These metabolites were annotated using the KEGG database (https://www.genome.jp/kegg/pathway.html), HMDB database (https://hmdb.ca/metabolites) and LIPIDMaps database (http://www.lipidmaps.org/). Principal components analysis (PCA) and Partial least squares discriminant analysis (PLS-DA) were performed at metaX[9] (a flexible and comprehensive software for processing metabolomics data). We applied univariate analysis (t-test) to calculate the statistical significance (P-value). FC refers to the fold change, which is the ratio of the mean of all biological repeated quantitative values of each metabolite in the comparison group. The differential metabolites were screened using VIP, P-value and FC. The specific standard outlined in Table 5.3 of the report.
UHPLC-MS/MS analyses were performed using a Vanquish UHPLC system (ThermoFisher, Germany) coupled with an Orbitrap Q ExactiveTM HF mass spectrometer, Orbitrap Q ExactiveTM HF-X mass spectrometer, Orbitrap Exploris 120 mass spectrometer or Orbitrap Exploris 480 mass spectrometer (Thermo Fisher, Germany) in Novogene Co., Ltd. (Beijing, China). Samples were injected onto a Hypersil Gold column (100 x 2.1 mm, 1.9 μm) using a 12-min linear gradient at a flow rate of 0.2 mL/min. The eluents for the positive and negative polarity modes were eluent A (0.1% FA in Water) and eluent B (Methanol). The solvent gradient was set as follows: 2% B, 1.5 min; 2-85% B, 3 min; 85-100% B, 10 min; 100-2% B, 10.1 min; 2% B, 12 min.
Fecal samples were extracted with 80% methanol aqueous solution. The mixture was vortexed, subjected to ultrasonication, and centrifuged at 15000 x g for 20 min at 4 °C. The supernatant was collected for LC-MS detection. Pooled QC samples and solvent blank samples were prepared and processed identically alongside experimental samples.
"],"organism":["Larimichthys crocea"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15718"],"author":["Dehua Wang.","Tongxin Xie. ocean university of china. 13936317310@163.com.","Qingjuan Tang."],"data_transformation_protocol":["The data files generated by UHPLC-MS/MS were processed by XCMS to perform
peak alignment, peak picking, and quantitation for each metabolite. Then, based on
adduct ions and setting mass deviation to 10 ppm[6], a comparison was made between
these data and the self-built high-quality secondary spectrum database (NovoMetDB)
to obtain results for metabolite identification. Metabolites with more than 50%
missing values in the samples were first filtered out and the remaining missing values
were imputed using KNN. After eliminating background ions according to blank
samples, the raw quantitative results were further processed to obtain relative peak
areas, which included normalization and filtering out compounds whose relative peak
areas exhibited a coefficient of variation (CV) greater than 30% in the quality control
(QC) samples[8]. Relative peak areas = Raw quantitative value of samples/ (The sum
of quantitative value of samples/ The sum of quantitative value of QC1). Data
processing is based on the Linux operating system (CentOS version 6.6), using R and
Python. For details on specific packages and software versions used, please refer to
the README file included in the results.
Treated tissue samples of large yellow croaker were collected, transferred into sterile centrifuge tubes, immediately frozen, and stored at −80 °C until metabolite extraction.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","pooled quality control sample","Metabolomics","Multi-omics study","Q Exactive HF/Q Exactive HF-X/Orbitrap Exploris 120/ Orbitrap Exploris 480","Larimichthys crocea","untargeted analysis","muscle","experimental sample","untargeted metabolite profiling"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","pooled quality control sample","Metabolomics","Multi-omics study","Q Exactive HF/Q Exactive HF-X/Orbitrap Exploris 120/ Orbitrap Exploris 480","Larimichthys crocea","untargeted analysis","muscle","experimental sample","untargeted metabolite profiling"],"mass_spectrometry_protocol":["The m/z scan range was set at 100-1500. The ESI source parameters were configured as follows: Spray Voltage: 3.5 kV; Sheath gas flow rate: 35 psi; Aux Gas flow rate: 10 L/min; Capillary Temp: 320 °C; S-lens RF level: 60; Aux gas heater temp: 350 °C. Polarity: positive and negative. MS/MS acquisition was performed using data-dependent scans. Q ExactiveTM HF mass spectrometer was operated in positive/negative polarity mode with spray voltage of 3.5 kV, capillary temperature of 320 °C, sheath gas flow rate of 35 arb and aux gas flow rate of 10 arb, S-lens RF level of 60, Aux gas heater temperature of 350 °C.