Hi James,

Google, or in this case, Progensis is your friend. Go to their website and find the references link (below). Most companies do this type of thing to promote their products.

http://www.nonlinear.com/progenesis/qi/evidence-it-works/references/

Thanks for suggestion. I do

Could you please suggest me future work which can follow the result from pro genesis QI?

After running control total protein and treated sample protein now i do have list of protein with their fold change value. what further i can do to make this data more significant? any analysis in-vitro or in-vivo or computational?

Your next steps depend on the system you are investigating and what tools are available to you. Western Blotting is a popular method for verification, even though there are many problems associated with the technique. It's odd that something as specific as mass spec is "validated" by WB when so many antibodies show a distinct lack of specificity.

That aside, you could use SRM, but that also seems an odd way of validating. ie. we validated our MS data with MS data. It is common though since the techniques are complimentary and people seem to have more confidence in SRM data as the technique has been in use for a long period.

Further computational analysis will likely give you pretty figures, but do they mean anything? It all depends on what question you are asking. You can do all sorts of analysis, but ultimately you have to decide what question you are asking and how to go about answering that question in the best way possible.

Good luck,

Peter