GNPS DEIMoS: an open-source tool for processing high-dimensional mass spectrometry data

LC-IMS-MS/MS data from a large study of human plasma samples consisting of 40 quality control samples from the NIST Standard Reference Material 1950 and 112 study samples. An internal standard mixture consisting of D4-malonic acid, D4-succinic acid, D5-glycine, D4-citric acid, 13C6-fructose, D5-L-tryptophan, D4-lysine, D7-alanine, D35-stearic acid, D5-benzoic acid, and D15-octanoic acid was added prior to extraction. Each sample was spiked with 50 uL of a solution of the internal standards at 0.166 mg/mL in water. Metabolites and lipids were extracted with concomitant protein precipitation using the Matyash protocol. The metabolite layer was removed and dried in vacuo. Lipid and protein layers were not analyzed. An Agilent 1260 Infinity II high flow liquid chromatography system was used to inject and chromatographically separate samples prior to introduction to the ion mobility spectrometry-mass spectrometry instrument. A steady flowrate of 0.300 mL/min was delivered through a Millipore-Sigma SeQuant Zic-pHILIC column (15 cm length, 2.1 mm inner diameter, packed with 5 um particles). Ion mobility spectrometry-tandem mass spectrometry analysis was performed using an Agilent 6560 Ion Mobility LC/Q-TOF system. Spectra were acquired separately in both positive and negative ionization modes. Fixed collision energies were employed at 10, 20, and 40 eV on alternating frames.