Dataset: Extracellular reef seawater metabolites from the Jardines de la Reina reef-system

Name: Sampling and accession information for extracellular reef seawater metabolites collected from the Jardines de la Reina reef-system, Cuba in November of 2017
Published: 2023-10-20
Keywords: metabolomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.843270.1

Spatial Extent: N:21.3033 E:-78.3811 S:20.5065 W:-79.5911

Temporal Extent: 2017-11-05 - 2017-11-20

Project:

RAPID/MRI: Acquisition of a Triple-Quad Mass Spectrometer for Quantitative Identification of Dispersants and Water-Soluble Oil in the Gulf of Mexico (RAPID Mass Spec for Dispersants)

Signature exometabolomes of Caribbean corals and influences on reef picoplankton (Coral Exometabolomes)

Principal Investigator:

Amy Apprill (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Elizabeth Kujawinski (Woods Hole Oceanographic Institution, WHOI)

Scientist:

Laura Gray (Woods Hole Oceanographic Institution, WHOI)

Contact:

Laura Gray (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-10-20

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Sampling and accession information for extracellular reef seawater metabolites collected from the Jardines de la Reina reef-system, Cuba in November of 2017

Abstract:

This dataset contains sampling and accession information for extracellular reef seawater metabolites collected from two different depths across 9 different shallow forereefs in the Jardines de la Reina reef-system, Cuba. Reef seawater samples, collected in duplicate per depth and location, were subjected to targeted and untargeted liquid chromatography mass spectrometry (LC-MS) methods in addition to a suite of biogeochemical measurements (see Related Datasets for access to the biochemistry data). Raw and .mzML data files from the LC-MS methods are located at MetaboLights database, using accession number MTBLS1820.(Accessible from https://www.ebi.ac.uk/metabolights/MTBLS1820/). These data were published in Weber et al. (2020).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-10-20	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.843270.1	2023-10-26

Description

Funding Description:

Dalio Foundation (now ‘OceanX’) (awarded to Amy Apprill)
National Science Foundation (OCE-1736288) (awarded to Amy Apprill)

Mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility using instruments funded by the National Science Foundation (grant OCE-1058448 awarded to Elizabeth B. Kujawinski and Melissa Kido Soule) and the Simons Foundation (Award ID #509042, awarded to Elizabeth B. Kujawinski)

Methods & Sampling

Location: Jardines de la Reina reef system south of the island of Cuba; General location: 20.8333° N, 78.9167° W

Sampling and analytical procedure summary:

Reef seawater microbial biogeochemistry and extracellular metabolite compositions were surveyed at nine, shallow (6 – 14 m in depth) forereef sites during a cruise to Jardines de la Reina (JR), Cuba in November of 2017. Seawater was also collected from two surface ‘off reef’ sites (800 – 1600 m depth).

Methods and data access for the biogeochemistry data are available from Related Dataset "Extracellular reef seawater biogeochemistry from the Jardines de la Reina reef-system" (see "Related Datasets" section).

Surface and reef depth seawater samples were also collected to quantify concentrations of known metabolites using a targeted metabolomics method and survey trends in untargeted metabolite feature composition using an untargeted method. Exometabolite extracts were subjected to reverse-phase liquid chromatography mass spectrometry after filtering and solid-phase- extraction.
Note: term "benthic" and "reef depth" are used interchangeably in columns "reef" and "Depth"

Targeted metabolomics analysis was completed using a UPLC (Accela Open Autosampler and Accela 1250 Pump, Thermo ScientificTM) coupled to a heated electrospray ionization source (H-ESI) and a triple stage quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher ScientificTM), operated in selective reaction monitoring (SRM) mode. For chromatography, a Waters Acquity HSS T3 column (2.1 mm × 100 mm, 1.8 μm), equipped with a Vanguard pre-column, was used for chromatographic separation at 40 °C.

