Gcmssolution software

Approximately 1 g of minced raw meat from DAB with or without the fungal-rub inoculation was placed into 15 mL glass vials with a PTFE/silicone septum and stored at −80 °C until analysis. The volatile compounds were prepared and then analyzed using a gas chromatograph-mass spectrometer (SHIMADZU GC-MS-QP2010) according to a previously described method [8 (link)]. The obtained mass spectra were deconvoluted using AMDIS GC/MS Analysis (version 2.73) (The National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA) and matched to those in the Massbank of North America GC-MS Spectra. Additionally, the mass spectra were compared with those in the commercial GC-MS libraries, such as NIST05 and NIST05s, using Shimadzu GC-MS solution software.

Mass chromatographic features were extracted with xcms (Smith et al., 2006 (link)) and subsequently processed with TargetSearch software (Cuadros-Inostroza et al., 2009 (link)) using Golm Metabolite Database (available from http://www.mpimp-golm.mpg.de/). Briefly, this software calculates RI for all compounds in chromatograms based on tabulated RI values for the constituents of the FAME mix and then matches RI and mass fragments of compounds in samples with those found in databases. Identified metabolites were cross-referenced in chromatograms using GCMS-solution software (Shimadzu Corp.). Peak areas of identified metabolites were normalized to the IS (ribitol) area before statistical analyses.

Composition analysis of volatile oil was performed by gas chromatography-mass spectrometry (GC-MS) using Shimadzu GCMS-TQ8040 (Shimadzu Corporation, Japan) on a Rxi-5MS capillary column (30 m × 0.25 mm id, film thickness 0.25 μm; Shimadzu, Japan). The carrier gas was helium (flow rate of 1.36 ml/min). GC-MS was carried out using the following temperature program: initial temperature was set at 180 °C and held for 3 min, followed by 6 °C/min ramp to 240 °C and hold for 3 min, followed by 3 °C/min ramp to 275 °C and hold for 3 min, followed by 5 °C/min ramp to 300 °C and hold for 3 min, followed by 5 °C/min ramp to a final temperature of 330 °C and hold for 5 min. The injection temperature was set at 290 °C and the injection volume was 1 μl (splitless mode). Detector parameters used for GC-MS analyses were as follows: interface temperature, 320 °C; ion source temperature, 300 °C; mass spectrometry was performed using Q3 scan with an m/z 45-500 scanning range. Chromatograms and mass spectra were evaluated using the GCMS solution software (Shimadzu Corporation, Japan).

GC/MS-analysis was performed on a QP2010 Plus Gas Chromatograph/Mass Spectrometer (Shimadzu, Duisburg, Germany) equipped with a fused silica capillary column (Equity TM-5; 30 m × 0.25 mm, 0.25 μm film thickness; SUPELCO, Bellafonte, PA) and a quadrupol detector working with electron impact ionization at 70 eV. One μl of the solution containing TBDMS amino acids was injected in 1:10 split mode at an interface temperature of 260°C and a helium inlet pressure of 70 kPa. The column was developed at 150°C for 3 min and then with a temperature gradient of 10°C min⁻¹ to a final temperature of 260°C that was held for 3 min. With a sampling rate of 0.5 s, selected ion monitoring was used. Data were collected using the GC/MS solution software (Shimadzu). All samples were measured three times. ¹³C-Excess and isotopologue abundances were calculated as described before (Lee et al., 1991 (link); Eylert et al., 2008 (link)) including: (i) determination of the TBDMS-derivate spectrum of unlabeled amino acids, (ii) determination of mass isotopologue distributions of labeled TBDMS-amino acids, and (iii) correction of ¹³C-incorporation concerning the heavy isotope contributions due to the natural abundances in the TBDMS-moiety and the amino acid atoms.

The Supelco 37 component FAME Mix (Sigma-Aldrich Corp., St. Louis, MO, USA) served as the standard during free fatty acid analysis by means of gas chromatography-mass spectrometry (GCMS). We used a gas chromatograph (GC-2010Plus), a mass spectrometer (GCMS-QP2010Ultra), a GCMS auto-sampler (AOC-20s), a GCMS auto-injector (AOC-20i), and GCMSsolution software (all from Shimadzu Corp., Kyoto, Japan). The extract solution was fractionated in terms of free fatty acids using solid phase cartridges. After methyl esterification, each fatty acid was analyzed (via GCMS) as its fatty acid methyl ester. The mass range was mass-to-charge ratio (m/z) 33–450. Saturated and branched-chain fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids were measured using mass spectrum base peaks (m/z peaks) of 74, 55 and 81, respectively, in the mass chromatogram.

Metabolomics analyses of CSF samples from the MDD and control groups were performed at the Chemicals Evaluation and Research Institute, Japan (CERI, Tokyo, Japan) using an GC-MS/MS based multiple reaction monitoring metabolomics platform. GC/MS/MS analysis was performed using a GCMS-TQ8030 (Shimadzu Co., Kyoto, Japan) with a fused silica capillary column (BPX-5; 30 m × 0.25 mm inner diameter, film thickness: 0.25 µm; SGE Analytical science by Trajan Scientific Australia Pty Ltd). Quantifications of the metabolites were conducted with the built-in GCMS Solution software (Ver.4.20, Shimadzu) and GC/MS/MS Smart Metabolites Database (Ver. 2.0, Shimadzu). In this study, 475 major metabolic compounds from various pathways (glycolytic system, pentose phosphate pathway, citric acid cycle, urea cycle, polyamine-creatine metabolism pathway, purine metabolism pathway, glutathione metabolism pathway, nicotinamide metabolism pathway, choline metabolism pathway and diverse amino acid metabolism pathway) were selected for metabolomics analysis (Table S1).