Dataset: Mass spectrometry metabolomics data

Name: MS-based polar metabolomics on diatom response to allelopathic chemicals from red tide dinoflagellate (Karenia brevis)
Published: 2018-03-21
Keywords: biota, oceans

Cite This Dataset

Project:

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

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)

Version:

21 March 2018

Version Date:

2018-03-21

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

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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

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 Files

File
metabolomics_data.csv (Comma Separated Values (.csv), 268 bytes) MD5:8acaa3dfdc3755594b083fef70187d33 Primary data file for dataset ID 537359

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
EN496	GoM2011	2011-07-02	R/V Endeavor	Joseph Montoya (Chief Scientist)	data info
EN509		2012-05-25	R/V Endeavor	Joseph Montoya (Chief Scientist)	data info

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

Date and time formats are described in python strftime() syntax.

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

Status message

Database

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Dataset: Mass spectrometry metabolomics data