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FFPE Tissue Proteomics

Mass Spectrometry and Selected Reaction Monitoring (SRM)

Mass spectrometry is the most sensitive and specific proteomic detection method available. In a typical experiment, proteins are digested with a protease, e.g., trypsin. The resulting peptides can then be analyzed using mass spectrometry. Selected Reaction Monitoring (SRM) is a mass spectrometry method for quantitation of proteins. It uses the actual sequences of target peptides unique to the protein or proteins of interest, not antibody-epitope interaction, to detect and measure them in the sample with absolute specificity. The technique can be used to measure the relative or the absolute presence of proteins. It is easily multiplexed to simultaneously measure large numbers of different proteins in a sample.

The Liquid Tissue® Process

The patented Liquid Tissue®-SRM assays are based on Expression Pathology’s proprietary processing technologies and Selected Reaction Monitoring, a powerful mass spectrometry analysis technique. The assays can be used to analyze protein expression directly in standard formalin-fixed paraffin-embedded (FFPE) patient tissue samples from tissue blocks or needle biopsies.

Formalin-fixed proteins in the dissected tissue are solubilized using the Liquid Tissue® protocol. The protocol overcomes the cross-linking, to give a completely solubilized tryptic digest, ready for mass spec analysis. Using advanced Triple Quad mass spectrometry instrumentation unique peptides are measured.

The patented Liquid Tissue® reagents and protocol integrate extraction of total proteins from FFPE samples with tryptic digestion so that samples can be analyzed by mass spectrometry. The samples are clear, dilutable, digests of the entire protein content, 100% representative of the collected material.

Cells are normally collected from a tissue section on a slide using needle dissection or microdissection. Formalin-fixation is an extremely powerful preservation agent. Once a tissue specimen is fixed, it can be stored at room temperature for a very long time. The Liquid Tissue® protocol can be used with new or old FFPE tissue samples for retrospective or prospective analysis, validation, or diagnostic purposes.