PNNL

Abstract

Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on fresh frozen or Optimal Cutting Temperature (OCT) embedded specimens. However, these specimens are often in limited supply and lack prospective patient information. Thus, the available archived formalin fixed, paraffin embedded (FFPE) tissue blocks from the Surveillance, Epidemiology and End Results (SEER) registries’ Residual Tissue Repositories represent a significant potential resource for population-based cancer studies. To examine the suitability of these tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with global proteomics and 18 with phosphoproteomics using isobaric labeling. All samples, regardless of age, yielded suitable protein mass after extraction for global analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although fewer protein and phosphopeptide identifications were made than from similar OCT specimens, we found no statistically significant differences in protein quality or quantity correlating with collection site or specimen age. These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for global proteomic investigations with some caveats.