Computational protocol: Correlative mass spectrometry imaging, applying time‐of‐flight secondary ion mass spectrometry and atmospheric pressure matrix‐assisted laser desorption/ionization to a single tissue section

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Protocol publication

[…] Image datasets from TOF‐SIMS (.ITM files from ION‐TOF were exported into. GRD by SurfaceLab software) and AP‐MALDI‐MS (.RAW file from Thermo Fisher Scientific) were converted into imzML using the “toImzmlModule” converter developed by Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA, Saclay, France), and the “RAW to imzML” converter developed by Justus Liebig University, respectively. As a result, the imzML files were processed using MSiReader, a free open‐source MSI software. This vendor‐neutral interface was built on Matlab by Robichaud et al. The ion selection bin width (m/z window) of the images generated from the MALDI‐MS dataset was Δm/z = 0.01, and Δm/z = 0.2 for the TOF‐SIMS dataset. Additional details of the imzML conversion and processing are available online. Note that the TOF‐SIMS and AP‐MALDI‐MS images have not been normalized or interpolated. […]

Pipeline specifications

Software tools raw to imzML converter, MSiReader
Application Mass spectrometry imaging
Organisms Homo sapiens
Chemicals Cholesterol, Fatty Acids, Phosphatidylcholines