Smart beam

The molecular weight of peptides in the eluted fractions was determined on an Ultraflex III MALDI-TOF/TOF time-of-flight mass spectrometer (Bruker Daltonics, Bremen, Germany) with a laser ionization source (SmartBeam, 355 nm). Sinapic acid (3,5-dimethoxy-4-hydroxycinnamic acid) was used as the matrix. Time-of-flight mass spectra were recorded in linear and reflection modes.

MALDI-TOF MS spectra of the peptide fractions obtained by RP-HPLC were recorded using an Ultra Flex III MALDI-TOF/TOF mass spectrometer (Bruker, Bremen, Germany) with a nitrogen laser (Smart Beam, 355 nm), reflector, and the potential LIFT™ tandem modes of operation. Sinapinic acid was used as a matrix. An external calibration was employed using a peptide sample [56 (link)] with m/z 6107 Da and its doubly-charged variant at m/z 3053 Da.

Tissue sections were imaged using a MALDI-TOF/TOF ultrafleXtreme mass spectrometer (Bruker Daltonik, Bremen) equipped with a smartbeam II™ laser operating at 1 kHz repetition rate. Ions were accelerated at 25 kV with PIE time of 100 ns. Spectra were acquired in positive reflectron mode in the 800–4000 mass range for peptide imaging or in the 300–1200 mass range for lipid imaging; external calibration with Bruker’s Peptide Calibration Standard or cesium triiodide clusters was performed for peptide and lipid imaging, respectively. A raster width of 100 µm was applied, 400 spectra were collected from each ablation point. Compass 1.4 for FLEX series (Bruker Daltonik, Bremen) was employed for spectra acquisition, processing and creation of primary images. After analysis slides were rinsed twice in 100% ethanol to remove the matrix, stained with hematoxylin and eosin, and scanned for co-registration with MALDI images using FlexImaging 4.1 software (Bruker Daltonik, Bremen). Original files with spectra were converted into .txt files using FlexAnalysis 1.4 software (Bruker Daltonik, Bremen) for further analyses.