title: High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue.
abstract: 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.
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Alice
authors.initials: A
authors.lastname: Ly
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Achim
authors.initials: A
authors.lastname: Buck
authors.affiliation: Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Balluff
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Na
authors.initials: N
authors.lastname: Sun
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Karin
authors.initials: K
authors.lastname: Gorzolka
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Annette
authors.initials: A
authors.lastname: Feuchtinger
authors.affiliation: Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany.
authors.forename: Klaus-Peter
authors.initials: KP
authors.lastname: Janssen
authors.affiliation: Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.
authors.forename: Peter J K
authors.initials: PJ
authors.lastname: Kuppen
authors.affiliation: Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.
authors.forename: Cornelis J H
authors.initials: CJ
authors.lastname: van de Velde
authors.affiliation: Institute of Pathology, Technische Universität München, Munich, Germany.
authors.forename: Gregor
authors.initials: G
authors.lastname: Weirich
authors.affiliation: Institute of Pathology, Technische Universität München, Munich, Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Erlmeier
authors.affiliation: Institute of Pathology, Technische Universität München, Munich, Germany.
authors.forename: Rupert
authors.initials: R
authors.lastname: Langer
authors.affiliation: Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Aubele
authors.affiliation: Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Horst
authors.initials: H
authors.lastname: Zitzelsberger
authors.affiliation: Centre for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, the Netherlands.|Fondazione Pisana per la Scienza ONLUS, Pisa, Italy.
authors.forename: Liam
authors.initials: L
authors.lastname: McDonnell
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Aichler
authors.affiliation: Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Axel
authors.initials: A
authors.lastname: Walch
mesh_terms: D000585:Aminacrine / Q000378:metabolism; D005557:Formaldehyde / Q000378:metabolism*; D005583:Fourier Analysis; D006801:Humans; D055432:Metabolomics / Q000379:methods*; D008970:Molecular Weight; D016612:Paraffin Embedding; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D016707:Tissue Fixation
chemical_list: D005557:Formaldehyde; D000585:Aminacrine