Formalin-fixation is also considered to be a superior preservative, since formaldehyde quickly and easily penetrates and fixes tissues because of its small molecular size, it causes minimal tissue shrinkage and distortion, and produces exceptional staining results in histopathology. The current universal tissue preservation method of choice is formalin-fixation and paraffin-embedment, to avoid tissue auto-proteolysis and putrefaction, and to allow tissue specimens to be analyzed and examined at a later stage. Tissues from biopsies, resections and/or surgery are routinely taken from patients as a treatment option and/or to facilitate more accurate diagnosis. Block age mainly affects initial protein extraction yields and does not extensively impact on subsequent label-free LC-MS/MS analysis results. The results indicate that the amount of protein extracted is significantly dependent on block age ( p 0.1). Data are available via ProteomeXchange with identifier PXD017198.
Data were evaluated in terms of protein concentration extracted, peptide/protein identifications, method reproducibility and efficiency, sample proteome integrity (due to storage time), as well as protein/peptide distribution according to biological processes, cellular components, and physicochemical properties. A sample size of n = 17 patients per experimental group (with experiment power = 0.7 and α = 0.05, resulting in 70% confidence level) was selected. This study investigated protein extraction efficiency of 1, 5, and 10-year old human colorectal carcinoma resection tissue and assessed three different gel-free protein purification methods for label-free LC-MS/MS analysis. In addition, the optimal sample preparation techniques required for accurate and reproducible results from label-free LC-MS/MS analysis across block ages remains unclear. However, the effect of long-term storage, at resource-limited institutions in developing countries, on extractable protein quantity/quality has not yet been investigated. FFPE blocks can be stored under ambient conditions for decades, while retaining cellular morphology, due to modifications induced by formalin. Since most pathology institutes routinely preserve biopsy tissues by standardized methods of formalin fixation and paraffin embedment, these archived FFPE tissues are important collections of pathology material that include patient metadata, such as medical history and treatments. To elucidate cancer pathogenesis and its mechanisms at the molecular level, the collecting and characterization of large individual patient tissue cohorts are required.
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