This depends on your protein and your needs. I guess you would like to do an affinity purification? Is your protein tagged? This can help a lot as you can find pre-established systems for the purification that only need minor changes for a good pourification. Purifying untagged proteins can be a lot more work to do.

But anyway it depends on what is important for you: binding capacity, resolution or scalability, etc. I would say there are no best techniques there are only techniques more suitable for a specific application than others.

Dear Shakthi,

Can you please provide a few more information on the purpose of protein purification? Would you like to isolate a certain protein for in-depth studies or prospective applications? Do you already have information about it, for instance its molecular weight? Do you have a detection or an activity assay? Which level of purity do you need in the end? Or do you want to study all proteins included in the mixture, for instance to search for different enzymatic activities?

If you don't want to answer these questions I would suggest ion exchange chromatography or hydrophobic interaction chromatography, and finally a size exclusion chromatography.

The go-to method for protein purification is usually fast protein liquid chromatography (FPLC) or conventional liquid chromatomatography (e.g. with a gravity or peristaltic pump fed agarose/sepharose-based column). While crude purifications can be generated by various precipitation steps (e.g. Spermidine precipitation, sulfate cuts), such preps require further cleaning before they are suitable for most uses.

There are no "best" techniques, the choice depends on the protein, the desired amount, the desired purity, and available resources/time.

If what you are asking about is how best to prepare protein extracts from B. cereus, then I suggest you take a look at the techniques used by people doing bacterial proteomics.

Shakthi,

You have asked a very vague/general question. There are many ways to purify proteins, each with their advantages and disadvantages, each more suited to certain proteins/sources than others. There is no single best technique, and to explain about all of them well enough to help you make a good choice is probably like writing a book chapter!

In fact, I am sure you will find detailed resources in your dept/univ library. There are also plenty of resources online - you just have to try looking.

Good luck!

EDIT: For some reason all these older replies did not show up when I was replying - so I did not know that everyone had already said it! 

Well.. Thanks for your response.. I am provided with the strains of bacillus cereus and asked to purify a specific protein known as Haloacid dehalogenase... I didn't find its molecular weight yet and I am at the starting point of my research and am planning to do some genome wide analysis of the protein.. 

You can find details of your protein of interest at: http://www.uniprot.org

You can find publications describing the purification of haloacid dehalogenase at: http://www.ncbi.nlm.nih.gov/pubmed/

It seems like people typically clone this particular protein from the original bacteria into E. coli first (which allows them to obtain large quantities of the protein by using a suitable expression plasmid), and then purify it by salting out using ammonium sulfate.