Summary of Study ST001356
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000926. The data can be accessed directly via it's Project DOI: 10.21228/M80H4K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001356 |
| Study Title | Diel Metabolites in the North Pacific Subtropical Gyre (KM1513) |
| Study Type | Diel metabolomics |
| Study Summary | Diverse organisms within the marine microbial communities show 24-hour cycles of gene expression, likely driven by the need to harness energy from sunlight and to cope with dramatic fluctuations in solar radiation over the course of the day. Metabolites are the direct product of metabolic activity; they are therefore expected to both reflect and influence the daily cycle of the microbial community. Here we measure the intracellular metabolome of the microbial community of the North Pacific Subtropical Gyre, sampled at 4-hour intervals for 8 days. Concentrations of some metabolites common to many organisms exhibit diel periodicity, revealing synchrony of community-level metabolism. Comparing these data to gene expression data reveals temporal offsets between gene transcription and cellular activity, and ties some metabolites to the activities of specific organisms. For example, the dramatic fluctuations of the disaccharide trehalose likely reflect the daily cycles of {Crocosphaera}, a photosynthesizing cyanobacteria that needs to store energy during the day to fuel nighttime nitrogen-fixation. This study illustrates how pairing multiple types of 'omics and environmental data can provide insight into how the activities of individual organisms lead to community functions such as net primary productivity and nitrogen fixation. |
| Institute | University of Washington |
| Department | Oceanography |
| Laboratory | Ingalls Lab |
| Last Name | Boysen |
| First Name | Angela |
| Address | 1502 NE Boat St |
| aboysen@uw.edu | |
| Phone | 3037461944 |
| Submit Date | 2020-03-23 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-07-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN002255 | AN002256 | AN002257 | AN002258 | AN002259 |
|---|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC | HILIC |
| Chromatography system | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class | Waters Acquity I-Class |
| Column | Waters Acquity UPLC HSS Cyano (CN) ( 50 x 2.1mm,1.8um) | Waters Acquity UPLC HSS Cyano (CN) ( 50 x 2.1mm,1.8um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Orbitrap | Triple quadrupole | Triple quadrupole | Orbitrap |
| MS instrument name | Waters Xevo-TQ-S | Thermo Q Exactive HF hybrid Orbitrap | Waters Xevo-TQ-S | Waters Xevo-TQ-S | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | Normalized Peak Area Per L Seawater Filtered | Normalized Peak Area Per L Seawater Filtered | Normalized Peak Area Per L Seawater Filtered | Normalized Peak Area Per L Seawater Filtered | Normalized Peak Area per L of SW filtered |
Chromatography:
| Chromatography ID: | CH001657 |
| Chromatography Summary: | RP |
| Methods Filename: | Ingalls_Metabolomics_MS_Parameters_2015.pdf |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters Acquity UPLC HSS Cyano (CN) ( 50 x 2.1mm,1.8um) |
| Column Temperature: | 35 C |
| Flow Gradient: | 5% B for 2 minutes, ramped to 100% B over 16 minutes, held at 100% B for 2 minutes, and equilibrated at 5% B for 5 minutes |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 20 min |
| Preconditioning: | equilibrated at the starting conditions for at least 10 minutes; several water blanks were run before |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001658 |
| Chromatography Summary: | HILIC |
| Methods Filename: | Ingalls_Metabolomics_MS_Parameters_2015.pdf |
| Chromatography Comments: | In marine samples, a major salt peak elutes at approximately 23 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. |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 30 C |
| Flow Gradient: | 100% A for 2 minutes, ramped to 100% B over 18 minutes, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes |
| Flow Rate: | 0.15 mL/min |
| Solvent A: | 85% acetonitrile/15% water; 10 mM ammonium carbonate |
| Solvent B: | 40% acetonitrile/60% water; 10 mM ammonium carbonate |
| Analytical Time: | 25 min |
| Preconditioning: | , the column was equilibrated at the starting conditions for at least 30 minutes |
| Chromatography Type: | HILIC |
