The efficiency of several mechanical-based lysis and extraction techniques, such as Adaptive Focused Acoustics (AFA), probe sonication, and bead beating from yeast isolates was compared for (i) total protein yield, (ii) preservation of enzymatic activity, (iii) fragmentation of proteins, and (iv) protein bias (i.e., the failure to isolate specific proteins). Protein bias was determined from both the number and relative abundance of proteins separated by SDS PAGE and by two-dimensional gel electrophoresis (2-DE) analysis.