Dataset: SPOT Cobalamins

Name: Quantification of different chemical forms of cobalamin from San Pedro Ocean Time Series (SPOT) cruises on R/V Nerissa and R/V Yellowfin from March to December 2017
Published: 2019-06-26
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.771777.1

Spatial Extent: N:33.55 E:-118.4 S:33.55 W:-118.4

Temporal Extent: 2017-03-15 - 2017-12-15

Project:

The role of organic and metal cofactors on the biogenic synthesis of halogenated volatile hydrocarbons (Volatile_Hydrocarbons)

Principal Investigator:

Sergio A. Sanudo-Wilhelmy (University of Southern California, USC)

Contact:

Laura Gómez-Consarnau (University of Southern California, USC)

BCO-DMO Data Manager:

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

Version:

Version Date:

2019-06-26

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Quantification of different chemical forms of cobalamin from San Pedro Ocean Time Series (SPOT) cruises on R/V Nerissa and R/V Yellowfin from March to December 2017

Abstract:

This dataset contains data on quantifying different chemical forms of cobalamin from San Pedro Ocean Time Series (SPOT) cruises on R/V Nerissa and R/V Yellowfin from March to December 2017.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2019-06-26	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.771777.1	2021-01-04

Methods & Sampling

Samples for quantification of the different cobalamin forms were collected at a six of depths within the euphotic zone (5-250m). Seawater was collected from each CTD depth using Niskin bottles and immediately filtered. Cobalamins were analyzed as in 1 Suffridge et al. (2017). Two liters of seawater were filtered through µm pore-size filters and then preconcentrated using a C18 resin (HF Bondesil (Agilent Technologies) and analyzed by liquid chromatography/triple mass spectrometry (LC/MS/MS/MS). The LC-MS system consists of a ThermoTSQ Quantum Access electro-spray ionization triple quadrupole mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography system. The LC system used a stable- bond C18 reversed-phase column (DiscoveryHSC18 10cm × 2.1mm,5 μm column, Supelco Analytical) with a100 μL sample loop.In order to increase the sensitivity and precision,theLC/MS was run in full-loop mode (100 μl/injection).

The LC-MS system used for the pigment quantification consists of a Thermo TSQ Quantum Access electro-spray ionization triple quadruple mass spectrometer, coupled to a Thermo Accela High Speed Liquid Chromatography pump and auto-sampler.

Data Processing Description

The LC-MS data was processed using Xcalibur and LCQUAN quantitative softwares from Thermo Scientific.

BCO-DMO Processing:
- modified parameter names (removed units, renamed date and time columns);
- re-formatted date to yyyy-mm-dd (was m/dd/yyyy);
- split time column into start and end times;
- converted lat and lon from degrees and minutes to decimal degrees.

Data Files

File
SPOT_Cobalamins.csv (Comma Separated Values (.csv), 3.44 KB) MD5:74af458717317e8be8855e83793eb267 Primary data file for dataset ID 771777

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1559276

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SPOT_Nerissa_Cruises_2017		2017-03-15	R/V Nerissa		data info
SPOT_Yellowfin_Cruises		2005-01-19	R/V Yellowfin		data info

Instruments

Mass Spectrometer

Supplied Name: ThermoTSQ Quantum Access

Supplied Description:

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.

Niskin bottle

Supplied Name: Niskin bottles

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise name and date	unitless	cruise_id
Date	Date; format: yyyy-mm-dd	unitless	date
Time_Start	Start time; format: HH:MM	unitless	time
Time_End	End time; format: HH:MM	unitless	time
Longitude	Longitude	decimal degrees	lon
Latitude	Latitude	decimal degrees	lat
Depth	Sample depth	meters (m)	depth
AB12	Average Adenosyl-B12 (Adenosylcobalamin) concentrations of triplicate analytical replicates using HPLC-MS.	picomoles per liter (pM)	no_bcodmo_term
HB12	Average Hydroxy-B12 (Hydroxycobalamin) concentrations of triplicate analytical replicates using HPLC-MS.	picomoles per liter (pM)	no_bcodmo_term
MB12	Average Methyl-B12 (Methylcobalamin) concentrations of triplicate analytical replicates using HPLC-MS.	picomoles per liter (pM)	no_bcodmo_term
CB12	Average Vitamin B12 (as Cyanocobalamin) concentrations of triplicate analytical replicates using HPLC-MS.	picomoles per liter (pM)	no_bcodmo_term
MET	Average Methionine concentrations of triplicate analytical replicates using HPLC-MS.	picomoles per liter (pM)	no_bcodmo_term

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Database

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Dataset: SPOT Cobalamins