Identifying Protein Complexes by Affinity Purification and Mass Spectrometry Analysis in the Rice Blast Fungus

Affinity purification and mass spectrometry analyses have been used in various organisms to identify �protein complexes and determine protein–protein interactions in vivo. In comparison with the TAP (tandem affinity purification) tag, the 3� FLAG is a relatively small epitope tag. It has been used to systematically identify protein–protein interactions in the budding yeast. We have used the 3� FLAG tag to isolate proteins co-purified with a number of genes in the rice blast fungus, including TIG1 , MST50 , PMK1 , and MST12 . For the example given in the text, five genes homologous to components of the yeast Set3C complex were identified by mass spectrometry analysis.