Dataset: GT10 - Cysteine Glutathione
Deployment: KN199-04

Dissolved cysteine and glutathione across the US GEOTRACES North Atlantic Zonal Section

Principal Investigator:

Chad Hammerschmidt (Wright State University)

Carl Lamborg (Woods Hole Oceanographic Institution, WHOI)

Contact:

Chad Hammerschmidt (Wright State University)

Carl Lamborg (Woods Hole Oceanographic Institution, WHOI)

Gretchen Swarr (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

U.S. GEOTRACES North Atlantic Transect (GA03) (U.S. GEOTRACES NAT)

Current State:

Final no updates expected

Version:

21 Jan 2013

Deployment Synonyms:

GA03, GT10, USGT-NAT-2010, KN199-4, GNAT, U.S. GEOTRACES NAZT Leg 1, knorr199-4/5, Section Cruise (GA03), 316N20101015

Version Date:

2013-03-05

Data URL:

https://www.bco-dmo.org/dataset-deployment/455736/data

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Description

This dataset included concentrations of filtered cysteine and glutathione (the only two thiols detected) from 21 full stations across the cruise path. The current dataset (as of Dec 2012) contains only results from 2010 cruise (8 stations) and primarily in the upper 1000 meters. Deeper water samples were collected at most stations, but analysis of a few deep water samples has indicated that most of these samples are below detection, and we have therefore elected not to analyze many of the deeper samples.

Methods & Sampling

Dataset acquisition description

Detailed method descriptions can be found in Kading, 2012.
Sample collection: 125 mL filtered (0.45 µm) from the ODF rosette, frozen immediately after collection and held that way until analysis. Samples pre-concentrated on C-18 columns the day of derivitization, extracted with methanol.
Sample bottles/cleaning: Kading, 2012
Analysis:
     Dupont et al., 2006, Kading, 2012, Tang et al., 2003
     Agilent 1200 HPLC, 4.6 x 250 mm Waters Spherisorb 5 ?m column with attached 4.6 x 10 mm guard column, 100 uL sample loop, gradient was 8% acetonitrile in 0.1% TFA to 35% acetonitrile linearly over 47 minutes and then rinsed for 5 minutes in 80% acetonitrile in 0.1% TFA. The column was conditioned for 30 minutes with 92% 0.1% trifluoroacetic acid (TFA) and 8% acetonitrile at 1 mL min-1 between each sample analyzed.
     Detection limit: 0.015 nM for cysteine and 0.01 nM for glutathione
     Procedural duplicates: 15% r.s.d.
     Recovery of known additions: 100%

Data Processing Description

Dataset Processing Description

"lt_DL” indicates that a sample was below the method detection limit.

Related files and references:
Dupont, C.L., Moffett, J.W., Bidigare, R.R. and Ahner, B.A., 2006. Distributions of dissolved and particulate biogenic thiols in the subartic Pacific Ocean. Deep-Sea Research Part I-Oceanographic Research Papers, 53(12): 1961-1974.

Kading, T., 2012. Distribution of thiols in the northwest Atlantic Ocean, WHOI-MIT Joint Program, Woods Hole, MA.

Tang, D.G., Shafer, M.M., Vang, K., Karner, D.A. and Armstrong, D.E., 2003. Determination of dissolved thiols using solid-phase extraction and liquid chromatographic determination of fluorescently derivatized thiolic compounds. Journal of Chromatography A, 998(1-2): 31-40.

BCO-DMO processing notes:
These changes were made to the submitted data file:
- added cruise_id
- inserted nd for blanks
- renamed variables to better match those in Master list
- adjusted formats: lat/lon
- changed '>DL' to lt_DL

Additional GEOTRACES Processing:
After the data were submitted to the International Data Management Office, BODC, the office noticed that important identifying information was missing in many datasets. With the agreement of BODC and the US GEOTRACES lead PIs, BCO-DMO added standard US GEOTRACES information, such as the US GEOTRACES event number, to each submitted dataset lacking this information. To accomplish this, BCO-DMO compiled a 'master' dataset composed of the following parameters: station_GEOTRC, cast_GEOTRC (bottle and pump data only), event_GEOTRC, sample_GEOTRC, sample_bottle_GEOTRC (bottle data only), bottle_GEOTRC (bottle data only), depth_GEOTRC_CTD (bottle data only), depth_GEOTRC_CTD_rounded (bottle data only), BTL_ISO_DateTime_UTC (bottle data only), and GeoFish_id (GeoFish data only). This added information will facilitate subsequent analysis and inter comparison of the datasets.

