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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Download all metabolite data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (Contains raw data)
Study IDST001356
Study TitleDiel Metabolites in the North Pacific Subtropical Gyre (KM1513)
Study TypeDiel metabolomics
Study SummaryDiverse 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
DepartmentOceanography
LaboratoryIngalls Lab
Last NameBoysen
First NameAngela
Address1502 NE Boat St
Emailaboysen@uw.edu
Phone3037461944
Submit Date2020-03-23
Raw Data AvailableYes
Raw Data File Type(s).mzXML
Analysis Type DetailLC-MS
Release Date2020-07-21
Release Version1
Angela Boysen Angela Boysen
https://dx.doi.org/10.21228/M80H4K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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) (2.1 mm X 50 mm, 1.8 µm) Waters Acquity UPLC HSS Cyano (CN) (2.1 mm X 50 mm, 1.8 µm) 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_LC_Parameters_2015.txt
Instrument Name:Waters Acquity I-Class
Column Name:Waters Acquity UPLC HSS Cyano (CN) (2.1 mm X 50 mm, 1.8 µm)
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:0.1% formic acid in water
Solvent B:0.1% formic acid in acetonitrile
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_LC_Parameters_2015.txt
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:10 mM ammonium carbonate in 85:15 acetonitrile to water
Solvent B:10 mM ammonium carbonate in 60:40 water to acetonitrile
Analytical Time:25 min
Preconditioning:, the column was equilibrated at the starting conditions for at least 30 minutes
Chromatography Type:HILIC
  logo