FFPE tissue analysis

Formalin fixation and paraffin-embedded (FFPE) is the most common way to preserve clinical specimens and archived tissue banks represent a huge potential for protein biomarker studies. 

Explore how robust workflows combined with short gradients on the Evosep One is a perfect match for the analysis of large cohorts of patient samples.

The big value of FFPE

FFPE is a specific way of preservation and preparation of biopsy specimens that can be used in several ways, for example examination, diagnostic and experimental research.

The tissue sample is fixed in formalin to preserve the proteins and the vital structures of the tissue. Then the sample is covered in a paraffin wax block to ease the process of slicing it for microscopic examination.

FFPE samples can be stored in biobanks and represent a valuable source of material to facilitate the study of biomarkers for targeted therapies as the proteins are very efficiently stored in FFPE over several years.


While large biobanks offer an invaluable resource for clinical and biomarker research, it has been challenging to integrate FFPE tissue samples with proteomics studies.

Sensitive and reproducible workflows are needed for clinical studies in general, but more important for sample types as FFPE, where the biggest issue is to reverse the crosslinks and efficiently extract proteins.

The Evotip is an essential part of the Evosep technology, which serves as a disposable trap column. This is a significant advantage for challenging samples like FFPE to ensure a robust pipeline.


Researchers from the Kuster Group at the Technical University of Munich have established a robust workflow to support the analysis of large cohorts of patient samples using FFPE tissue.

They focused on finding a reasonable balance between achieving high proteome depth and limiting the overall analysis time. By taking advantage of the Evotip, they compared online gas phase fractionation by FAIMS to be on par with classic stagetip based high-pH fractionation but requiring 50% less sample and reducing sample handling.

They were able to identify 5000-6000 proteins from lymph node, lung and prostate tissues respectively in less than 3 hours of analysis time.

Read publication here


FFPE tissue analysis on evosep One

FFPE tissue analysis on the Evosep One

available on demand

In this webinar, we focus on how robust workflows combined with short gradients on the Evosep One is a perfect match for the analysis of large cohorts of FFPE samples.

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Evosep One solves the proteomics dilemma – covering high throughput analysis and proteome depth
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end-to-end, fully automated digestion protocol and evotip pure workflow on the opentrons ot-2
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fully automated, rapid, robust sample loading on evotip pure with the agilent assaymap bravo
EVOSEP ONE: A Standardized Separation
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