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Qproteome FFPE Tissue Kit

For isolation of full-length proteins from formalin-fixed tissues
  • Standardized, quantitative extraction from FFPE tissue
  • Full-length proteins
  • Low sample requirements

The Qproteome FFPE Tissue Kit uses innovative proprietary chemistry to reverse the crosslinking process of fomalin fixation and deliver full-length proteins ready for subsequent analysis.

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Cat No./ID: 37623
Qproteome FFPE Tissue Kit (20)
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For 20 protein preparations from formalin-fixed, paraffin-embedded tissue samples: Extraction Buffer, Collection Tubes, Collection Tube Sealing Clips
The Qproteome FFPE Tissue Kit is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

Yields comparable to frozen material.

Protein yields from FFPE tissues using the Qproteome kit are comparable to those from frozen material. Protein yields from frozen and FFPE tissues were compared by processing material in parallel, separation by SDS-PAGE, and western blotting. Controls were lysates from SW480 colorectal adenocarcinoma cells (colon), Huh7 human hepatoma cells (liver), SH-SY5Y neuroblastoma cells (rat brain).

Standardized and reproducible protein extraction.

The Qproteome Kit provides standardized and reproducible extraction from FFPE sections. Six FFPE colon tissue samples were processed in parallel. Equal volumes of extracted protein were separated by SDS-PAGE. Proteins were detected using β-actin and Erk2 antibodies after western blotting.

Tissue-specific biomarker identifcation.

Identification of a biomarker specific to certain types of lymphoma. The transcription factor E2A was detected after western blotting of proteins extracted from FFPE lymphoma preparations. E2A was detected in the B-cell lymphoma samples, but was absent in the T-cell lymphoma preparations. The housekeeping gene β-actin was analyzed as a control. (Data kindly provided by Susan Eckerle, Institute for Pathology, University Clinic, Frankfurt, Germany.)

Efficient protein extraction from FFPE tissue.

Proteins are efficiently extracted from FFPE tissue. Samples were obtained from formalin-fixed paraffin-embedded liver preparations using a 1 mm diameter punch, and proteins extracted using the Qproteome FFPE Tissue Kit. Four samples of each size were processed. Protein concentration in the final supernatant was determined using a BCA assay. Data kindly provided by Prof. Dr. Anja Bosserhoff, Institute of Pathology/Molecular Pathology, University of Regensburg, Germany.

Compare FFPE tissue samples at the protein level.

Protein extraction enables comparison of histological samples on the protein level. Two breast cancer biopsy samples, both scored 2+ for the receptor tyrosine kinase HER2 by immunohistochemistry, were processed using the Qproteome FFPE Tissue Kit and analyzed by protein lysate array and western blotting. In sample B, HER2 gene amplification was confirmed by FISH (data not shown). The housekeeping gene β-actin was analyzed as a control. Data kindly provided by Karl-Friedrich Becker and Christina Schott, Technical University of Munich, Germany.


The Qproteome FFPE Tissue Kit delivers efficient protein extraction from FFPE tissue using a standardized protocol for reproducible protein yields (see figure "Standardized and reproducible protein extraction"). Using the Qproteome FFPE Tissue Kit, protein yields are comparable to frozen material, enabling, for example, comparison between different tissues for identification of disease-specific markers (see figure "tissue-specific biomarker identification").



As the standard method for histological tissue preparation, millions of formalin-fixed paraffin-embedded (FFPE) samples are classified and archived each year. Previously, their analysis was limited to histochemical techniques. The Qproteome FFPE Tissue Kit opens this vast, highly valuable resource up to proteomic and protein expression analysis by enabling efficient extraction of full-length proteins suitable for western blotting, protein arrays, and mass spectrometry. For the very first time, proteins or pathway of interest can be investigated in archived FFPE tissues. Probing blots or arrays with multiple antibodies enables simultaneous investigation of proteins, providing a detailed picture of multiple protein expression profiles, for example, in signaling transduction cascades.

Formalin fixation creates chemical crosslinks, stabilizing samples for histological analysis, but rendering any subsequent protein separation (e.g., by SDS-PAGE) impossible. The Qproteome FFPE Tissue Kit uses innovative proprietary chemistry to reverse the crosslinking process and deliver full-length proteins ready for analysis by western blotting or protein array, with subsequent immunodetection (see figure “Compare FFPE Tissue Samples at the Protein Level”).


Sections are deparaffinized and incubated in an Extraction Buffer. After centrifugation, extracted proteins are recovered in the supernatant. Recovered proteins can be mixed directly with sample buffer and loaded onto an SDS-PAGE gel, just like conventional protein samples. No extra expensive equipment or additional processing is required.


The Qproteome FFPE Tissue Kit offers a unique tool for analysis of samples whose pathological status has been determined, but whose precise protein makeup has until now remained inaccessible. Such samples — for example, taken over a course of treatment or from different groups of probands — offer a rich source of information for comparative proteomics and biomarker studies.


Applications SDS-PAGE, Western-Blot, mass spectrometry
Binding capacity/yield 20–80 µg
Fractions isolated One fraction
Sample size 2–3 x 100 mm2 per prep
Start material Formalin-fixed tissues

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Critical factors for molecular analysis of FFPE samples
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