If you are looking at a specific modified protein and/or modification site, Western Blotting. For many frequently interrogated sites such as Histone mods there are antibodies available.

Generic analysis is more difficult. For phosphorylation there are stains that can be used to highlight phosphoproteins on 2D gels, however it is difficult then later to connet the staining to a protein identity and mod position (which is then usually done by MS/MS again).

The above made suggestion is indeed the best alternative. But there some others as well. If your focus on functional importance of the modification in question, you can use some biochemical and molecular biology approaches. For example, by mutating certain amino acids and growing the cells in the presence of 33P or 32P or  (simple pulse chase will do) you can change the relative levels of overall phosphorylation of your protein by either PhosphorImager or autoradiography (the protein of interest needs to be immunoprecipitated before SDS PAGE). You can also employ certain site-specifc proteases to analyze the relative degree of cleavage that will depend on the modification status of the amino acid in question. Functional importance can be verified by checking for known activities of your protein wt vs specific mutation(s). Such experiments can be performed in vitro as well. 

Thank you very much for the suggestion, they were helpful

But to be specific , i need to know how can I study the change in protein-protein interaction specificities by altering the acetylation or phosphorylation of a protein using a drug. There are phospho antibodies available for the protein and I also have the acetylated lysine antibody. The protein is not a histone in this case. 

Hi,

I think such change in interaction can be assessed by immunoprecipitation followed by western blot with the proteins of interest in samples +/- the drug. specific phospho or acetyl mutants of the protein can be generated by site directed mutagenesis and their interactions with the partner can subsequently be checked for further confirmation.