Metadata Report for BODC Series Reference Number 2004371
Metadata Summary
Problem Reports
Data Access Policy
Narrative Documents
Project Information
Data Activity or Cruise Information
Fixed Station Information
BODC Quality Flags
SeaDataNet Quality Flags
Metadata Summary
Data Description |
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Data Identifiers |
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Time Co-ordinates(UT) |
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Parameters |
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Definition of BOTTFLAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
BOTTFLAG | Definition |
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0 | The sampling event occurred without any incident being reported to BODC. |
1 | The filter in an in-situ sampling pump physically ruptured during sample resulting in an unquantifiable loss of sampled material. |
2 | Analytical evidence (e.g. surface water salinity measured on a sample collected at depth) indicates that the water sample has been contaminated by water from depths other than the depths of sampling. |
3 | The feedback indicator on the deck unit reported that the bottle closure command had failed. General Oceanics deck units used on NERC vessels in the 80s and 90s were renowned for reporting misfires when the bottle had been closed. This flag is also suitable for when a trigger command is mistakenly sent to a bottle that has previously been fired. |
4 | During the sampling deployment the bottle was fired in an order other than incrementing rosette position. Indicative of the potential for errors in the assignment of bottle firing depth, especially with General Oceanics rosettes. |
5 | Water was reported to be escaping from the bottle as the rosette was being recovered. |
6 | The bottle seals were observed to be incorrectly seated and the bottle was only part full of water on recovery. |
7 | Either the bottle was found to contain no sample on recovery or there was no bottle fitted to the rosette position fired (but SBE35 record may exist). |
8 | There is reason to doubt the accuracy of the sampling depth associated with the sample. |
9 | The bottle air vent had not been closed prior to deployment giving rise to a risk of sample contamination through leakage. |
Definition of Rank |
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Problem Reports
No Problem Report Found in the Database
Data Access Policy
Open Data supplied by Natural Environment Research Council (NERC)
You must always use the following attribution statement to acknowledge the source of the information: "Contains data supplied by Natural Environment Research Council."
Narrative Documents
Thermo Scientific Accela High Performance Liquid Chromatograph
The Accela high performance liquid chromatography system provides fast separations at pressures of up to 18,130 psi and at flow rates of 1 to 5000 µL/min. The system consists of an analytical pump, an autosampler, an optional PDA detector or UV/Vis detector and a solvent platform.
There is a choice of three analytical pumps to use with the system (the Accela Pump, Accela 600 Pump and Accela 1250 Pump) with each pump having a built-in degassing unit which is remotely controlled from the data system computer via USB. The autosampler automates sample injections and sample preparation and includes a built-in column oven, with a temperature range of 5 to 95°C, and a sample temperature control (0 to 60°C). Within the autosampler there is the capacity for 200 samples across five sample trays. There is a choice to use a PDA detector which in combination with the 5 or 1 cm LightPipe flowcell, provides the highest level of sensitivity available in photodiode array detection for HPLC. The second detector that can be used is a UV/Vis detector which can monitor two wavelength channels. Both detectors have a dual-lamp optical bench that covers the UV-visible spectrum from 190 to 800 nm. The solvent platform is located on top of the system stack and holds four 1 L solvent reservoir bottles and one 1 L wash bottle.
Please see the manufacturer's user's guide and product sheet for further details.
Niskin Bottle
The Niskin bottle is a device used by oceanographers to collect subsurface seawater samples. It is a plastic bottle with caps and rubber seals at each end and is deployed with the caps held open, allowing free-flushing of the bottle as it moves through the water column.
Standard Niskin
The standard version of the bottle includes a plastic-coated metal spring or elastic cord running through the interior of the bottle that joins the two caps, and the caps are held open against the spring by plastic lanyards. When the bottle reaches the desired depth the lanyards are released by a pressure-actuated switch, command signal or messenger weight and the caps are forced shut and sealed, trapping the seawater sample.
Lever Action Niskin
The Lever Action Niskin Bottle differs from the standard version, in that the caps are held open during deployment by externally mounted stainless steel springs rather than an internal spring or cord. Lever Action Niskins are recommended for applications where a completely clear sample chamber is critical or for use in deep cold water.
Clean Sampling
A modified version of the standard Niskin bottle has been developed for clean sampling. This is teflon-coated and uses a latex cord to close the caps rather than a metal spring. The clean version of the Levered Action Niskin bottle is also teflon-coated and uses epoxy covered springs in place of the stainless steel springs. These bottles are specifically designed to minimise metal contamination when sampling trace metals.
Deployment
Bottles may be deployed singly clamped to a wire or in groups of up to 48 on a rosette. Standard bottles and Lever Action bottles have a capacity between 1.7 and 30 L. Reversing thermometers may be attached to a spring-loaded disk that rotates through 180° on bottle closure.
AMT23 (JR20131005) pigment composition by HPLC analysis from CTD bottle samples
Data Acquisition and Analysis
Samples for analysis of phytoplankton pigment concentration were collected from each CTD cast during the cruise. Two samples were collected from each cast, with one sample from around 8-10 m, and the other from around 22-24 m depth.
Samples (1-4L) were vacuum filtered onto GF/F filters, flash frozen in liquid nitrogen and stored at -80 °C. Pigments were extracted from the sample filters into 2 mL 90% acetone using an ultrasonic probe (35 s; 50W). Extracts were clarified and analysed by reversed phase HPLC using a Thermo Accela Series HPLC system with chilled autosampler (4 °C) and photodiode array detector. The HPLC was calibrated using a suite of standards purchased from DHI (Denmark). Pigments were identified based on retention time and spectral match using photo-diode array, following the methods in Zapata et al. (2000).
Instrumentation Description
Thermo Accela Series HPLC system
BODC Data Processing Procedures
Data were submitted to BODC in Microsoft Excel spreadsheet format and saved to the archive with reference PML150156. The file was provided to BODC with cruise, CTD number, CTD bottle number, station, sequential day of year, depth, time, latitude and longitude as metadata. Sample metadata were checked against information held in the database - there were no discrepancies.
The following parameters were provided in the file but only the parameters that were not derived from the summation of other parameters in the dataset were loaded into the database. The absent data value was recorded as the effective limit of detection (LOD). The effective limits of detection, calculated for a filter volume of 3L are given in the table below.
Originator's Parameter | Originator's description | Sum of | Effective LOD (µg/L) | Database load |
---|---|---|---|---|
[TChl a] | Total chlorophyll a | [Chlide a] + [DVChl a] + [Chl a] | - | No |
[TChl b] | Total chlorophyll b | Total chlorophyll b = [DVChl b] + [Chl b] | - | No |
[TChl c] | Total chlorophyll c | Total chlorophyll c = [Chl c2] + [Chl c3] | - | No |
[ßß-Car] | Carotenes (beta-beta-Car) | - | 0.001 | Yes |
[ßE-Car] | Carotenes (beta-epsilon-Car) | - | 0.001 | Yes |
[Caro] | Carotenes (beta-beta-Car + beta-epsilon-Car) | [ßß-Car] + [ßE-Car] | - | Yes |
[But fuco] | 19'-Butanoyloxyfucoxanthin | - | 0.001 | Yes |
[Hex fuco] + [Pras] | 19'-Hexanoyloxyfucoxanthin + Pras | 19'-Hexanoyloxyfucoxanthin + Prasinoxanthin | - | No |
[Hex fuco] | 19'-Hexanoyloxyfucoxanthin | - | 0.001 | Yes |
[Pras] | prasinoxanthin | - | 0.001 | Yes |
[Asta] | astaxanthin | - | 0.001 | Yes |
[Antha] | antheraxanthin | - | 0.001 | Yes |
[Chlide a] | chlorophyllide-a | - | 0.002 | Yes |
[Allo] | Alloxanthin | - | 0.001 | Yes |
[Diad] | Diadinoxanthin | - | 0.001 | Yes |
[Diato] | Diatoxanthin | - | 0.001 | Yes |
[Fuco] | Fucoxanthin | - | 0.001 | Yes |
[Perid] | Peridinin | - | 0.002 | Yes |
[Zea] | Zeaxanthin | - | 0.001 | Yes |
[Viola] | violaxanthin | - | 0.001 | Yes |
[Neo] | neoxanthin | - | 0.001 | Yes |
[Chl a] | Chlorophyll a | - | 0.003 | Yes |
[Chl b] | Chlorophyll b | - | 0.003 | No |
[DVChl a] | Divinyl chlorophyll a | - | 0.002 | Yes |
[Chl b] + [DVChl b] | Chlorophyll b + Divinyl chlorophyll b | - | 0.003 | Yes |
[Chl c1] | chlorophyll c1 | - | 0.001 | Yes |
[Chl c2] | chlorophyll c2 | - | 0.001 | Yes |
[Chl c3] | chlorophyll c3 | - | 0.001 | Yes |
[Lut] | lutein | - | 0.001 | Yes |
[TChl] | Total Chlorophyll | [TChl a] + [TChl b] + [TChl c] | - | No |
[PPC] | Photoprotective carotenoids | [Allo]+[Diad]+[Diato]+[Zea]+[Caro] | - | No |
[PSC] | Photosynthetic carotenoids | [But]+[Fuco]+[Hex fuco]+Perid] | - | No |
[PSP] | Photosynthetic pigments | [PSC]+[TChl] | - | No |
[TAcc] | Total accessory pigments | [PPC]+[PSC]+[TChl b]+[TChl c] | - | No |
[TPig] | Total pigments | [TAcc]+[TChl a] | - | No |
There were duplicate data provided for cast 064, depth 2 m, bottle position 24 and the mean and standard deviation for these values were entered into the database.
Parameter codes defined in BODC parameter dictionary were assigned to the variables as shown in the table below. The data were provided in µg l-1 units that were converted to ng l -1 for all parameters but chlorophyll-a.
Data loaded into BODC's database without any further changes.
Originator's Parameter | Units | Description | BODC Parameter Code + SD Code | Units | Comments |
---|---|---|---|---|---|
[Caro] | µg l-1 | Concentration of beta,epsilon-carotene+beta,beta-carotene {alpha-beta-carotene alpha+beta-carotene} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | ABCRHPP1 ABCRSDP1 | ng l-1 | Unit conversion x1000 applied |
[Allo] | µg l-1 | Concentration of alloxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | ALLOHPP1 ALLOSDP1 | ng l-1 | Unit conversion x1000 applied |
[But fuco] | µg l-1 | Concentration of 19'-butanoyloxyfucoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | BUTAHPP1 BUTASDP1 | ng l-1 | Unit conversion x1000 applied |
[Diad] | µg l-1 | Concentration of diadinoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | DIADHPP1 DIADSDP1 | ng l-1 | Unit conversion x1000 applied |
[Diato] | µg l-1 | Concentration of diatoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | DIATHPP1 DIATSDP1 | ng l-1 | Unit conversion x1000 applied |
[Fuco] | µg l-1 | Concentration of fucoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | FUCXHPP1 FUCXSDP1 | ng l-1 | Unit conversion x1000 applied |
[Hex fuco] | µg l-1 | Concentration of 19'-hexanoyloxyfucoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | HEXOHPP1 HEXOSDP1 | ng l-1 | Unit conversion x1000 applied |
[Perid] | µg l-1 | Concentration of peridinin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | PERIHPP1 PERISDP1 | ng l-1 | Unit conversion x1000 applied |
[Zea] | µg l-1 | Concentration of zeaxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | ZEOXHPP1 ZEOXSDP1 | ng l-1 | Unit conversion x1000 applied |
[Chl a] | µg l-1 | Concentration of chlorophyll-a {chl-a} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CPHLHPP1 SDCLHPP1 | mg m-3 | n/a |
[DVChl a] | µg l-1 | Concentration of divinyl chlorophyll-a per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | DVCAHPP1 DVCASDP1 | ng l-1 | Unit conversion x1000 applied |
[Chlide a] | µg l-1 | Concentration of chlorophyllide-a {CAS 14897-06-4} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CIDAHPP1 CIDASDP1 | ng l-1 | Unit conversion x1000 applied |
[Chl b + DVChl b] | µg l-1 | Concentration of chlorophyll-b+divinyl chlorophyll-b per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CBDVHPP1 CBDVSDP1 | ng l-1 | Unit conversion x1000 applied |
[Chl c1] | µg l-1 | Concentration of chlorophyll-c1 {chl-c1 per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CHLC1HP1 CHLC1HSD | ng l-1 | Unit conversion x1000 applied |
[Chl c2] | µg l-1 | Concentration of chlorophyll-c2 {chl-c2} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CLC2HPP1 CLC2SDP1 | ng l-1 | Unit conversion x1000 applied |
[Chl c3] | µg l-1 | Concentration of chlorophyll-c3 {chl-c3} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CLC3HPP1 CLC3SDP1 | ng l-1 | Unit conversion x1000 applied |
[BE-car] | µg l-1 | Concentration of beta,epsilon-carotene {alpha-carotene CAS 432-70-2} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | BECAHPP1 BECASDP1 | ng l-1 | Unit conversion x1000 applied |
[BB-car] | µg l-1 | Concentration of beta,beta-carotene {beta-carotene CAS 7235-40-7} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | BBCAHPP1 BBCASDP1 | ng l-1 | Unit conversion x1000 applied |
[Lut] | µg l-1 | Concentration of lutein per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | LUTNHPP1 LUTNSDP1 | ng l-1 | Unit conversion x1000 applied |
[Neo] | µg l-1 | Concentration of neoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | NEOXHPP1 NEOXSDP1 | ng l-1 | Unit conversion x1000 applied |
[Viola] | µg l-1 | Concentration of violaxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | VILXHPP1 VILXSDP1 | ng l-1 | Unit conversion x1000 applied |
[Pras] | µg l-1 | Concentration of prasinoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | PRSXHPP1 PRSXSDP1 | ng l-1 | Unit conversion x1000 applied |
[Anth] | µg l-1 | Concentration of antheraxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | ANTHHPP1 ANTHSDP1 | ng l-1 | Unit conversion x1000 applied |
[Asta] | µg l-1 | Concentration of astaxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | ASTAXHP1 ASTAXHSD | ng l-1 | Unit conversion x1000 applied |
Data Quality Report
Quality assurance procedures for pigment analysis at PML were put in place for samples collected after 1st May 2011. Values of precision were given where replicate samples were available. The whole dataset conforms to the quality assurance criteria set out in Aiken et al. 1999 (DSRII 56, 899-917). The absent data value is given as 0.000 in the dataset. For pigment analysis, the absent data value is considered to be the effective limit of detection. The pigment profile of AMT23 surface samples frequently contained an unknown component with an absorption maximum at 418 nm, that coeluted with [Chl c3]. The unknown component was particularly abundant relative to [Chl c3] in surface samples from CTDs 2-23. The unknown component was not observed from CTDs 55-65. The unknown component, when present, affected the quantification of [Chl c3].
