Return to study ST002834 main page
MB Sample ID: SA307068
| Local Sample ID: | Pos_QC5 |
| Subject ID: | SU002943 |
| Subject Type: | Bacteria |
| Subject Species: | Bacteroides thetaiotaomicron |
| Taxonomy ID: | 818 |
| Subject Comments: | Fecal derived communities and isolates, supernatant was assayed |
| Species Group: | Bacteria |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004629 | AN004630 |
|---|---|---|
| Chromatography ID | CH003483 | CH003483 |
| MS ID | MS004375 | MS004376 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Agilent Zorbax SB-C18 (100 x 3.0 mm, 1.8 um) | Agilent Zorbax SB-C18 (100 x 3.0 mm, 1.8 um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | counts, height | counts, height |
Chromatography:
| Chromatography ID: | CH003483 |
| Chromatography Summary: | Bacterial supernatant were analyzed via reversed phase (C18) coupled to a Thermo Q-Exactive HF high resolution mass spectrometer. Prepared samples were injected onto an Agilent Zorbax SB-C18 column (100 mm length × 3 mm id; 1.8 μm particle size) with an additional Phenomenex KrudKatcher pre-column (2 μm depth x 0.004in ID) maintained at 40°C coupled to an Thermo Vanquish UPLC. The mobile phases were prepared with 0.1% formic acid in either 100% LC-MS grade water for mobile phase (A), 100% water or mobile phase (B), 100% acetonitrile. Gradient elution was performed as follows 3% (B) maintained 0–0.43 min to 97% (B) at 9 min, maintained until 11 min, returning to initial conditions at 11.5 min and equilibrating until the end of the run at 14 min. Flow rate is maintained at 0.4 mL/min. Each sample was analyzed in both positive and negative ionization modes (ESI+, ESI-) via subsequent injections. Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60 (https://www.nature.com/articles/s41587-020-0531-2) and queried against a combination of our in-house MS2 library and MassBank of North America, the largest freely available spectral repository (https://doi.org/10.1002/mas.21535). Features were excluded from analysis if peak height was not at least 5-fold greater in one or more samples compared to the procedural blank average. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Agilent Zorbax SB-C18 (100 x 3.0 mm, 1.8 um) |
| Column Temperature: | 40C |
| Flow Gradient: | Gradient elution was performed from 100% (B) at 0–2 min to 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until 16.75 min with a column flow ofGradient elution was performed as follows 3% (B) maintained 0–0.43 min to 97% (B) at 9 min, maintained until 11 min, returning to initial conditions at 11.5 min and equilibrating until the end of the run at 14 min. |
| Flow Rate: | 0.4 mL/min. |
| Solvent A: | Water + 0.1% formic acid |
| Solvent B: | Acetonitrile + 0.1% formic acid |
| Chromatography Type: | Reversed phase |
