Return to study ST001410 main page
MB Sample ID: SA115664
| Local Sample ID: | U7_A |
| Subject ID: | SU001484 |
| Subject Type: | Other |
| Subject Species: | Natural mixed marine microbial community |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001484 |
| Subject Type: | Other |
| Subject Species: | Natural mixed marine microbial community |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| U7_A | SA115664 | FL014416 | 15 | Depth_m |
| U7_A | SA115664 | FL014416 | 10 | Vol_L |
Collection:
| Collection ID: | CO001479 |
| Collection Summary: | Samples for particulate metabolites from cruise KOK1606 were collected aboard the Ka’imikai-O- Kanoloa research vessel from April 20 to May 2, 2016, all at 15 m. At each sampling location, single, duplicate, or triplicate filters were collected using either niskins attached to a conductivity, temperature, depth array (CTD) or the underway intake. Samples (10-15 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. Blank PTFE filters were extracted alongside samples as methodological blanks. |
| Sample Type: | Suspended Marine Particulate Matter |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR001499 |
| Treatment Summary: | No treatment - this was a study of the of natural marine microbial population in the surface ocean from the North Pacific Subtropical Gyre to North Pacific Transition Zone. |
Sample Preparation:
| Sampleprep ID: | SP001492 |
| 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 | AN002358 | AN002359 | AN002360 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | HILIC | HILIC |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | Waters Acquity UPLC HSS Cyano (100 x 2.1mm,1.8um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| 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 | POSITIVE | NEGATIVE |
| Units | Adjusted and normalized peak areas | Adjusted and normalized peak areas | Adjusted and normalized peak areas |
Chromatography:
| Chromatography ID: | CH001729 |
| Chromatography Summary: | See attached protocol |
| 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 |
| Chromatography ID: | CH001730 |
| Chromatography Summary: | See attached protocol |
| 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 |
MS:
| MS ID: | MS002200 |
| Analysis ID: | AN002358 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002201 |
| Analysis ID: | AN002359 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002202 |
| Analysis ID: | AN002360 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | See attached protocol. |
| Ion Mode: | NEGATIVE |
