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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

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Site-to-Site Reproducibility and Spatial Resolution in MALDI-MSI of Peptides from Formalin-Fixed Paraffin-Embedded

Alice Ly1, Rémi Longuespée2, Rita Casadonte3

  • 1Bruker Daltonik GmbH, Bremen, Germany.

Proteomics. Clinical Applications
|November 9, 2018
PubMed
Abstract

Insights

Standardizing matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) workflows for formalin-fixed paraffin-embedded (FFPE) tissues improves spatial resolution and site-to-site reproducibility for clinical applications.

Area of Science:

  • Biomedical Imaging
  • Analytical Chemistry
  • Pathology

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for clinical applications of MALDI-MS Imaging (MALDI-MSI).
  • Optimizing in situ tryptic digestion is essential for high-quality MALDI-MSI of FFPE samples.
  • Ensuring reproducibility across different sites is vital for clinical translation.

Purpose of the Study:

  • To enhance in situ tryptic digestion for MALDI-MSI of FFPE tissues.
  • To assess the reproducibility of MALDI-MSI results from different geographical sites.
  • To establish a standardized workflow for reliable clinical application of MALDI-MSI.

Main Methods:

  • FFPE tissues (mouse intestine, human ovarian teratoma, tissue microarrays) were analyzed using MALDI-MSI.
  • Automated spraying with trypsin and CHCA matrix, coupled with deliquescence-based incubation, was employed.
  • Analysis involved a rapifleX MALDI Tissuetyper at 50 µm spatial resolution, with data processed using flexImaging, SCiLS, and R.

Main Results:

  • Trypsin application and digestion were identified as key sources of variation and loss of spatial resolution.
  • The developed workflow successfully discriminated discrete histological features in various tissues.
  • Different sites achieved comparable image quality, as validated by spatial segmentation and Principal Component Analysis (PCA).

Conclusions:

  • A standardized MALDI-MSI workflow is critical for maintaining spatial resolution and achieving site-to-site reproducibility.
  • This standardization facilitates the transition of MALDI-MSI from basic research to clinical practice.
  • The findings support the reliable use of MALDI-MSI for analyzing FFPE tissues in diverse clinical settings.
Keywords:
MALDIformalin-fixed paraffin embedded tissuereproducibilitytissue typingworkflow

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