Mouse skin lipid MALDI imaging with trapped ion mobility (TIMS) dataset

This dataset serves as an exemplary case study data set for the TIMSImaging (Cardinal) software for processing Bruker raw files (.d) from TimsTOF fleX (Bruker). Wild-type mice on C57 Bl/6 :129sv background were used. The mice were kept in SPF facility with 12h light dark cycle and food and water as libitum. Forepaws from 12-week-old mice were used. After collection the paws snap-frozen in optimal cutting temperature medium. 5 um cryo sections were cut on super-frost microscopic glass slides. The collection of material were approved by Regierungspraesidium Freiburg approval number X-22/02F. Cryosections were stored at -80°C until usage. First, slides were dried for 1h in a vacuum desiccator and afterwards spray covered with MALDI matrix. 2,5-dihydroxybenzoic acid (DHB) was used as MALDI matrix in a concentration of 40mg/ml in 70% acetoniltrile, 30% water, 0.1% trifluoroacetic acid. DHB matrix was sprayed with the M3 + sprayer (HTX Technologies, Chapel Hill, NC, USA) with the following parameters: temperature 75°C, nozzle velocity 1200 mm/min, flow rate 100 μL/min, number of passes 8, track spacing 3 mm, pattern CC, drying time 10 s, and nitrogen gas pressure set to 10 psi. MALDI TIMS MS1 imaging datasets were acquired in the positive-ion reflector mode using a timsTOF fleX mass spectrometer (Bruker Daltonics, Bremen, Germany) at a pixel size of 20 × 20 μm, using 600 shots and a laser frequency of 10 kHz. The m/z range was set to m/z 300–1350, the 1/K0 range to 0.7 – 1.96 V•s/cm2 with a ramp time of 200 ms. Tuning parameters were set as follows: MALDI plate offset 50 V, deflection 1 delta 70 V, funnel 1 RF 500 Vpp, funnel 2 RF 350 Vpp, multiple RF 300 Vpp, collision energy 10 eV, collision RF 1800 Vpp, ion energy 5 eV, transfer time 85 ms, and pre pulse storage 10 μs.