1 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada. marcos.difalco@concordia.ca.

Proteomics is the large-scale analysis of proteins rendered possible by modern mass spectrometry analysis methods capable of identifying thousands of peptides/proteins in a fast high-throughput manner. Here I describe protocols for the preparation of fungal culture protein samples for mass spectrometry-based proteomics analysis including protein sample cleanup, proteolytic digestion, LC-MS/MS separation, and database search protein identification.