I don't have an idea about mass specs of proteins but am curious to know if it is possible to have a relative abundance of phosphorylated/unphosphorylated protein from mass spec data?
If you don't know what phospho sites you want to quantify before hand, this is a good method:
"A large-scale method to measure absolute protein phosphorylation stoichiometries."
http://www.nature.com/nmeth/journal/v8/n8/abs/nmeth.1636.html
If you do know the phospho sites/states you can use SRM-MS. Here is a paper that came out of my lab a few months ago using SRM-MS:
"Gli protein activity is controlled by multisite phosphorylation in vertebrate Hedgehog signaling."
http://www.sciencedirect.com/science/article/pii/S221112471300733X
Let me know if this answers your question or if you have any more questions.
Article A large-scale method to measure absolute protein phosphoryla...
Article Gli Protein Activity Is Controlled by Multisite Phosphorylat...
If your question is just "how many phosphorylated proteins are there in this sample", then yes, that's pretty easy. If you actually find all proteins that are phosphorylated may still be the question, it depends on the techniques used to fractionate your sample, the MS itself etc. But it's a very well established thing to do in MS.
http://lab.rockefeller.edu/chait/pdf/01/01_McLachlin_current-opinions.pdf
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