The effect of polyethylene glycol 20,000 on protein extraction efficiency of formalin-fixed, paraffin-embedded tissues

The optimal conditions and procedures for efficient and reproducible protein extraction of FFPE tissues have not yet been standardised and new sensitive techniques are continually being developed and improved upon. To our knowledge, there is no general agreement as to the choice of detergent or buffer system (and/or addition of PEG 20,000) required for efficient and reproducible protein extraction from human FFPE tissues. Moreover, the effect of PEG 20,000 on protein extraction efficiency has not been evaluated using human FFPE colorectal cancer tissues. This study therefore aims to assess the impact of PEG 20,000 on the protein extraction efficiency, reproducibility, and protein selection bias of the protein extraction buffer used for FFPE colonic resection tissue in label-free LC-MS/MS analysis. The sample pellets were also tested for residual protein, not extracted in the initial extraction. The results show that the absence of PEG 20,000 increases the number of peptides and proteins identified by unfractionated LC-MS/MS analysis, and the method is more reproducible. However, no significant differences were observed with regard to protein selection bias. We propose that studies generating high protein yields would benefit from the absence of PEG 20,000 in the protein extraction buffer.