title: MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation.
abstract: MALDI imaging mass spectrometry (MALDI-imaging) has emerged as a spatially-resolved label-free bioanalytical technique for direct analysis of biological samples and was recently introduced for analysis of 3D tissue specimens. We present a new experimental and computational pipeline for molecular analysis of tissue specimens which integrates 3D MALDI-imaging, magnetic resonance imaging (MRI), and histological staining and microscopy, and evaluate the pipeline by applying it to analysis of a mouse kidney. To ensure sample integrity and reproducible sectioning, we utilized the PAXgene fixation and paraffin embedding and proved its compatibility with MRI. Altogether, 122 serial sections of the kidney were analyzed using MALDI-imaging, resulting in a 3D dataset of 200GB comprised of 2million spectra. We show that elastic image registration better compensates for local distortions of tissue sections. The computational analysis of 3D MALDI-imaging data was performed using our spatial segmentation pipeline which determines regions of distinct molecular composition and finds m/z-values co-localized with these regions. For facilitated interpretation of 3D distribution of ions, we evaluated isosurfaces providing simplified visualization. We present the data in a multimodal fashion combining 3D MALDI-imaging with the MRI volume rendering and with light microscopic images of histologically stained sections.
  
  
  CONCLUSIONS
  Our novel experimental and computational pipeline for 3D MALDI-imaging can be applied to address clinical questions such as proteomic analysis of the tumor morphologic heterogeneity. Examining the protein distribution as well as the drug distribution throughout an entire tumor using our pipeline will facilitate understanding of the molecular mechanisms of carcinogenesis.
authors.affiliation: Steinbeis Innovation Center SCiLS (Scientific Computing in Life Sciences), Bremen, Germany.
authors.forename: Janina
authors.initials: J
authors.lastname: Oetjen
authors.forename: Michaela
authors.initials: M
authors.lastname: Aichler
authors.forename: Dennis
authors.initials: D
authors.lastname: Trede
authors.forename: Jan
authors.initials: J
authors.lastname: Strehlow
authors.forename: Judith
authors.initials: J
authors.lastname: Berger
authors.forename: Stefan
authors.initials: S
authors.lastname: Heldmann
authors.forename: Michael
authors.initials: M
authors.lastname: Becker
authors.forename: Michael
authors.initials: M
authors.lastname: Gottschalk
authors.forename: Jan Hendrik
authors.initials: JH
authors.lastname: Kobarg
authors.forename: Stefan
authors.initials: S
authors.lastname: Wirtz
authors.forename: Stefan
authors.initials: S
authors.lastname: Schiffler
authors.forename: Herbert
authors.initials: H
authors.lastname: Thiele
authors.forename: Axel
authors.initials: A
authors.lastname: Walch
authors.forename: Peter
authors.initials: P
authors.lastname: Maass
authors.forename: Theodore
authors.initials: T
authors.lastname: Alexandrov
mesh_terms: D000818:Animals; D030562:Databases, Protein; D007668:Kidney / Q000737:chemistry / Q000378:metabolism*; D008279:Magnetic Resonance Imaging; D051379:Mice; D020543:Proteome / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D020543:Proteome
keywords: 3D MALDI imaging mass spectrometry; 3D spatial segmentation; Histology; MRI; Mouse kidney; PAXgene fixation