Training dataset: MALDI imaging of N-glycans in murine kidney sections

The files provided here are all adopted from the PRIDE PXD009808 datasets and the corresponding publication: Ove J. R. Gustafsson, Matthew T. Briggs, Mark R. Condina, Lyron J. Winderbaum, Matthias Pelzing, Shaun R. McColl, Arun V. Everest-Dass, Nicolle H. Packer, Peter Hoffmann. “MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney.” Analytical and Bioanalytical Chemistry (2015) 407: 2127. https://doi.org/10.1007/s00216-014-8293-7

Three 6µm sections of formalin-fixed paraffin-embedded murine kidney tissue specimens were prepared for MALDI imaging. To release N-linked glycans, PNGase F was printed onto two kidney sections. In the third section one area was printed with buffer to serve as a control and another area was covered with N-glycan calibrants (Gustafsson et al., Figure 4 a-c). 2,5-DHB matrix was sprayed onto the tissue sections and MALDI imaging was performed with 100 µm spatial resolution using a MALDI-TOF/TOF instrument.

We processed the original imzML files to make them concise but meaningful as training data sets in the Galaxy training network (https://galaxyproject.github.io/training-material/).
We reduced the m/z range to 1250 – 2310 and resampled the m/z values with a step size of 0.1. The main part of the training is based on the control and first treated kidney file for which we selected representative pixels to further decrease file size (files: ‘control’, ‘treated1’). To test the results on the complete dataset we also provide a file in which both treated kidney sections, the control and the calibrant files are combined after decreasing and resampling the m/z range as described above. The combined file was normalized to the total ion current (TIC) (file: ‘all_files’). All processing steps were performed on https://usegalaxy.eu with the tools ‘MSI filtering’, ‘MSI combine’ and ‘MSI preprocessing’ in version 1.12.1.3).
Additionally, the LC-MS/MS results were extracted from table S2 of the publication by Gustafsson et al. and are provided as tabular file to enable the N-glycan identification (file: 'Glycan_IDs').