issue on the accuracy of the phospho proteomics data

Question

[alwayshope]

Dear guys,

Do you have any idea for the accuracy of the phosphoproteomics data?

When trying to analyze the data, the protein abundance matrix observed a lot of heterogenous, say,

the protein x can increase a lot (31 to 127, > 4 fold) in biological 1,

but decreased at biological replicate 2 (26 to 12, >2 fold) ;

and decreased at biological replicate 3 (371 to 163, >2 fold);

Many other proteins have the same issue, mess increase/decrease.

Is the abundance matrix normal, or maybe miss labeling in the sequencing process??

Thanks a lot!