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MB Sample ID: SA256454
| Local Sample ID: | Arabic Gum-C43-01-6685 |
| Subject ID: | SU002653 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004204 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Bruker timsTOF |
| Column | Bruker Intensity Solo 2 C18 (100 mm × 2.1 mm , 1.8 μm) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker timsTOF |
| Ion Mode | POSITIVE |
| Units | AU |
MS:
| MS ID: | MS003951 |
| Analysis ID: | AN004204 |
| Instrument Name: | Bruker timsTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The LC-MS/MS analysis was performed using an ultra-high-performance liquid chromatography system (UHPLC) (Bruker Daltonik GmbH, Bremen, Germany) connected to a quadrupole time-of-flight mass spectrometer (QTOF). An electrospray ionization (ESI) source, a solvent delivery systems pump (HPG 1300), an autosampler, and a thermostat column compartment were all included in the system. The computer operating system was Windows 10 Enterprise 2016 LTSB. Bruker Compass HyStar 5.0 SR1 Patch1 (5.0.37.1), Compass 4.1 for otofSeries, and otof Control Version 6.2 software were used for data management. Mobile phases A (water with 0.1% formic acid) and B (acetonitrile with 0.1% formic acid) were employed. The gradient program was: 0–2 min, 99% A: 1% B; 2–17 min, 99–1% A: 1–99% B; 17–20 min, 99% B: 1% A. The flow rate. Subsequently, 20–20.1 min 99% B to 99% A; 20.1–28.5 min, 99% A: 1% B at 0.35 mL/min flow rate; 28.5–30 min; 99% A: 1% B at 0.25 mL/min. A 10 μL aliquot of the sample was injected, and the separation was performed on a Hamilton® Intensity Solo 2 C18 column (100 mm × 2.1 mm × 1.8 μm) at a column oven temperature set at 35 °C. For each injection, the ESI source circumstances were as follows: The capillary voltage was adjusted to 4500 V; the drying gas flow rate was 10.0 L/min at a temperature of 220 °C; and the nebulizer pressure was 2.2 bar. The collision energy stepping for the MS2 acquisition varied between 100 and 250% fixed at 20 eV and an end plate offset of 500 V. [35]. For the external calibration step, sodium formate was utilized as a calibrant. For the calibrant sodium formate, the auto MS scan segment of the acquisition lasted from 0 to 0.3 minutes, and the auto MS/MS segment, which included fragmentation, lasted from 0.3 to 30 minutes. The acquisition in both segments was performed using the positive mode at 12 Hz. The automatic in-run mass scan range was from 20 to 1300 m/z, the width of the precursor ion was ±0.5, the number of precursors was 3, the cycle time was 0.5 s, and the threshold was 400 cts. Active exclusion was excluded after 3 spectra and released after 0.2 min. The data was processed using MetaboScape® 4.0 software (Bruker Daltonics, Billerica, MA, USA) (37). The following were the T-ReX 2D/3D workflow bucketing parameters for the processed data: intensity threshold of 1000; peak length of 7 spectra; and using peak area for quantifying the feature. Mass spectra were calibrated in 0-0.3 minutes using features from at least 48 to 187 samples. However, the auto MS/MS scan was carried out using the average method. The retention time and mass ranges for the scan were 0.3 to 25 minutes and 50 to 1000 m/z, respectively. By using LC-QTOF to analyze every sample in duplicate, 88 samples from both groups undergoing examination were combined to create a data set with 3487 characteristics. Based on the mapping of the MS/MS spectra and retention time in the HMBD 4.0, an annotated database created to meet the demands of the metabolomics community, metabolites were identified. A total of 102 distinct metabolites were selected after MetaboScape® filtration (Supplementary Table S1). The peak intensities of each metabolite were used to quantify the data matrix. Only significant compounds recorded in the HMDB 4.0 with p < 0.05 were included in the metabolite datasets. The online website HMDB (https://hmdb.ca/metabolites/HMDB0059911) was used to filter the human metabolites or Arabic gum metabolites. Following HMDB filtration, 92 unique metabolites remained (Supplementary Table S2). The software MetaboAnalyst 5.0 (Mcgill University, Montreal, QC, Canada), a comprehensive platform for metabolomics data analysis, was used to import the metabolite datasets after exporting them as a CSV file [36]. To help classify the samples, the most discriminating features in the studied group were chosen using the sPLS-DA method in MetaboAnalyst. The rate of false positives was reduced, and multiple hypothesis testing was corrected using the false discovery rate (FDR) approach. The Arabic gum group's significantly altered metabolites were found using a two-tailed independent students t-test in comparison to the control group. As a result, a volcano plot was created to display the statistical significance and fold change for cellular metabolite dysregulation. The threshold for significance was p<0.05. Functional Enrichments were constructed using metaboanalyst (https://www.metaboanalyst.ca). |
| Ion Mode: | POSITIVE |
