1We would like to study the phosphoproteome under control and treatment condition towards which we are looking for literature on the possible methodologies using Pro Q staining with subsequent sypro ruby staining. Could you provide us with this.

2. Subsequent to staining, how would the analysis be done, could you suggest possible softwares available and how these softwares work.

3. How do we rule out differences in phosphorylation status contributed by differential expression of the proteins ( false positives) or could you elaborate on possible normalization strategies.

4. Can Pro Q staining be used in combination with DIGE to study changes in phosphorylation.

Hi Rahul,
Pro Q is a good method to use.
You can do first SyproRuby take a photo with any of your UV imager and then do the Pro Q just after washing the gel 3 times. Then image the phosphrilated proteins.
There are many softwares that you can use. Personaly I used the Image Master from GE. best for doing 2D.
It is easy to use. You just need to download the image you captured and then you need to follow a good help page. If you did not do it before it will take some time to master it.
Normalisation is always difficult in 2D image analysis. There are many ways to normelise . One of the ways is to put a known control in the sample before runing the gel.
Other ways is to load a known amount of protein concentration to all samples.
For the last question yes it can be used for DIEG
Guy