Compound discoverer 3.1 cd

The 100 mg liver samples (six replicates per group) were ground separately in liquid nitrogen, and 500 μL of precooled 80% methanol was resuspended using well vortex to homogenize. The liver samples were ice-bathed for 5 min, followed by centrifugation at 15,000× g for 20 min at 4 °C. The supernatants were diluted with mass-spectrometry-grade water to a methanol content of 53% and then centrifuged (15,000× g, 20 min, 4 °C). Thus, the supernatants were injected into the UPLC–MS/MS system for analysis. UPLC–MS/MS analyses were conducted at Gene Denovo Ltd. (Guangzhou, China), and a Vanquish UPLC system (ThermoFisher, Berlin, Germany) and an Orbitrap Q ExactiveTM HF-X mass spectrometer (Thermo Fisher, Berlin, Germany) were used.
The raw data files were processed using UPLC–MS/MS with Compound Discoverer 3.1 (CD3.1, Thermo Fisher) performing peak alignment, peak extraction, and quantification for each metabolite. Peak was matched to mzCloud (https://www.mzcloud.org/, accessed on 16 February 2022), mz Vault, and Mass List database to obtain accurate qualitative and relative quantitative results. We used the statistical software R (R-3.4.3 version), Python (Python version 2.7.6), and CentOS (CentOS version 6.6) for statistical analysis. A normal transformation was attempted using the area normalization method when the data were not normally distributed.

Each storage root sample (100 mg) was ground in liquid nitrogen and the homogenate was resuspended in 500 μL prechilled 80% methanol using vigorous vortexing. After processing, the supernatant was analyzed using liquid chromatography tandem mass spectrometry (LC–MS/MS) [42 (link),43 ].
The LC–MS/MS analyses were performed using a Vanquish ultrahigh-performance liquid chromatograph (UHPLC) (Thermo Fisher Scientific, Waltham, MA, USA) coupled with an Orbitrap Q Exactive TM HF-X mass spectrometer (Thermo Fisher Scientific) by Gene Denovo Co., Ltd. (Guangzhou, China) [44 (link)]. The raw data files generated using UHPLC–MS/MS were processed using Compound Discoverer 3.1 (CD3.1, Thermo Fisher Scientific) to perform peak alignment, peak-picking, and quantification for each metabolite. The normalized data were used to predict the molecular formula based on additive ions, molecular ion peaks, and fragment ions. Peaks were matched with data in online spectral libraries (mz Cloud (https://www.mzcloud.org/, accessed on 31 May 2022); mz Vault) and the Mass List database to obtain accurate qualitative and relative quantitative results. Statistical analyses were performed using the statistical software R (R version R-3.4.3), Python (Python 2.7.6 version), and CentOS (CentOS release 6.6). When data were not normally distributed, the area normalization method was applied.