Dataset Open Access

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

Föll, Melanie

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').

Files (568.4 MB)
Name Size
all_files.ibd
md5:d94de769b9c9322bdfee29a347ee10d8
466.4 MB Download
all_files.imzml
md5:1bcc064b7893afafb361a127c4843e51
16.8 MB Download
all_files_annotation.tabular
md5:10860d950903e8c999fec74274e5e04e
169.3 kB Download
combined_image_all_files.pdf
md5:337c9c08529c4aa463c5993347f6a6bc
53.7 kB Download
conrol.imzml
md5:ea72cc1743f8f2b034fc7b991badcd09
770.1 kB Download
control.ibd
md5:36159b018af8e2998fcf0beb8cd61652
21.4 MB Download
Glycan_IDs.tabular
md5:16a3cb320ac7400c359b3c9d20117cf2
1.5 kB Download
treated1.ibd
md5:580bfed3ca5ab53514fcf32c3be30427
60.6 MB Download
treated1.imzml
md5:0524443ff39eb97e115ce742d46ecedf
2.2 MB Download
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