You will have two major concerns:
Coverage: Can the mass spectrometry technique(s) deliver high sequence coverage? With higher coverage, there is a greater statistical chance to detect and identify the peptide containing a modification group.
Occupancy of the modification site: What percent of the protein preparation is modified? If it is low, then the chance of detecting the modified peptide decreases. If the occupancy is high (>30%), then this works in the favor of identifying a modification site.

First, note that, due to its unique sequences, every protein has a different potential to be mapped at high sequence coverage.
Coverage for all proteins increases by:
a)    Starting with a higher amount of protein (>5 μg of protein is desirable) for MS analysis
b)    Making sure that the protein is pure
c)    Using multiple MS instruments/techniques for analysis will increase coverage
d)    Enriching the phosphopeptides using a TiO2 column