Computational protocol: Distinct deposition of amyloid-β species in brains with Alzheimer’s disease pathology visualized with MALDI imaging mass spectrometry

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Protocol publication

[…] Frozen tissue sections were cut on a cryostat (CM1950, Leica Microsystems, Wetzlar, Germany) at a 10 μm thickness using indium-tin-oxide–coated glass slides (Bruker Daltonics, Bremen, Germany). Prior to washing, stored samples were placed in a vacuum chamber to dry. To remove endogenous lipids and inorganic salts, dried samples were immersed in 70% ethanol for 30 s, pure ethanol for 30 s, Carnoy’s solution for 3 min, pure ethanol for 30 s, 0.1% TFA for 1 min, and pure ethanol for 30 s. Prior to matrix coating, treated with a formic acid vapor. Sinapinic acid was used as a matrix. For mass spectrometric measurements, tissue areas were defined using the FlexControl 3.8 and FlexImaging 5.0 software packages (both Bruker Daltonics). Spectra were acquired using the rapifleX MALDI Tissuetyper (Bruker Daltonics) in positive linear mode, where ions were detected in a mass range of m/z 2000 to 20,000, with spatial resolution of 20 and 100 μm, respectively. A ready-made protein standard was used for spectra calibration (Bruker Daltonics). Visualization and statistical analysis were completed using FlexImaging and SciLS Lab 2016a (SCiLS, Bremen, Germany). […]

Pipeline specifications

Software tools flexImaging, SCILS Lab
Application Mass spectrometry imaging
Organisms Homo sapiens
Chemicals Amino Acids, Pyrrolidonecarboxylic Acid