtain a better separation of protein, and so a higher number of identified protein.