For a specific phosphosite, maybe we can find several phosphopeptides containing such a phosphosite in phosphoproteomics data, but these phosphopeptides are different and thereby have different detected values (See the picture below).
How do you usually quantify the fold change of the phosphosite if such a site from different peptides (e.g. S27 in the picture)?
From your example, the phosphopeptides all contain more than one phosphosite, so it may cause different quantified results.
you'll have to quantify separately the difference phosphopeptides. if you see 2 fold difference in one peptide and 4 fold difference in the other, you can say that you have 8 fold on that one site. however, you have to normalize it to the changes in the protein in the sample. it may be that the overall protein quantity has fallen and not the phosphorylation.
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