What are the disadvantages of using antibody arrays to analyze phosphorylated proteins?

There are several disadvantages of using antibody arrays to analyze phosphorylate proteins. Another disadvantage of these arrays is that they are not cost-efficient, especially when a large quantity of samples or phosphorylation sites need to be analyzed. The availability of antibodies is another issue in regard to these arrays. Antibodies with high specificity and sensitivity may not be readily available for all phosphorylated proteins of interest. This limits the use of these arrays for certain experiments. Another limitation is that antibody arrays have limited coverage of the whole phosphoproteome. This is because they target a predefined set of proteins or phosphorylation sites, which may not capture the entire diversity of phosphorylation activity in a sample. Scientists often combine antibody array techniques with mass spectrometry techniques to try and overcome these limitations. There is also complex data interpretation which requires unique software and training. Lastly, MS provides low throughput as only a few to tens of samples are able to be analyzed per day.