The Xcalibur 4.0 workstation software (Thermo Fisher Scientific) was used for raw data recording and processing. Using Compound Discoverer 3.3 (Thermo Fisher Scientific), post-processing of the data was performed to extract the metabolite-related datasets based on the structural correlation between the drug and its metabolites. A maximum tolerance of 5 ppm was set for the mass error. Using blank samples, the workflow subtracted the chemical backgrounds, aligned the retention times, and found the expected compounds and metabolites. Fragment ion search (FISH) scoring was used, and each annotation was then manually evaluated based on the HCD, DDA spectra, molecular formula, and FISH coverage.
Xcalibur 4.0 workstation
Manufactured by Thermo Fisher Scientific
The Xcalibur 4.0 workstation is a software platform for data acquisition, processing, and management in analytical laboratories. It provides a unified interface for control and operation of Thermo Fisher Scientific mass spectrometry instruments.
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3 protocols using xcalibur 4.0 workstation
1
Metabolite Profiling Using Xcalibur
2
Metabolite Identification by High-Resolution Mass Spectrometry
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A Thermo Xcalibur 4.0 workstation was used for the data acquiring and processing. In order to get more fragment ions of the metabolites, the peaks detected with intensity over 10,000 were selected for identification. The chemical formulas for all parent ions of the selected peaks were calculated from the accurate mass using a formula predictor by setting the parameters as follows: C [0–40], H [0–50], O [0–50], S [0–4], N [0–4], Cl [0–4].
3
Quantitative Metabolomic Analysis of FbP
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Levels of FbP for NCM3722 grown in succinate, sorbitol or acetate as a sole carbon source were analyzed by a targeted mass spectrometry‐based quantitative metabolomic approach in biological duplicate with four samples per group of assay. Briefly, for each sample, cell pellets (3–4×109) were resuspended in 3:1 MeOH:H2O (v/v), subjected to sonication with 500 W for 10 min, and next centrifuged for 10 min at 4 °C. The supernatant was collected and dried in a lyophilizer. The powder was resuspended in 2:8 MeOH:H2O (v/v) and centrifuged for 10 min at 4°C, and then, the supernatant was ready for detection. FbP analysis was performed using 10 μl of sample loaded into a Nexera UPLC (SHIMADZU) with an ACQUITY UPLC C18 column (100 × 2.1 mm, 1.7 μm, Waters) and underwent gradient elution procedures; then the sample was ionized by ESI and detected by QE high‐resolution mass spectrometer (Thermo) with Xcalibur 4.0 workstation in the negative ion mode, scanning precursor ion m/z 338.99 for FbP. The amount of FbP in unknown samples was calculated by peak areas when compared with that of an FbP standard.
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