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MB Sample ID: SA098729
| Local Sample ID: | mtab_alm_UW_072718_52 |
| Subject ID: | SU001431 |
| Subject Type: | Other |
| Subject Species: | Wastewater |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001431 |
| Subject Type: | Other |
| Subject Species: | Wastewater |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| mtab_alm_UW_072718_52 | SA098729 | FL013951 | UW N4B61 neg | Sample type |
Collection:
| Collection ID: | CO001426 |
| Collection Summary: | Samples were collected from street-level manholes located outside of three buildings: one multipurpose-use building (Building 7 = building 1), and two residential buildings (Buildings 61 and 84 = buildings 2 and 3). We used a commercial peristaltic pump (Boxer) to continuously collect wastewater samples for 3 hours starting from 9:00 AM for Building 1 and 8:00 AM for Buildings 2 and 3. The peristaltic pump was programmed to pump wastewater at a rate of 5.55 mL/min over a 3-hour period into a 1 L polycarbonate bottle (Thermo Scientific) stored on ice, for a total volume of 1 L of wastewater. |
| Sample Type: | Wastewater |
Treatment:
| Treatment ID: | TR001446 |
| Treatment Summary: | 100 mL of each sample were filtered separately through a 0.2 μM PTFE membrane filter (Millipore) using a glass filtration apparatus (Glassco) to remove bacteria and debris. All filtration glassware and polycarbonate bottles were acid washed with hydrochloric acid and autoclaved prior to filtration. |
Sample Preparation:
| Sampleprep ID: | SP001439 |
| Sampleprep Summary: | The filtrate from the previous step was collected in amber glass vials, the pH was adjusted to between 2 and 3, and stored at -80 ࿁C, all in less than 2 hours post sampling. |
Combined analysis:
| Analysis ID | AN002260 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Fusion Orbitrap |
| Ion Mode | NEGATIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH001659 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002104 |
| Analysis ID: | AN002260 |
| Instrument Name: | Thermo Fusion Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data was collected in negative ionization mode with data-dependent secondary mass spectra (MS/MS) obtained via high-energy collisional dissociation (HCD, mass resolution 15,000 and collision energy of 35 arbitrary units, automatic gain control, AGT, of 5.0e4 and max injection time, IT, of 22 ms). The full MS resolution was 120,000 at 200 mz with an AGT target of 4.0e5 and a maximum IT of 50 ms. The quadrupole isolation width was set at 1.0 m/z. ESI was carried out at a source voltage of 2600 kV for negative ion mode with a capillary temperature of 350 ࿁C, vaporizer temperature of 400 ࿁C, and sheath, auxiliary, and sweep gases at 55, 20, and 1 arbitrary units, respectively. Python 3.6.5 with scikit-learn version 0.19.1 as well as R 3.5.1 were used for processing and analysis. Following data acquisition, all data files were converted to an open source file format (.mzML) via a custom wrapper (msconvert_ee.py) of the program MSConvert in the ProteoWizard suite. All files were then processed as a single batch with a custom python wrapper script (full_ipo_xcms.py) of both IPO and then subsequent XCMS processing. The parameters for XCMS were: CentWave (ppm=10, peakwidth=(5,15), snthresh=(100), prefilter=(4,10000), mzCenterFun=wMean, integrate=2, mzdiff=-0.005, noise=50,000), ObiwarpParam (binsize=0.1, response=1, distFun=cor_opt, gapInit=0.3, gapExtend=2.4, factorDiag=2, factorGap=1), PeakDensityParam (bw=10, minFraction=0.05, minSamples=1, binSize=0.002, maxFeatures=50), mode (negative). In addition to aligning and extracting peak information, this program automatically extracted all MS/MS spectra and saved as a separate .mgf file for use in the metabolite naming pipeline. Mentioned python scripts can be found at: https://github.com/ethanev/Metabolite_lookup |
| Ion Mode: | NEGATIVE |
