Metadata Report for BODC Series Reference Number 2005104

• 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

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.

AMT24 (JR20140922) pigment composition by HPLC analysis from CTD bottles

Originator's Protocol for Data Acquisition and Analysis

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

Data were submitted to BODC in Microsoft Excel spreadsheet format and saved to the archive with reference PML160094. 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.

The data were reformatted and marked up with BODC parameter codes. The data were provided in µg/L units that were converted to ng/L for all parameters but chlorophyll-a. Data were loaded into BODC's samples database under Oracle Relational Database Management System using established BODC data banking procedures.

The originator variables were mapped to appropriate BODC parameter codes as follows:

Data Quality Report

Quality assurance procedures for pigment analysis at PML were put in place for samples collected after 1st May 2011. The whole dataset conforms to the quality assurance criteria set out in Aiken et al. (2009). 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 AMT24 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 8, 10, 19, 34, and 50. The unknown component was not observed from CTDs 32, 48, and 54-68. The unknown component, when present, affected the quantification of [Chl c3], and where this is relevant the data have been flagged using BODC flag 'L'.

Data were also flagged by BODC where they were at or below the Effective LOD as '<'.

Information on the bottle numbers the water samples were taken from was not available so BODC chose the final bottle to be sampled on the CTD Rosette to assign the data to based on water depth and correspondence with the data originator.

References

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, 195, 29-45.

Aiken et al., (2009) Phytoplankton pigments and functional types in the Atlantic Ocean: A decadal assessment, 1995-2005. Deep Sea Research II: Topical Studies in Oceanography, 56, 899-917.

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

BODC Sample Metadata Report for JR20140922_CTD_CTDS066

Please note:the supplied parameters may not have been sampled from all the bottle firings described in the table above. Cross-match the Sample Reference Number above against the SAMPRFNM value in the data file to identify the relevant metadata.

Related Data Activity activities are detailed in Appendix 1

Cruise

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:

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Appendix 1: JR20140922_CTD_CTDS066

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.