Dataset: Mass spectrometry metabolomics data
Deployment: EN509

MS-based polar metabolomics on diatom response to allelopathic chemicals from red tide dinoflagellate (Karenia brevis)

Principal Investigator:

Julia Kubanek (Georgia Institute of Technology, GA Tech)

Co-Principal Investigator:

Facundo Fernandez (Georgia Institute of Technology, GA Tech)

Brook L. Nunn (University of Washington, UW)

Contact:

Julia Kubanek (Georgia Institute of Technology, GA Tech)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Waterborne chemical cues in the plankton: a systems biology approach (Plankton Chemical Cues)

Current State:

Final no updates expected

Version:

31 Oct 2014

Version Date:

2014-10-31

Data URL:

https://www.bco-dmo.org/dataset-deployment/537499/data

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Description

These mass spec data files are in Thermo-Finnigan .raw format. Vendor software can be used to view these files, and there are free viewers that can also be used (one example is PVIEW). The files can also be converted to mzXML files using MSconvert.

Note: Data files in .raw format are also available from the Chorus repository (https://chorusproject.org) under project ID number 650 (project name: "Diatom response to allelopathy"), experiment ID number 848. See: https://chorusproject.org/anonymous/download/experiment/8464697144662088343

Methods & Sampling

Dataset acquisition description

Field assemblages of plankton were sampled during two cruises (EN496 and EN509), and shipboard experiments were conducted to test the community-level effects of Karenia brevis allelopathy on Gulf of Mexico plankton. The sampling and shipboard experiments are described fully in:
Poulson-Ellestad et al. 2014. Are offshore phytoplankton susceptible to Karenia brevis allelopathy? J. Plankton Res. 36:1344-1356. doi: 10.1093/plankt/fbu064

See related publication:
Poulson-Ellestad, K.L., Jones, C.M., Roy, J., Viant, M.R., Fernandez, F.M., Kubanek, J., & Nunn, B.L. 2014. Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. PNAS Proc Natl Acad Sci USA, 111(24): 9009-14. doi:10.1073/pnas.1402130111

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1060300	NSF Division of Ocean Sciences

Instruments

Mass Spectrometer

Supplied Name: Xevo G2 QTOF Mass Spectrometer

Supplied Description:

A Xevo G2 QTOF Mass Spectrometer was used.

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
description	Description of the file package	dimensionless	brief_desc
file_size	Approximate file size	gigabytes (GB)	file_size
download_link	Link to download the file	dimensionless	file_link

Database

Contribute Data

Dataset: Mass spectrometry metabolomics data
Deployment: EN509

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Mass spectrometry metabolomics dataDeployment: EN509

Dataset acquisition description

Dataset Processing Description

Dataset: Mass spectrometry metabolomics data
Deployment: EN509