Why is it difficult to compare phosphorylation in proteins and peptides?

In a recent project, I wanted to find out in what way phosphorylation of certain peptides is influenced by a specific environmental cue. So in a published research article I came across a list which included a number of phosphoproteins that correlated well with the given cue. However, when I compared the levels of phosphorylation in those phosphoproteins with my phosphopeptides that I had shown to correlate with the given cue as well, there was almost no overlap. Since I am not from the proteomics field, I lack basic knowledge to understand what exactly is the problem with this comparison. Any explanation or suggestion for readings (research paper/book) would be much appreciated!