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Keywords:

  • Liquid extraction surface analysis;
  • Microproteomics;
  • Shotgun proteomics;
  • Signaling pathway;
  • Tubo-ovarian cancer

Purpose

We have developed a new method for rapid analysis of a specific region on formalin fixed and paraffin embedded (FFPE) tissue sections. This method combines advantages of direct tissue MS analysis keeping histological information and conventional proteomics approaches for confident identification of proteins in complex sample.

Experimental design

After histological annotation, heat-induced antigen retrieval is performed on FFPE tissue. Using a chemical inkjet printer, trypsin is deposited on discrete regions of less than 1 mm2. After protein digestion, a liquid extraction is performed to retrieve all the peptides. Data coming from identification of proteins in cancer and benign region are compared.

Results

In total, 3649 unique peptides were identified (with a peptide strict false discovery rate less than 1%) corresponding to 983 and 792 nonredundant protein groups identified in benign and cancer region, respectively. A total of 123 protein groups are found only in cancer region and 315 are specific to the benign part. From these data, it has been possible to obtain different important signaling pathways involved in cancer processes and some proteins already known as biomarkers.

Conclusions and clinical relevance

This new approach using a combination of localized on-tissue protein digestion and liquid microextraction followed by LC-MS/MS analysis is useful for advancing our understanding of cancer biology. It is a rapid and innovative technique that will contribute positively to clinical proteomics.