Clinically relevant formalin-fixed and paraffin-embedded (FFPE) tissues have not 
been widely used in neuroproteomic studies because many proteins are presumed to 
be degraded during tissue preservation. Recent improvements in proteomics 
technologies, from the 2D gel analysis of intact proteins to the "shotgun" 
quantification of peptides and the use of isobaric tags for absolute and 
relative quantification (iTRAQ) method, have made the analysis of FFPE tissues 
possible. In recent years, iTRAQ has been one of the main methods of choice for 
high throughput quantitative proteomics analysis, which enables simultaneous 
comparison of up to eight samples in one experiment. Our objective was to assess 
the relative merits of iTRAQ analysis of fresh frozen versus FFPE nervous 
tissues by comparing experimental autoimmune encephalomyelitis (EAE)-induced 
proteomic changes in FFPE rat spinal cords and frozen tissues. EAE-induced 
proteomic changes in FFPE tissues were positively correlated with those found in 
the frozen tissues, albeit with ∼50% less proteome coverage. Subsequent 
validation of the enrichment of immunoproteasome (IP) activator 1 in EAE spinal 
cords led us to evaluate other proteasome and IP-specific proteins. We 
discovered that many IP-specific (as opposed to constitutive) proteasomal 
proteins were enriched in EAE rat spinal cords, and EAE-induced IP accumulation 
also occurred in the spinal cords of an independent mouse EAE model in a 
disability score-dependent manner. Therefore, we conclude that it is feasible to 
generate useful information from iTRAQ-based neuroproteomics analysis of 
archived FFPE tissues for studying neurological disease tissues.