Measuring pCO₂ in water

Once you've completed the initial configuration (see Preparing for measurements), you can configure the measurement sequence. Click Exp. Config to view the options for measuring the CO₂ concentration of gas standards, atmospheric air, and seawater.

Configuring the measurement sequence

To configure the measurement sequence:

1. Enter PROJECT INFO, including the Project, Operator, and a Memo.

   These details are saved with each data file. Project and Memo are recorded at the start of a new data file, which can be at the start of the automatic measurement sequence and after 1000 rows of data. Operator is recorded on each data row.

2. Enter CO₂ Standard Values, which are the CO₂ concentrations of the standard gases.

   Up to five CO₂ standard gases are allowed. Port 3 refers to Standard 1, Port 4 refers to Standard 2, and so on. Enter values from the tank for each port that is connected to a gas standard. Leave ports blank if there is no gas connected; the software will skip ports that are left blank. Click Set to apply the settings.

3. Under Chlorophyll Setting, set the Fluorescence Gain of the chlorophyll sensor.

   Choose the gain setting most appropriate for the chlorophyll in the sample. See Setting the gain for details.

4. Configure the EXPERIMENTAL SETTINGS.

   When settings are changed, the frame turns blue to indicate unsaved changes. Click SET in the corresponding box to save the changes. Click Reset (at the bottom right corner of the box) to discard changes and revert to the last saved values.

   

   1. Measurement Cycle Settings are the number of events and repeats.

      • Air Measurements: Enter the number of air samples to be measured.
      • Seawater Measurements: Enter the number of seawater samples to be measured.
      • Air-Seawater Repeats: The number of times to repeat the air and seawater measurements before measuring the next group of standards.
      • Cycle Repeats: The default setting is to measure the sequence continuously until you click Stop Sample. Click Continuous to change the setting to a number. The program will stop the measurements after 10 cycles (or whatever is entered in Cycle Repeats).

      For every single analysis, the default setting is 60 seconds for air, water, and the standard. This setting determines the frequency of measurements. You can adjust it to a larger or smaller value to change the recording frequency.

      In the open ocean, since the seawater pCO₂ is relatively stable, you can take relatively more measurements of air. However, in coastal waters, where pCO₂ changes very rapidly, you may need to take more measurements of water.

   2. Purge and Measurement Interval Settings specify the duration of wait times and purge times between measurements.

      The New Source Purging time allows the system to thoroughly flush tubing after switching from one air source to another. The default is 240 seconds (180 seconds minimum recommended). You can set it to a larger value if necessary - and you may need to if you change the flow rate.

   3. Flow Rate Setting is the air flow rate through the pCO₂ system (not including the gas analyzer subsample loop).

      If you reduce the flow rate, you should increase the purge times to ensure that tubing is completely purged between measurements.

   4. Standard Passing Criteria establishes the number of times to repeat a reading and the standard deviation for passing.

      If the computed standard deviation is greater than the entered value, it continues measuring standards as a running average including the most recent measurements until achieving the passing criteria or until the maximum number of repeats, at which point it will stop. If the instrument stops without passing, you might need to do some troubleshooting.

5. Start the measurement sequence.

   Once all values are set, click Start Sample to start the measurement sequence. Three alarm graphics, Overflow, Cooling and Water Flow, are to the left of the status fields.

   • Overflow is triggered when the water level is high for 4 seconds continuously.
   • Cooling is triggered when the temperature in the cooler is below 0 °C or above 10 °C.
   • Water flow is triggered if the water flow rate drops to below 1 L/min.

   Red indicates an alarm is triggered. Green indicates OK.

6. Stop the measurement sequence.

   Click Stop Sample to stop the measurement.

   The LI-5405A will finish the current reading and stop the sequence. Then a message prompts you to either run a set of standards or stop all measurements. If there is no response for 2 minutes, it will proceed with a set of standards.

7. If you're done taking measurements, follow the shutdown procedure (see After measurements).

8. Finish data processing.

   To compute final results, follow the steps in .

After measurements

Before powering off the components, run DI water through the system to completely flush seawater. Typically, this takes a few minutes. Wipe away any water spilled on the base plate of the system.

Drain and rinse the system

Drain the tube for the chlorophyll and dissolved oxygen sensor. The tube is connected to the drain valve on one end; the other end is the drain. Direct the opening of the tube to a waste water container and then open the valve to release the water.

Powering off

Power of the pCO₂ module and gas analyzer. Keep the power cable disconnected during storage. If you are storing or shipping the gas analyzer, be sure to read the relevant details in the gas analyzer instruction manual.

Final data processing

After recording raw data, you'll have all of the information required to compute final results. One post-processing step is completed and reported in the data file (see Computing corrected CO2 from measured CO2). Two additional steps are required for the final results (see Convert xCO2 to 100% humidity pCO2 and Normalize measured pCO2 to in-situ surface seawater temperature).

Computing corrected CO₂ from measured CO₂

The values in the column Compensated CO₂ (ppm) are corrected following the procedure below.

The measured xCO₂ (mole fraction CO₂ concentration of seawater, atmosphere, or standard in the dried sample gas flow in ppm) needs to be corrected based on the measured values of the standards. It is recommended that the concentration range of the standard gases covers the range of the measured pCO₂ values to generate accurate corrections.

Equation 4‑1 shows how to correct the measured xCO₂ to accurate values using the measured standard values (R1, R2, R3, etc) and the standard values (S1, S2, S3, etc.):

4‑1

where the Corrected xCO₂ means the value after correction, Raw stands for raw data measured by the CO₂ analyzers, S is the true CO₂ value of the standard gas, and R is the measured CO₂ value of the standard gas by CO₂ analyzers.

For instance, three standards and two different sample gases are measured, with the results listed in Table 4‑1.

Table 4‑1. Standards and sample gases.

Source	Standard xCO2	CO2 reading	Calibrated Sample CO2
Standard 1	S1 = 200	R1 = 202.1
Standard 2	S2 = 360	R2 = 362.0
Standard 3	S3 = 550	R3 = 551.3
Equilibrator		Raw 1 = 350.7	(348.7)
Air		Raw 2 = 386.4	(384.5)

For the sample gases measured from the equilibrator (CO₂ = 350.7 ppm), the value is between the first and the second standards. Substituting values from Table 4‑1 into equation 4‑1 gives:

4‑2

The final result is 348.7 ppm.

For the air sample gas (CO₂ = 386.4 ppm), the value is between the second (S2) and third (S3) standard values. Use these two standards for the correction.

4‑3

The final result is 384.5 ppm.

Convert xCO₂ to 100% humidity pCO₂

The partial pressure of CO₂ in seawater at the temperature of equilibration (inside the equilibrator), pCO₂ eq) in μatm, is calculated as:

4‑4pCO₂(eq) = xCO₂(water) × [P_b(eq) – P_w(eq)]

where xCO₂ (water) is the mole fraction concentration of seawater CO₂ in the dried sample gas flow read by the gas analyzer (after correction) in ppm; P_b (eq) is the barometric pressure at equilibration in atm; and P_w (eq) is the water vapor pressure at equilibration in atm that is calculated using salinity and temperature of equilibration, which is assumed to be equal to the salinity and temperature measured by the SBE 45. While there is a thermometer installed inside the equilibrator, it is not as accurately calibrated as that of the SBE 45.

Atmospheric xCO₂ should be measured once every 2 to 4 hours.

The partial pressure of CO₂ in the air, pCO₂ (air) in μatm, is then calculated as:

4‑5pCO₂(air) = xCO₂(air) × [P_b(sea surface) – P_w(sea surface)]

where xCO₂(air) is the mole fraction concentration of the atmospheric CO₂ in the dried sample gas flow in ppm, P_b (sea surface) is the barometric pressure at the sea surface in atm, and P_w(sea surface) is the water vapor pressure at sea surface in atm calculated from the temperature and salinity measured at the ship’s water intake. In a small vessel, data from the SBE 45 can be used instead.

Normalize measured pCO₂ to in-situ surface seawater temperature

The partial pressure of CO₂ in seawater at the in-situ temperature can be calculated as (Takahashi et al., 2002):

4‑6pCO₂(water) = pCO₂(eq) × exp[0.0423 × (SST - T_eq)]

where SST is the in-situ Sea Surface Temperature measured at the ship’s water intake point in °C and T_eq is the temperature at equilibration in °C. In a small vessel, data from the SBE 45 data can be used instead.