Download these files to open these two example datasets in SCiLS™ Lab:
SCiLS Example Datasets
Hepatocellular & Breast Cancer Sample
Two MALDI Imaging datasets of a hepatocellular carcinoma and a breast cancer tissue, resp., provided by the team of Rick Drake from Medical University of South Carolina, Charleston, South Carolina. To enable spatially correlated glycan profiling from tissue sections, MALDI MSI measurements have been performed after the FFPE tissue was dewaxed, washed, subjected to antigen retrieval, treated with PNGase F and sprayed with CHCA matrix. The dataset was recorded using a timsTOF fleX in positive ion mode with m/z range of 700-4000, and a spatial resolution of 150 μm resulting in 17836 spectra (breast cancer) and 21548 spectra (liver carcinoma).
Matching glycan data against the target list “N-Glycan human”, it can be shown that glycans with specific structural motifs are unique to pathologies within and across tissue types.
We gratefully thank Jade MacDonald and Peggi Angel from MUSC for providing us with this dataset for demo purposes.
Colon Tumor Sample
A MALDI Imaging dataset of a human colon tumor specimen provided by Professor Axel Walch from the Institute of Pathology at Helmholtz Zentrum München, Germany. The dataset reveals distinct tissue types present in the section: tumor, mucosa, submucosa, muscularis propria, and subserosa.
The colon tissue sample was provided as formalin-fixed paraffin-embedded (FFPE) sample, MALDI MSI measurements have been performed after in situ enzymatic trypsin digestion of proteins. Altogether, 12,049 spectra were acquired with a lateral resolution of 150 μm, each spectrum covering a mass range of 600-4000 m/z. After MALDI MSI experiments, the section was hematoxylin and eosin (H&E) stained and microscopic images have been superimposed with the MALDI MSI data. For more details on tissue samples and data acquisition we refer to T. Alexandrov, S. Meding et al. (Journal of Proteomics, 2011).
We gratefully thank Dr. Stephan Meding, Dr. Benjamin Balluff, and Prof. Dr. Axel Walch for providing us with this dataset for demo purposes.
Download both files to open this example dataset in SCiLS™ Lab:
Rat Testis Dataset
A MALDI Imaging dataset of a rat testis sample measured on a high-resolution FT-ICR MS, provided by Dr. Corinna Henkel and Dr. Arndt Asperger (Bruker Daltonics). The data was acquired with a lateral resolution of 10 µm and contains 5670 spectra in the mass range of 150-3000 m/z, each spectrum containing 2,951,625 m/z-bins.
Download both files to open this example dataset in SCiLS™ Lab:
Traumatized Muscle Dataset
A MALDI Imaging dataset of injured skeletal muscles, provided by Dr. Oliver Klein from Charité – Universitätsmedizin Berlin, Germany. The dataset comprises eight muscle specimens containing primary trauma, trauma adjacent, and intact muscles regions.
The muscle samples were provided as formalin-fixed paraffin-embedded (FFPE) samples, MALDI MSI measurements have been performed after in situ enzymatic trypsin digestion of proteins. Altogether, 36,926 spectra were acquired with a lateral resolution of 80 μm, each spectrum covering a mass range of 800-3500 m/z. For more details on tissue samples and data acquisition, see O. Klein et al. (Proteomics, 2014).
We gratefully thank Dr. Oliver Klein for providing us with this dataset for demo purposes.
Download both files to open this example dataset in SCiLS™ Lab:
Mouse Pancreas Dataset
A MALDI Imaging dataset containing a cohort of six sections of mouse pancreas, provided by Prof. Dr. Kathrin Maedler and Dr. Janina Oetjen from the MALDI Imaging Lab, University of Bremen.
This dataset comprises three sections each from two conditions: Mouse pancreas of mice fed with a high fat/ high sucrose diet (HFD) and from normal diet control mice. The sections were covered with sinapinic acid as matrix and data was acquired in the mass range of 2–20 kDa with a lateral resolution of 75 µm. It contains 72,872 spectra with 7679 datapoints per spectrum.
We gratefully thank Prof. Dr. Kathrin Maedler and Dr. Janina Oetjen from the MALDI Imaging Lab, University of Bremen for providing us with this dataset for demo purposes.
Download both files to open this example dataset in SCiLS™ Lab:
Rat Kidney Dataset
A MALDI Imaging dataset of a 10 µm tissue section of a rat kidney. The dataset was acquired with a lateral resolution of 200 µm using sinapinic acid as matrix. It contains 3530 spectra in the mass range of 2–20 kDa, each spectrum containing 7680 m/z bins.
We thank Dr. Lena Hauberg-Lotte and Dr. Janina Oetjen from the MALDI Imaging Lab, University of Bremen for providing us with this dataset for demo purposes.
Download both files to open this example dataset in SCiLS™ Lab: