Dataset: HPLC Pigments - Underway

Name: Underway HPLC pigments from the RVIB Nathaniel B. Palmer NBP1302 cruise in the Ross Sea during 2013 (TRACERS project)
Published: 2015-05-18
Keywords: oceans

Cite This Dataset

Spatial Extent: N:-54.796 E:168.689167 S:-76.52095 W:-83.12735

Project:

TRacing the fate of Algal Carbon Export in the Ross Sea (TRACERS)

Principal Investigator:

Giacomo DiTullio (Grice Marine Laboratory - College of Charleston, GML-CoC)

Contact:

Emily Cooper (Grice Marine Laboratory - College of Charleston, GML-CoC)

Giacomo DiTullio (Grice Marine Laboratory - College of Charleston, GML-CoC)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

18 May 2015

Version Date:

2015-05-18

Current State:

Preliminary and in progress

Underway HPLC pigments from the RVIB Nathaniel B. Palmer NBP1302 cruise in the Ross Sea during 2013 (TRACERS project)

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Description

HPLC pigment analyses of underway collected samples from the NBP1302 cruise (Ross Sea, Antarctica).

Methods & Sampling

Water samples were collected from underway samples.

Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100). Culture aliquots were filtered on Whatmann GF/F filters, flash frozen in liquid nitrogen, and stored at -80°C until analysis. Just prior to analysis, pigments were extracted overnight in acetone at -20°C. The following day extracted pigments were centrifuged and measured using a gradient elution method (DiTullio and Geesey, 2003), a modification of the Zapata et al 2000 method. Chromatographic separation was performed using a Waters C8 symmetry column, photodiode array and fluorescence detectors. The internal standard, β-Apo-8-carotenal-trans standard (Fluka Chemical Corp., USA) was added to extracted pigments as a peak reference. Individual pigment peaks were quantified with Chemstation software (revision B.03.01, Agilent) and our pigment action spectra library calibrated using pigment standards from DHI LABS (Hoersholm, Denmark) and in-house purifications of non-commercially available pigments. Coefficient of variation among replicate HPLC injections is < 3% and our limit of detection is approximately 1 ng L-1.

Nathaniel B. Palmer Systems and Specifications

Data Processing Description

Response factors for pigments were performed using dilutions of calibration standards. Full details of data processing and methods used can be found in:
DiTullio, G. R. & Geesey, M. E. (2002) Photosynthetic pigments in marine algae and bacteria. In: BITTON, G. (ed.) The Encyclopedia of Environmental Microbiology. New York: John Wiley & Sons Inc.

BCO-DMO Processing Notes:
- Generated from original .xlsx file "NPB1302 BCO-DMO.xls, sheet: Underway Final" contributed by Emily Cooper
- Parameter names edited to conform to BCO-DMO naming convention found at Choosing Parameter Name
- Blanks (missing data) replaced with "nd" meaning "no data";
- Date reformmated to YYYYMMDD
- Time reformatted to HHMM
- Added ISO_DateTime_UTC column from original DATE and TIME fields
- Lat/Lon whole degs and minutes removed (decimal degrees preserved)
- Lat/Lons recalculated to reflect correct hemisphere signage

Data Files

File
HPLC_Pigments_UW.csv (Comma Separated Values (.csv), 31.60 KB) MD5:0e7d58273c7fbf010c30fa07e5a2bff6 Primary data file for dataset ID 558893

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Polar Programs	PLR-1142065

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
NBP1302	TRACERS 2013	2013-02-12	RVIB Nathaniel B. Palmer	Dennis Hansell (Chief Scientist)	data info

Instruments

Global Positioning System Receiver

Supplied Name: Trimble GPS - PCODE

Supplied Description:

Instrument Type

Generic Name: Global Positioning System Receiver

Acronym: GPS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/POS03/

Generic Description:

The Global Positioning System (GPS) is a U.S. space-based radionavigation system that provides reliable positioning, navigation, and timing services to civilian users on a continuous worldwide basis. The U.S. Air Force develops, maintains, and operates the space and control segments of the NAVSTAR GPS transmitter system. Ships use a variety of receivers (e.g. Trimble and Ashtech) to interpret the GPS signal and determine accurate latitude and longitude.

High-Performance Liquid Chromatograph

Supplied Name: HPLC

Supplied Description:

Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100).

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.

Pump - Surface Underway Ship Intake

Supplied Name: Underway Seawater System

Supplied Description:

The seawater system supplies underway seawater to the Aquarium Room, Wet Lab,
Hydro Lab, Helo Deck, Helo Hangar, and Baltic Room. Green strand piping, a non-metal-
lic, chemically resistant material has been used throughout the system to minimize algae
and bacterial growth.
It also maintains its structural integrity under low temperatures. Large diameter piping and
a minimum of 90° turns helps prevent frazil ice formation in the system. The seawater
system is also equipped with a centrifugal ice strainer/de-bubbler.

Instrument Type

Generic Name: Pump - Surface Underway Ship Intake

Acronym: Pump-Ship Intake

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/31/

Generic Description:

The 'Pump-underway ship intake' system indicates that samples are from the ship's clean water intake pump. This is essentially a surface water sample from a source of uncontaminated near-surface (commonly 3 to 7 m) seawater that can be pumped continuously to shipboard laboratories on research vessels. There is typically a temperature sensor near the intake (known as the hull temperature) to provide measurements that are as close as possible to the ambient water temperature. The flow from the supply is typically directed through continuously logged sensors such as a thermosalinograph and a fluorometer. Water samples are often collected from the underway supply that may also be referred to as the non-toxic supply. Ideally the data contributor has specified the depth in the ship's hull at which the pump is mounted.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Num	Sample Number	integer	sample
Date	Date (GMT)	YYYYMMDD	date
Time	Time (GMT)	HHMM	time
ISO_Date_Time	Date/Time (GMT (ISO formatted)	YYYY-MM-DDTHH:MM:SS[.xx]Z	ISO_DateTime_UTC
Latitude	Latitude (South is negative)	decimal degrees	lat
Longitude	Longitude (West is negative)	decimal degrees	lon
Filt_vol	Volume Filtered	liters	vol_filt
Chl_C3	Chlorophyll c3	ng/L	chl_c3
Chl_lide	Chlorophyllide	ng/L	chlide
MgDvp	Magnesium-2;4-divinyl	ng/L	mg_dvp_a5
Chl_C2	Chlorophyll c2	ng/L	chl_c2
Chl_C1	Chlorophyll c1	ng/L	chl_c1
Peridinin	Peridinin	ng/L	peridinin
Ph_ide	Pheophorbide a	ng/L	p_phorbide
But19	19'-butanoyloxyfucoxanthin	ng/L	fucox_but
Fuco	Fucoxanthin	ng/L	fucox
Neo	Neoxanthin	ng/L	neox
Prasino	Prasinoxanthin	ng/L	prasinox
Viola	Violaxanthin	ng/L	violax
Hex19	19'-hexanoyloxyfucoxanthin	ng/L	fucox_hex
DD	Diadinoxanthin	ng/L	diadinox
cis_Fuco	cis-Fucoxanthin	ng/L	cis_fucox
Allo	Alloxanthin	ng/L	allox
Diato	Diatoxanthin	ng/L	diatox
Monad	Monadoxanthin	ng/L	monad
Zeax	Zeaxanthin	ng/L	zeax
Lutein	Lutein	ng/L	lutein
Croco	Crocoxanthin	ng/L	crocox
Chl_b	Chlorophyll b	ng/L	chl_b
Chlorophyll_c2_MGDG	Chlorophyll c2 MGDG	ng/L	chl_c2
Chlorophyll_a_allomer	Chlorophyll a allomer	ng/L	chl_a
DV_Chl_a	Divinyl chlorphyll a	ng/L	chl_a2
Chl_a	Chlorophyll a	ng/L	chl_a
Ph_tin	Phaeophytin a	ng/L	p_phytin
a_Car	Alpha-carotene	ng/L	carotene_a
b_Car	Beta-carotene	ng/L	carotene_b
Total_Chl_a	Total Chlorophyll a	ng/L	chl_a_tot

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Dataset: HPLC Pigments - Underway