A method for MSE differential proteomic analysis of archival formalin-fixed celloidin-embedded human inner ear tissue

► We have developed a liquid chromatography-mass spectrometry method for tissue sections embedded with celloidin. ► Five different tissue extraction methods were used to evaluate formalin de-cross-linking. ► Four methods were used to evaluate celloidin removal for liquid chromatography-mass spectrometry. ► The methods judged best were applied to formalin-fixed celloidin-embedded sections of mouse inner ear samples, and human inner ear and human otic capsule bone sections. ► Proteins from all major cellular components were detected in the formalin-fixed celloidin-embedded archival human temporal bone sections.