Two key methods to preserve tumor tissues in biobanks are broadly adopted: formalin-fixation and paraffin-embedding (FFPE) and optimal cutting-temperature compound (OCT)- embedding and subsequent freezing, of the tissue specimens. Multiple proteins can be quantified simultaneously from the same sample using mass spectrometry (MS). However, applying MS to FFPE and OCT samples carries several technical challenges such as background artifacts from embedding materials and protein alteration. The differences in the. quality of retrieved protein expression data from FFPE compared to matched OCT samples are not well-characterized.