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Related Experiment Video

Updated: Dec 26, 2025

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
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A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

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A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis.

Fabian Coscia1,2, Sophia Doll2, Jacob Mathias Bech3

  • 1Clinical Proteomics Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

The Journal of Pathology
|March 11, 2020
PubMed
Summary
This summary is machine-generated.

Formalin fixation and paraffin-embedding (FFPE) tissue analysis via mass spectrometry (MS) proteomics is now efficient. This streamlined workflow enables rapid, quantitative profiling of large FFPE tissue cohorts for patient phenotyping.

Keywords:
FFPE tissueadenomabiobank sampleshigh-throughput, protocol, biomarker discoverymass spectrometryproteomics

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Area of Science:

  • Biomedical research
  • Proteomics
  • Histopathology

Background:

  • Formalin fixation and paraffin-embedding (FFPE) is standard for tissue preservation in clinical diagnostics.
  • FFPE archives are crucial for research, but protein extraction and mass spectrometry (MS)-based proteomics analysis remain challenging.
  • Efficient and streamlined MS-based proteomic workflows are needed for large FFPE tissue cohorts.

Purpose of the Study:

  • To develop and validate a streamlined MS-based proteomic workflow for quantitative profiling of FFPE tissues.
  • To demonstrate the workflow's applicability to diverse clinical pathology specimens and sample amounts.
  • To assess the feasibility of analyzing large FFPE tissue cohorts efficiently.

Main Methods:

  • Development of an MS-based proteomic workflow for direct analysis of FFPE tissues from histopathology slides.
  • Utilized state-of-the-art data dependent acquisition (DDA) and data independent acquisition (DIA) MS techniques.
  • Applied the workflow to clinical pathology specimens, including low-input samples from laser microdissection.

Main Results:

  • The workflow enables quantitative proteomic profiling of FFPE tissues in rapid, single-run analyses (100 min).
  • Broad applicability demonstrated across various sample types and amounts, including challenging low-input tissues.
  • Analysis of a >100-sample adenoma cohort was completed in less than a day.
  • Protein identification showed a slight decrease in samples stored >15 years, but proteomic subtypes were independent of archival duration.

Conclusions:

  • FFPE tissues hold significant promise for patient phenotyping through unbiased proteomics.
  • The developed workflow is robust, timely, and streamlined for analyzing large FFPE tissue cohorts.
  • This approach facilitates efficient utilization of FFPE archives for biomedical research and clinical insights.