Untargeted metabolomics analysis was completed using an ultra-high performance liquid chromatography system (Vanquish UHPLC, Thermo ScientificTM) coupled with an Orbitrap Fusion Lumos Tribid mass spectrometer (Thermo ScientificTM) using the same chromatographic conditions as used for targeted metabolomics.

Detailed methods are included on the MetaboLights project page (Project MTBLS1820) and within the open access paper, Weber et al. (2020).

BCO-DMO Processing

BCO-DMO Data Manager Processing Notes:
* Sheet 1 of file "Cuba2017_metabdata_BCODMO_date_latlong.xlsx" was imported into the BCO-DMO data system with values "NaN" as missing data values. This file version was submitted to BCO-DMO 2023-09-06.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* date format changed to ISO format
* Column "MetaboLights_Study_Number" was added with value "MTBLS1820" as discussed with submitter.
* Column "reef" and "site" added to correspond to related dataset, biogeochemistry data column "reef". See related dataset description. Reef values added from information in the sample identifier. Logic and the resulting reef column was reviewed by the submitter.

Data Files

File
MTBLS1820 samples filename: 843270_v1_mtbls1820_samples.csv (Comma Separated Values (.csv), 24.85 KB) MD5:0ed217f36cf305fbc0ef1d288f4e26e8 Primary data table for dataset 843270 version 1. MTBLS1820 is the study identifier in the associated Metabolights repository.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1736288
NSF Division of Ocean Sciences	OCE-1058448

Deployments

None available yet

Instruments

Mass Spectrometer

Supplied Name: Orbitrap Fusion Lumos (Thermo Fisher Scientific)

Supplied Description:

Mass spectrometry samples were analyzed on a Vanquish UHPLC system (Thermo Fisher Scientific) coupled via heated electrospray ionization (H-ESI) to an ultrahigh resolution tribrid mass spectrometer, the Orbitrap Fusion Lumos (Thermo Fisher Scientific).

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.

Mass Spectrometer

Supplied Name: Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer

Supplied Description:

Extracts prepared for targeted metabolomics were analyzed using UPLC (Accela Open Autosampler and Accela 1250 Pump, Thermo Scientific) coupled to a heated electrospray ionization source (H-ESI) and a triple stage quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher Scientific), operated in selective reaction monitoring (SRM) mode.

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

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

Generic Description:

Ultra high-performance liquid chromatography

Supplied Name: Vanquish UHPLC system (Thermo Fisher Scientific)

Supplied Description:

Instrument Type

Generic Name: Ultra high-performance liquid chromatography

Acronym: UHPLC

Generic Description:

Ultra high-performance liquid chromatography: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small (< 2 microm) particles and the inlet pressure is relatively high.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
MetaboLights_Study_Number	MetaboLights study number	unitless	accession_number
Sample_Name	Name of sample	unitless	sample
reef	sample name of reef (site identifier and sample depth; "surf" for surface or "benthic" for reef depth).	unitless	Site_ID
site	Site identifier	unitless	site
Seawater_collection_date	Date of sample collection Format: %Y-%m-%d	unitless	date
Latitude	sampling location latitude	decimal degrees	lat
Longitude	sampling location longitude	decimal degrees	lon
Sample_type	sample type	unitless	sample_descrip
Seawater_sampling_location	description of sampling location relative to the coral reef	unitless	sample_descrip
Depth	categorical sampling depth (e.g. pooled QC, reef depth, surface)	unitless	depth_n
Replicate	Indicates if a duplicate sample was collected for this location and depth	unitless	replicate
Profiling_mode	Type of method used - either targeted or untargeted	unitless	sampling_method
Ion_mode	Type of ionization used - either positive or negative	unitless	sampling_method
raw_file_name	full file name for the raw data file that can be downloaded from MetaboLights (extension .raw)	unitless	file_name
derived_file_name	full file name for the derived data file that can be downloaded from MetaboLights (extension .mzML)	unitless	file_name