Return to study ST001409 main page
MB Sample ID: SA115648
| Local Sample ID: | S7E41D180_1 |
| Subject ID: | SU001483 |
| Subject Type: | Other |
| Subject Species: | Natural mixed marine microbial community |
| Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001483 |
| Subject Type: | Other |
| Subject Species: | Natural mixed marine microbial community |
| Gender: | Not applicable |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S7E41D180_1 | SA115648 | FL014409 | 180 | Depth_m |
| S7E41D180_1 | SA115648 | FL014409 | 4 | Vol_L |
Collection:
| Collection ID: | CO001478 |
| Collection Summary: | Samples for particulate metabolites were collected from 10 depths between 30 and 250 m on June 3, 2017 aboard the R/V Marcus Langseth. At each sampling location and depth, single, duplicate, or triplicate filters were collected using either niskins attached to a conductivity, temperature, depth array (CTD) or the underway intake. Samples (4 L) were collected into polycarbonate carboys, filtered onto 147 mm 0.2 μm PTFE filters using peristaltic pumps, polycarbonate filter holders, and Masterflex PharMed BPT tubing (Cole-Parmer). Filters were flash frozen in liquid nitrogen and stored at -80°C until extraction. In addition to our samples, we filtered seawater through two 0.2 μm PTFE filters in series, using the second filter as a methodological blank. This blank is especially important to parse signals from the salt matrix that would be present after sorption to the filter. |
| Sample Type: | Suspended Marine Particulate Matter |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001498 |
| Treatment Summary: | No treatment, this is a study of the natural marine microbial population in the North Pacific Transition Zone. |
Sample Preparation:
| Sampleprep ID: | SP001491 |
| Sampleprep Summary: | Each sample was extracted using a modified Bligh-Dyer extraction. Briefly, filters were cut up and put into 15 mL teflon centrifuge tubes containing a mixture of 100 µm and 400 µm silica beads. Heavy isotope-labeled internal standards were added along with ~2 mL of cold aqueous solvent (50:50 methanol:water) and ~3 mL of cold organic solvent (dichloromethane). The samples were shaken on a FastPrep-24 Homogenizer for 30 seconds and chilled in a -20 °C freezer repeatedly for three cycles of bead-beating and a total of 30 minutes of chilling. The organic and aqueous layers were separated by spinning samples in a centrifuge at 4,300 rpm for 2 minutes at 4 °C. The aqueous layer was removed to a new glass centrifuge tube. The remaining organic fraction was rinsed three more times with additions of 1 to 2 mL of 50:50 methanol:water. All aqueous rinses were combined for each sample and dried down under N2 gas. The remaining organic layer was transferred into a clean glass centrifuge tube and the remaining bead beating tube was rinsed two more times with cold organic solvent. The combined organic rinses were centrifuged, transferred to a new tube, and dried under N2 gas. Dried aqueous fractions were re-dissolved in 380 µL of water. Dried organic fractions were re-dissolved in 380 µL of 1:1 water:acetonitrile. 20 µL of isotope-labeled injection standards in water were added to both fractions. Blank filters were extracted alongside samples as methodological blanks. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Bligh-Dyer |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002355 | AN002356 | AN002357 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
| Units | Adjusted and normalized peak areas | Adjusted and normalized peak areas | Adjusted and normalized peak areas |
Chromatography:
| Chromatography ID: | CH001727 |
| Chromatography Summary: | See attached summary. |
| Methods Filename: | CH_Ingalls_Lab_LC_Methods.txt MS_Ingalls_Lab_MS_Methods.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 30 |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 85% acetonitrile/15% water; 10 mM ammonium carbonate |
| Solvent B: | 15% acetonitrile/85% water; 10 mM ammonium carbonate |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH001728 |
| Chromatography Summary: | See attached summary. |
| Methods Filename: | CH_Ingalls_Lab_LC_Methods.txt MS_Ingalls_Lab_MS_Methods.txt |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) |
| Column Temperature: | 35 |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002197 |
| Analysis ID: | AN002355 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002198 |
| Analysis ID: | AN002356 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002199 |
| Analysis ID: | AN002357 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
