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Fixation and Sectioning01:03

Fixation and Sectioning

Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...
Preparation of Samples for Electron Microscopy01:20

Preparation of Samples for Electron Microscopy

To be visualized by an electron microscope, either transmission or scanning, biological samples need to be fixed (stabilized) so the electron beam does not destroy them and dried thoroughly (desiccated/dehydrated) so the vacuum does not affect them. Fixation needs to be done as quickly as possible because the sample properties will start changing as soon as it is removed from its natural environment. For example, in a tissue sample, the oxygen levels begin decreasing, causing an altered...

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Related Experiment Video

Updated: May 8, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
09:20

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

Proteomic sample preparation from formalin fixed and paraffin embedded tissue.

Jacek R Wiśniewski1

  • 1Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry.

Journal of Visualized Experiments : Jove
|September 12, 2013
PubMed
Summary

This study presents an optimized proteomic analysis protocol for formalin-fixed, paraffin-embedded (FFPE) tissues. The method enables large-scale quantitative proteomic investigation of human disorders from preserved clinical samples.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Pathology

Background:

  • Preserved clinical materials like FFPE tissues are valuable for proteomic research.
  • Investigating human disorders requires robust methods for analyzing proteins in these tissues.

Purpose of the Study:

  • To describe an optimized protocol for large-scale quantitative proteomic analysis of FFPE tissues.
  • To enable in-depth proteomic investigation of human disorders using preserved clinical samples.

Main Methods:

  • Optimized protocol involving FFPE tissue sectioning and microdissection.
  • Filter-aided sample preparation (FASP) for cell lysis and protein digestion with LysC and trypsin.
  • Peptide fractionation using pipette-tip microcolumns for enhanced proteomic depth.

Main Results:

  • Successful quantitative proteomic analysis of FFPE tissues.
  • Achieved depth of analysis covering up to 10,000 proteins from minute sample amounts.
  • Demonstrated a powerful workflow for system-wide disease study and biomarker/drug target identification.

Conclusions:

  • The described workflow is effective for large-scale quantitative proteomic analysis of FFPE tissues.
  • This technique facilitates comprehensive disease research and the discovery of potential biomarkers and drug targets.
  • Enables deep proteomic insights from limited preserved clinical material.