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MB Sample ID: SA323088
| Local Sample ID: | SH_10 |
| Subject ID: | SU003086 |
| Subject Type: | Other abiotic sample |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003086 |
| Subject Type: | Other abiotic sample |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SH_10 | SA323088 | FL038544 | pre-filter | Treatment |
| SH_10 | SA323088 | FL038544 | 1 | Batch |
Collection:
| Collection ID: | CO003079 |
| Collection Summary: | Two independently made batches of bacteria media was used for this study. For each batch, five aliquots from the same batch were used as replicates. Each aliquot was then split into halves for metabolite extraction. Following extraction, the one half was used as the pre-filtered controls and the other half was used for post-filtered sample that passed through the 0.2 micron filter membrane. |
| Sample Type: | bacterial media |
Treatment:
| Treatment ID: | TR003095 |
| Treatment Summary: | Metabolites extracted from mega medium, a rich and undefined bacterial medium, are filtered using a 96-well 0.2 micron filter plate. Here we compare the detection of metabolites in pre-filtered vs. post-filtered conditions from the same replicate, and five replicates are used for each of the two independent batches of media tested. |
Sample Preparation:
| Sampleprep ID: | SP003092 |
| Sampleprep Summary: | The sample preparation procedure is described in detail in our preprint of this metabolomic protocol: https://protocolexchange.researchsquare.com/article/pex-2055/v1 |
Combined analysis:
| Analysis ID | AN004882 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap Exploris 240 |
| Ion Mode | POSITIVE |
| Units | raw ion count |
Chromatography:
| Chromatography ID: | CH003684 |
| Chromatography Summary: | A published C18 reveres phase method was implemented with minor modifications. The C18 positive method (ESI+) used mobile phase solvents (LC-MS grade) consisting of 0.1% formic acid (Fisher) in water (A) and 0.1% formic acid in methanol (B). The gradient profile was from 0.5% B to 70% B in 4 minutes, from 70% B to 98% B in 0.5 minutes, and holding at 98% B for 0.9 minute before returning to 0.5% B in 0.2 minutes. The flow rate was 350 µL per minute. The sample injection volume was 5 µL. LC separations were made at 40C on separate columns fitted with a Vanguard pre-column of the same composition: Waters Acquity BEH 1.7 µm particle size, 2.1 mm id x 100 mm length (C18). Data were collected at a mass range of 70-1000 m/z at an acquisition rate of 2 spectra per second. Specific ion source parameters included Fragmentor (140V), Gas Temp (250oC), Sheath Gas Temp (200oC), and VCap (4000V). |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40C |
| Flow Gradient: | From 0.5% B to 70% B in 4 minutes, from 70% B to 98% B in 0.5 minutes, and holding at 98% B for 0.9 minute before returning to 0.5% B in 0.2 minutes. |
| Flow Rate: | 0.350 mL/minute |
| Solvent A: | 100% water + 0.1% formic acid |
| Solvent B: | 100% methanol + 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004626 |
| Analysis ID: | AN004882 |
| Instrument Name: | Thermo Orbitrap Exploris 240 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Please see step-by-step details in our preprint for this metabolomic protocol: https://protocolexchange.researchsquare.com/article/pex-2055/v1 |
| Ion Mode: | POSITIVE |
