Dataset: SPOT Cobalamins
Deployment: SPOT_Yellowfin_Cruises

Quantification of different chemical forms of cobalamin from SPOT cruises in 2017

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)

Project:

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

Data URL:

https://www.bco-dmo.org/dataset-deployment/771781/data

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Description

Methods & Sampling

Dataset acquisition description

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

Dataset 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.

More information about this dataset deployment

Funding

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

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

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

Database

Contribute Data

Dataset: SPOT Cobalamins
Deployment: SPOT_Yellowfin_Cruises

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SPOT CobalaminsDeployment: SPOT_Yellowfin_Cruises

Dataset acquisition description

Dataset Processing Description

Dataset: SPOT Cobalamins
Deployment: SPOT_Yellowfin_Cruises