Post-translational modifications are known to regulate protein properties in response to environmental or developmental changes. Current methods are inadequate to measure many modifications, so a proof of concept for an approach which determines the global degree of modification was performed. This was exemplified by monitoring the protein modification changes of Pyk1 in yeast. The associated mass spectrometric raw data and data processing code are here provided as described in the PhD thesis (Chapter 5) of Maxime den Ridder.