Figure 12.

Ideal design of an AP-MS experiment with negative controls and biological replicates. Hypothetical experiment involving the purification of four different baits (colored circles) and a negative control (grey circle). Each of the biological replicate experiments is performed for each of the baits in a single batch. Different biological replicates are performed on batches of cells harvested at different times, and for which purification and proteolysis is done on different days. Notice the randomization of the loading order of the samples on the mass spectrometer to help preventing bias (e.g. carry-over).