Purpose: To compare the proteomic profiles of formalin‐fixed, paraffin‐embedded (FFPE) liver biopsy material and matched frozen liver tissue from patients with nonalcoholic steatohepatitis (NASH).

Experimental design: A label‐free mass spectrometry‐based approach was used to profile global protein expression in FFPE and frozen liver biopsy specimens from five patients with NASH.

Results: Eight hundred and sixty proteins were identified with >75% confidence: 225 common proteins were identified in both the FFPE and frozen tissues, and an additional 142 and 493 proteins were identified in the FFPE and frozen tissues, respectively. Functional analyses revealed a general, nonspecific reduction in the number of proteins identified in FFPE tissue compared with frozen tissue. No bias toward proteins located in any specific subcellular compartments or implicated in any particular biological functions was observed. The relative abundance of several proteins with functions relating to the pathogenesis of NASH (peroxiredoxin‐1, fatty acid binding protein 1, fatty acid synthase, vimentin, catalase, and glutathione S‐transferase A1) was similar in FFPE and frozen liver tissues.

Conclusions and clinical relevance: FFPE liver biopsy material from NASH patients can be used for global proteomic analysis and biomarker identification studies, although a universal reduction in the number of identified proteins compared with frozen tissue is likely.