Primary tissue samples are valuable resources for investigators interested in 
understanding disease. In order to maximize the information content that can be 
gained from these precious samples, proper storage, handling, and preparation 
are essential. Some tissue preservation techniques utilize the cryopreservation 
medium, optimal cutting temperature (OCT) compound. While this medium provides 
benefits for traditional molecular studies, certain components can interfere 
with mass spectrometric analyses. Mass spectrometry based proteomics is a 
growing field with many applications for disease research. Our goal is to 
determine a reliable method for separating the proteins from the contaminating 
species in OCT embedded samples, thus making these samples compatible with mass 
spectrometric analyses. The novel applications of ether-methanol precipitation, 
filter-aided sample preparation (FASP), and SDS-PAGE provide researchers with 
protocols for removing OCT contaminating species from valuable samples. The 
results presented in this study show that all three methods reproducibly remove 
OCT; however, precipitation and FASP outperform SDS-PAGE by common proteomic 
metrics.