Based on two-dimensional electrophoresis and LC-MS/MS analysis, “protein fingerprinting” is a powerful approach for protein identification. Here we describe the application of this approach for the characterisation of cellulase cocktails. We report the protein map of a natural secretome, derived from P. decumbens, a fungal strain grown on lignocellulosic biomass; for comparison, protein maps for two commercial mixtures, Celluclast 1.5L and Novozymes SP188, are presented. A secretome protein map derived from P. decumbens can potentially serve as a guide for the design of commercial mixtures; it can be used to develop a standard for quality control to monitor available commercial enzymatic mixtures.