Published November 26, 2018 | Version v1
Dataset Open

MALDI imaging of mouse kidney peptides - test dataset

  • 1. Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
  • 2. Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany


This imzML test file is concise but meaningful as a training data set in the Galaxy training network (

One 6 µm thick section of formalin-fixed paraffin-embedded mouse kidney (from 6 month old, male, C57 black 6 mice) was mounted onto an indium-tin oxide (ITO) glass slide, deparaffinized and subjected to antigen retrieval in citric acid (pH 6, 100°C, 1h). Before and after antigen retrieval the sample was washed with 10mM ammonium bicarbonate buffer. After air drying, four 1 µl spots of Bombesin (0.01 mg/ml) were placed around the tissue to control digestion. Trypsin was sprayed onto the tissue with the iMatrix Sprayer and the sample was incubated for 2 h at 50°C in a humid chamber. Internal Calibrants (Angiotensin I, Substance P, [Glu]-Fibrinopeptide B, ACTH 18-39) were mixed with α-Cyano-4-hydroxycinnamic acid (CHCA) matrix and sprayed onto the sample.

The sample was measured with the Applied Biosystems/MDS SCIEX 4800 MALDI TOF/TOF™ Analyzer in reflector positive ion mode and a spatial resolution of 150 µm. The acquired Analyze7.5 file was loaded into Cardinal and filtered to reduce file size and decrease analysis time: Filtering was done for m/z values between 1220 and 1625 as well as pixel that represent about half of the kidney and one Bombesin digestion control spot. The data was exported in the common data format imzML.



Files (59.3 MB)

Name Size Download all
57.0 MB Download
2.3 MB Download