Journal Article

High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue

McDonnell, Liam, Walch, Axel, Zitzelsberger, Horst, Ly, Alice, Kuppen, Peter J K, van de Velde, Cornelis J H, Buck, Achim, Aichler, Michaela, Feuchtinger, Annette, Aubele, Michaela, Sun, Na, Janssen, Klaus-Peter, Balluff, Benjamin, Gorzolka, Karin, Weirich, Gregor, Langer, Rupert, Erlmeier, Franziska

2016

Overview

Formalin-fixed paraffin embedding (FFPE) of tissues has been assumed to alter the metabolite content or chemical state, hampering metabolomics studies. Here, Ly et al . describe reproducible metabolomic analysis of FFPE samples by mass spectrometry imaging. Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in metabolite content or chemical state due to tissue processing. We present a protocol for the in situ analysis of metabolite content from FFPE samples using a high-mass-resolution matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR-MSI) platform. The method involves FFPE tissue sections that undergo deparaffinization and matrix coating by 9-aminoacridine before MALDI-MSI. Using this platform, we previously detected ∼1,500 m / z species in the mass range m / z 50–1,000 in FFPE samples; the overlap compared with fresh frozen samples is 72% of m/z species, indicating that metabolites are largely conserved in FFPE tissue samples. This protocol can be reproducibly performed on FFPE tissues, including small samples such as tissue microarrays and biopsies. The procedure can be completed in a day, depending on the size of the sample measured and raster size used. Advantages of this approach include easy sample handling, reproducibility, high throughput and the ability to demonstrate molecular spatial distributions in situ . The data acquired with this protocol can be used in research and clinical practice.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/1647/245/2160 / 631/1647/296 / 631/45/320 / Aminacrine - metabolism / Analytical Chemistry / Biological Techniques / Computational Biology/Bioinformatics / Cyclotron resonance / Data acquisition / Embedding / Formaldehyde / Formaldehyde - metabolism / Fourier Analysis / Fourier transform infrared spectroscopy / Fourier transforms / Histology / Humans / Imaging / Investigations / Ionization / Ions / Lasers / Life Sciences / Mass spectrometry / Mass spectroscopy / Metabolism / Metabolites / Metabolomics / Metabolomics - methods / Microarrays / Molecular Weight / Organic Chemistry / Paraffin / Paraffin Embedding / Paraffins / Pathology / Protocol / Reproducibility / Scientific imaging / Spatial distribution / Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods / Spectroscopy / Tissue Fixation / Tissues