Dataset: Targeted metabolite abundances: dissolved
Deployment: KN210-04

Targeted dissolved metabolite abundances

Principal Investigator:

Elizabeth Kujawinski (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Krista Longnecker (Woods Hole Oceanographic Institution, WHOI)

Contact:

Elizabeth Kujawinski (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Project:

Dissolved Organic Matter Composition in the Deep Atlantic Ocean (Deep Atlantic DOM)

Deployment Synonyms:

DeepDOM

Data URL:

https://www.bco-dmo.org/dataset-deployment/700032/data

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Description

This dataset contains dissolved metabolite abundances from seawater samples collected during the R/V Knorr cruise KN210-04 between 29 Mar 2013 and 06 May 2013 along the eastern coast of South America.

See related dataset:
Targeted metabolite abundances: Particulate

Sample depth, lat, lon, station, time, and cast are from CTD profiles are also included in this dataset. For more information about the data from CTDs refer to the following datasets:
CTD
event log

Methods & Sampling

Dataset acquisition description

The filtrate from filtration through a 0.7 µm GF/F filter and a 0.2 um omnipore filter was acidified to pH 2-3 with 12 M hydrochloric acid and extracted using solid phase extraction (1 g Agilent Bond Elut PPL cartridge, 6 mL cartridge volume) and eluted with methanol (according to methods described in Dittmar et al., 2008; Longnecker et al., 2015). Extracts were stored at -20C until analysis.

A Phenomenex C18 reversed phase column (Synergi Fusion, 2.1 x 150 mm, 4 um) coupled via a heated ESI source to a triple quadrupole mass spectrometer (Thermo Scientific TSQ Vantage) was used to measure metabolites (Kido Soule et al., 2015).

Data Processing Description

Dataset Processing Description

Peaks were detected and integrated using MAVEN (Melamud et al., 2010). Metabolites were quantified using calibration curves and MQ blanks were subtracted. The dissolved metabolites were corrected to account for their solid phase extraction efficiencies (Johnson et al., 2017). For limits of detection please refer to Johnson et al., 2017.

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values replaced with no data value 'nd'
* changed micro (u) symbol to u in the data.
* lat/lon rounded to 5 decimal places
* time 0 padded if less than 4 numbers (731 -> 0731)
* added ISO_DateTime_UTC timestamp

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1154320	NSF Division of Ocean Sciences

Instruments

Mass Spectrometer

Supplied Name: Thermo Scientific TSQ Vantage

Supplied Description:

Phenomenex C18 reversed phase column (Synergi Fusion, 2.1 x 150 mm, 4 um) coupled via a heated ESI source to a triple quadrupole mass spectrometer (Thermo Scientific TSQ Vantage) was used to measure metabolites

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
cast	cast number	unitless	cast
station	station identifier	unitless	station
date_start_utc	date (UTC) in format yyyymmdd	unitless	date
time_start_utc	time (UTC) in format HHMM	unitless	time
ISO_DateTime_UTC	ISO timestamp based on the ISO 8601:2004(E) standard in format YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC)	unitless	ISO_DateTime_UTC
event_start	The event number from the ELOG maintained during the cruise.	unitless	event
lat_start	Latitude at the time the event started (from the cruise event log)	decimal degrees	lat
lon_start	Longitude at the time the event started (from the cruise event log); west is negative	decimal degrees	lon
depth	Sample depth from CTD. (Orignally called depSM)	meters (m)	depth
DHBA	2,3-dihydroxybenzoic acid concentration	picomolar (pM)	no_bcodmo_term
MPA	3-mercaptopropionate concentration	picomolar (pM)	no_bcodmo_term
PABA	4-aminobenzoic acid concentration	picomolar (pM)	no_bcodmo_term
PHBA	4-hydroxybenzoic acid concentration	picomolar (pM)	no_bcodmo_term
SAH	S-(5'-adenosyl)-L-homocysteine concentration	picomolar (pM)	no_bcodmo_term
MTA	5-methylthioadenosine concentration	picomolar (pM)	no_bcodmo_term
adenosine	adenosine concentration	picomolar (pM)	no_bcodmo_term
biotin	biotin concentration	picomolar (pM)	no_bcodmo_term
caffeine	caffeine concentration	picomolar (pM)	no_bcodmo_term
chitotriose	chitotriose concentration	picomolar (pM)	no_bcodmo_term
vitamin_B12	cyanocobalamin concentration	picomolar (pM)	no_bcodmo_term
PGA	D-(-)3-phosphoglyceric acid concentration	picomolar (pM)	no_bcodmo_term
desthiobiotin	desthiobiotin concentration	picomolar (pM)	no_bcodmo_term
folic_acid	folic acid concentration	picomolar (pM)	no_bcodmo_term
glyphosate	glyphosate concentration	picomolar (pM)	no_bcodmo_term
IAA	indole 3-acetic acid concentration	picomolar (pM)	no_bcodmo_term
inosine	inosine concentration	picomolar (pM)	no_bcodmo_term
glutathione	glutathione concentration	picomolar (pM)	no_bcodmo_term
leucine	leucine concentration	picomolar (pM)	Leu
Ac_Glu_OH	N-acetylglutamic acid concentration	picomolar (pM)	no_bcodmo_term
NAD	NAD concentration	picomolar (pM)	no_bcodmo_term
NADP	NADP concentration	picomolar (pM)	no_bcodmo_term
pantothenic_acid	pantothenic acid concentration	picomolar (pM)	no_bcodmo_term
phenylalanine	phenylalanine concentration	picomolar (pM)	no_bcodmo_term
pyridoxine	pyridoxine concentration	picomolar (pM)	no_bcodmo_term
riboflavin	riboflavin concentration	picomolar (pM)	no_bcodmo_term
taurocholate	taurocholate concentration	picomolar (pM)	no_bcodmo_term
thiamine	thiamine concentration	picomolar (pM)	no_bcodmo_term
thymidine	thymidine concentration	picomolar (pM)	no_bcodmo_term
tryptophan	tryptophan concentration	picomolar (pM)	no_bcodmo_term

Database

Contribute Data

Dataset: Targeted metabolite abundances: dissolved
Deployment: KN210-04

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Targeted metabolite abundances: dissolvedDeployment: KN210-04

Dataset acquisition description

Dataset Processing Description

Dataset: Targeted metabolite abundances: dissolved
Deployment: KN210-04