Bottle parameters in the master file were taken from the GT-C_Bottle_GT10, GT-C_Bottle_GT11, ODF_Bottle_GT10, and ODF_Bottle_GT11 datasets. Non-bottle parameters, including those from GeoFish tows, Aerosol sampling, and McLane Pumps, were taken from the Event_Log_GT10 and Event_Log_GT11 datasets. McLane pump cast numbers missing in event logs were taken from the Particulate Th-234 dataset submitted by Ken Buesseler.

A standardized BCO-DMO method (called "join") was then used to merge the missing parameters to each US GEOTRACES dataset, most often by matching on sample_GEOTRC or on some unique combination of other parameters.

If the master parameters were included in the original data file and the values did not differ from the master file, the original data columns were retained and the names of the parameters were changed from the PI-submitted names to the standardized master names. If there were differences between the PI-supplied parameter values and those in the master file, both columns were retained. If the original data submission included all of the master parameters, no additional columns were added, but parameter names were modified to match the naming conventions of the master file.

See the dataset parameters documentation for a description of which parameters were supplied by the PI and which were added via the join method.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0927274	NSF Division of Ocean Sciences
OCE-1132515	NSF Division of Ocean Sciences

Instruments

High-Performance Liquid Chromatograph

Supplied Name: High Performance Liquid Chromatograph

Supplied Description:

Agilent 1200 HPLC

Instrument Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

Generic Description:

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.

Trace Metal Bottle

Supplied Description:

Instrument Type

Generic Name: Trace Metal Bottle

Acronym: TM Bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	Official cruise identifier e.g. KN199-04 = R/V Knorr cruise number 199-04.	text	cruise_id
station_GEOTRC	GEOTRACES station number; ranges from 1 through 12 for KN199-04 and 1 through 24 for KN204-01. Stations 7 and 9 were skipped on KN204-01. PI-supplied values were identical to those in the intermediate US GEOTRACES master file. Originally submitted as 'STNNBR', this parameter name has been changed to conform to BCO-DMO's GEOTRACES naming conventions.	integer	station
cast_GEOTRC	Cast identifier, numbered consecutively within a station. PI-supplied values were identical to those in the intermediate US GEOTRACES master file. Originally submitted as 'CASTNO', this parameter name has been changed to conform to BCO-DMO's GEOTRACES naming conventions.	integer	cast
sample_GEOTRC	Unique identifying number for US GEOTRACES samples; ranges from 5033 to 6078 for KN199-04 and from 6112 to 8148 for KN204-01. PI-supplied values were identical to those in the intermediate US GEOTRACES master file. Originally submitted as 'GEOTRC_SAMPNO', this parameter name has been changed to conform to BCO-DMO's GEOTRACES naming conventions.	integer	sample
date	UTC date of sample collection	yyyymmdd	date_utc
time	UTC time	HHMM	time_utc
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
depth	sample depth; provided in original data submission.	meters	depth
Cys	concentration of cysteine	nanomoles/liter	amino_conc
Cys_rsd	cysteine error as percent relative standard deviation	percent	rsd
Cys_flag	cysteine quality flag: 2) ok 3) questionable 4) bad analysis 5) sample lost 6) mean of replicates 9) sample was not collected for thiol analysis	integer	flag
GSH	concentration of glutathione	nanomoles/liter	no_bcodmo_term
GSH_rsd	glutathione error as percent relative standard deviation	percent	rsd
GSH_flag	glutathione quality flag: 2) ok 3) questionable 4) bad analysis 5) sample lost 6) mean of replicates	integer	flag
event_GEOTRC	Unique identifying number for US GEOTRACES sampling events; ranges from 2001 to 2225 for KN199-04 events and from 3001 to 3282 for KN204-01 events. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	event
sample_bottle_GEOTRC	Unique identification numbers given to samples taken from bottles; ranges from 1 to 24; often used synonymously with bottle number. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	bot_Nis
bottle_GEOTRC	Alphanumeric characters identifying bottle type (e.g. NIS representing Niskin and GF representing GOFLO) and position on a CTD rosette. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	dimensionless	bottle
depth_GEOTRC_CTD	Observation/sample depth in meters; calculated from CTD pressure. Values were added from the intermediate US GEOTRACES master file (see Processing Description).	meters	depth
BTL_ISO_DateTime_UTC	Date and time (UTC) variable recorded at the bottle sampling time in ISO compliant format. Values were added from the intermediate US GEOTRACES master file (see Processing Description). This standard is based on ISO 8601:2004(E) and takes on the following form: 2009-08-30T14:05:00[.xx]Z (UTC time)	YYYY-MM-DDTHH:MM:SS[.xx][+/-TZ]	ISO_DateTime_UTC

Database

Contribute Data

Dataset: GT10 - Cysteine Glutathione
Deployment: KN199-04

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: GT10 - Cysteine GlutathioneDeployment: KN199-04

Dataset acquisition description

Dataset Processing Description

Dataset: GT10 - Cysteine Glutathione
Deployment: KN199-04