Computational protocol: The Distribution of Phosphatidylcholine Species in Superficial-Type Pharyngeal Carcinoma

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Protocol publication

[…] The matrix solution was prepared by dissolving 50 mg of 2,5-dihydroxybenzoic acid (DHB; Bruker Daltonics, Leipzig, Germany) in 1 mL 70% methanol and 20 mM potassium acetate. DHB is a widely used matrix for low-weight molecules. A thin matrix layer was applied to the surface of the tissue sections using a 0.2 mm nozzle airbrush (Procon Boy FWA Platinum; Mr. Hobby, Tokyo, Japan). The spraying distance was maintained at 15 cm from the tissue surface. The total amount of the matrix solution on each slide was 1 mL. The spraying technique enabled full matrix coverage over the entire tissue surface and facilitated cocrystallization of the matrix and biomolecules. [...] The tissue sections were analyzed using a matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight (MALDI-TOF/TOF) type instrument, Ultraflex II TOF/TOF (Bruker Daltonics), which was equipped with a 355 nm smartbeam laser at 200 Hz repetition. Data were acquired in the positive-ion mode using an external calibration method with ions from DHB, angiotensin II, and bradykinin, which covered a mass-to-charge ratio (m/z) range of 100 to 1200. Calibration proteins were deposited on the surfaces of sample sections. Each raster scan was automatically performed in the regions of cancer and normal tissue. The interval between data points was 50 μm, and 100 laser beam shots in a random walk mode for each data point were irradiated. The mass spectrometry parameters were manually optimized to obtain the highest sensitivity, with m/z values in the range of 500–900. All mass spectra were acquired automatically using FlexImaging 2.1 software (Bruker Daltonics). […]

Pipeline specifications

Software tools ProCon, flexImaging
Applications Miscellaneous, Mass spectrometry imaging
Organisms Homo sapiens
Diseases Carcinoma, Carcinoma in Situ, Carcinoma, Squamous Cell
Chemicals Fatty Acids, Phosphatidylcholines, Arachidonic Acid