Problem Report
This section is not relevant to this data set.
References Cited
Zapata, M., Rodriguez, F., Garrido, J.L. 2000. Separation of chlorophylls and carotenoids from marine phytoplankton: a new HPLC method using a reversed phase C8 column and pyridine-containing mobile phases. Marine Ecology Progress Series, vol. 195: 29-45.
Project Information
PML National Capability
The Plymouth Marine Laboratory National Capability focuses on long term science concerned with basin/decadal variability of the Ocean.
Data Activity or Cruise Information
Data Activity
Start Date (yyyy-mm-dd) | 2013-10-15 |
End Date (yyyy-mm-dd) | 2013-10-15 |
Organization Undertaking Activity | National Oceanography Centre, Southampton |
Country of Organization | United Kingdom |
Originator's Data Activity Identifier | JR20131005_CTD_CTD017 |
Platform Category | lowered unmanned submersible |
No Document Information Held for the Series
Related Data Activity activities are detailed in Appendix 1
Cruise
Cruise Name | JR20131005 (AMT23, JR300) |
Departure Date | 2013-10-01 |
Arrival Date | 2013-11-11 |
Principal Scientist(s) | Mikhail V Zubkov (National Oceanography Centre, Southampton) |
Ship | RRS James Clark Ross |
Complete Cruise Metadata Report is available here
Fixed Station Information
No Fixed Station Information held for the Series
BODC Quality Control Flags
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
Flag | Description |
---|---|
Blank | Unqualified |
< | Below detection limit |
> | In excess of quoted value |
A | Taxonomic flag for affinis (aff.) |
B | Beginning of CTD Down/Up Cast |
C | Taxonomic flag for confer (cf.) |
D | Thermometric depth |
E | End of CTD Down/Up Cast |
G | Non-taxonomic biological characteristic uncertainty |
H | Extrapolated value |
I | Taxonomic flag for single species (sp.) |
K | Improbable value - unknown quality control source |
L | Improbable value - originator's quality control |
M | Improbable value - BODC quality control |
N | Null value |
O | Improbable value - user quality control |
P | Trace/calm |
Q | Indeterminate |
R | Replacement value |
S | Estimated value |
T | Interpolated value |
U | Uncalibrated |
W | Control value |
X | Excessive difference |
SeaDataNet Quality Control Flags
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
Flag | Description |
---|---|
0 | no quality control |
1 | good value |
2 | probably good value |
3 | probably bad value |
4 | bad value |
5 | changed value |
6 | value below detection |
7 | value in excess |
8 | interpolated value |
9 | missing value |
A | value phenomenon uncertain |
B | nominal value |
Q | value below limit of quantification |
Appendix 1: JR20131005_CTD_CTD017
Related series for this Data Activity are presented in the table below. Further information can be found by following the appropriate links.
If you are interested in these series, please be aware we offer a multiple file download service. Should your credentials be insufficient for automatic download, the service also offers a referral to our Enquiries Officer who may be able to negotiate access.
Series Identifier | Data Category | Start date/time | Start position | Cruise |
---|---|---|---|---|
2003632 | Water sample data | 2013-10-15 13:42:30 | 26.65489 N, 25.06299 W | RRS James Clark Ross JR20131005 (AMT23, JR300) |
2010500 | Water sample data | 2013-10-15 13:42:30 | 26.65489 N, 25.06299 W | RRS James Clark Ross JR20131005 (AMT23, JR300) |