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MB Sample ID: SA299169
| Local Sample ID: | 180821_Smp_MS12C1DCM_C.mzML |
| Subject ID: | SU002896 |
| Subject Type: | Other organism |
| Subject Species: | Natural mixed marine microbial community |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002896 |
| Subject Type: | Other organism |
| Subject Species: | Natural mixed marine microbial community |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 180821_Smp_MS12C1DCM_C.mzML | SA299169 | FL036289 | Sample | Sample_type |
| 180821_Smp_MS12C1DCM_C.mzML | SA299169 | FL036289 | 12 | Station |
| 180821_Smp_MS12C1DCM_C.mzML | SA299169 | FL036289 | DCM | Depth |
Collection:
| Collection ID: | CO002889 |
| Collection Summary: | Samples were collected aboard the R/V Kilo Moana in June and July 2017. Water was collected with Niskin bottles attached to the CTD from the surface and the deep chlorophyll maximum (DCM), and 175 meters depth. Water was filtered onto a 0.2um pore size filter under gentle vacuum pressure prior to flash-freezing in LN2 before storage at -80 in precombusted aluminum foil. Samples were collected in two stages, the first of which was a transect across the entire eddy dipole from one edge to another while the second stage was a long-term Lagrangian occupation of the eddy centers (L1 = cyclone @ -12cm, L2 = anticyclone @ +25cm). Samples for the transect were collected throughout the day while the eddy center samples were all collected at about 6pm. |
| Sample Type: | Suspended Marine Particulate Matter |
| Collection Method: | CTD Niskin Bottle |
| Collection Location: | North Pacific |
| Volumeoramount Collected: | 10L |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002905 |
| Treatment Summary: | No experimental manipulations were performed on the samples. |
Sample Preparation:
| Sampleprep ID: | SP002902 |
| Sampleprep Summary: | Polar metabolites were extracted using a modified Bligh−Dyer extraction using 1:1 methanol/water and dichloromethane. A methodological blank was extracted and analyzed alongside. Isotope-labeled internal standards were added both before and after the extraction for all samples, blanks, and pooled samples. To evaluate the effect of obscuring variation due to different matrix strengths and analytical drift, pooled samples were run at both full and half concentration (diluted with water) at least three times during the run. This study ran the eddy center samples separately from the eddy transect samples but they were processed together. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Bligh-Dyer |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004538 | AN004539 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | SeQuant ZIC-HILIC (150 x 2.1mm, 5um) | SeQuant ZIC-HILIC (150 x 2.1mm, 5um) |
| 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 | normalized peak area per liter seawater filtered | normalized peak area per liter seawater filtered |
Chromatography:
| Chromatography ID: | CH003409 |
| Chromatography Summary: | A SeQuant ZIC-pHILIC column (5 um particle size, 2.1 mm x 150 mm, from Millipore) was used with 10 mM ammonium carbonate in 85:15 acetonitrile to water (Solvent A) and 10 mM ammonium carbonate in 85:15 water to acetonitrile (Solvent B) at a flow rate of 0.15 mL/min. This column was compared with a Waters UPLC BEH amide and a Millipore cHILIC column; the pHILIC showed superior reproducibility and peak shapes. The column was held at 100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total). The column was maintained at 30 C. The injection volume was 2 µL for samples and standard mixes. When starting a batch, the column was equilibrated at the starting conditions for at least 30 minutes. To improve the performance of the HILIC column, we maintained the same injection volume, kept the instrument running water blanks between samples as necessary, and injected standards in a representative matrix in addition to standards in water. After each batch, the column was flushed with 10 mM ammonium carbonate in 85:15 water to acetonitrile for 20 to 30 minutes. |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | SeQuant ZIC-HILIC (150 x 2.1mm, 5um) |
| Column Temperature: | 30 |
| Flow Gradient: | 100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total) |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 85% acetonitrile/15% water |
| Solvent B: | 15% acetonitrile/85% water |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004285 |
| Analysis ID: | AN004538 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolomic data was collected on a Thermo Q Exactive HF hybrid Orbitrap (QE) mass spectrometer. The capillary and auxiliary gas heater temperatures were maintained at 320°C and 100°C, respectively. The S-lens RF level was kept at 65, the H-ESI voltage was set to 3.3 kV and sheath gas, auxiliary gas, and sweep gas flow rates were set at 16, 3, and 1, respectively. Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. Calibration was performed every 3-4 days at a target mass of 200 m/z. All files were then converted to an open-source mzML format and centroided via Proteowizard’s msConvert tool. Skyline was used to for manual integration and QC of quantified data, while XCMS was used with a custom QC method for peak area data and each feature manually reviewed. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004286 |
| Analysis ID: | AN004539 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolomic data was collected on a Thermo Q Exactive HF hybrid Orbitrap (QE) mass spectrometer. The capillary and auxiliary gas heater temperatures were maintained at 320°C and 100°C, respectively. The S-lens RF level was kept at 65, the H-ESI voltage was set to 3.3 kV and sheath gas, auxiliary gas, and sweep gas flow rates were set at 16, 3, and 1, respectively. Polarity switching was used with a scan range of 60 to 900 m/z and a resolution of 60,000. Calibration was performed every 3-4 days at a target mass of 200 m/z. All files were then converted to an open-source mzML format and centroided via Proteowizard’s msConvert tool. Skyline was used to for manual integration and QC of quantified data, while XCMS was used with a custom QC method for peak area data with the model trained on positive mode data applied to these negative mode results. |
| Ion Mode: | NEGATIVE |
