Dissolved Gas Measurements by GC-FID

*This protocol is a work in progress. Please consult Julia Hart with any questions.*


This document describes how to collect and run CO2exetainer samples on “Louie,” the greenhouse gas-configured GC in the HEEL lab. Prior to fieldwork, exetainers must be flushed with helium to remove all, even trace amounts, of atmospheric O2; follow the protocol “Preparing Exetainers for the Field.” These samples are pre-acidified with 50% v/v H3PO4. Zinc chloride (ZnCl2) can be added to the Exetainers as a preservative ahead of time. Alternatively, it can be injected through the septa at the time sampling.


This protocol uses compressed gases. If you are unfamiliar about how to work with compressed gases, you must first take the Online Compressed Gas Safety Course. You will be using a mild, but concentrated phosphoric acid. You may also be using concentrated zinc chloride (ZnCl2), which is both acidic and corrosive.  Familiarize yourself with the MSDS for both of these chemicals before you begin.  We no longer use mercuric chloride (HgCl2).


In the Field

  • Collection bucket
  • 5-mL syringe
  • Needles
  • Prepared Exetainers
  • 1-mL syringe
  • Needles
  • Apiezon grease (M or N type)

In the Lab

  • 5-mL syringe
  • Needles


Exetainers should have been prepared according to the “Preparing Exetainers for the Field” protocol, with a single caveat. Exetainers intended for GHG sample collection may be pre-acidified with 50ml of 50% v/v H3PO4. Simply add the acid to the open exetainer just prior to entering the glove bag.


  1. Collect your water sample carefully so as not to unnecessarily disturb the water (which would introduce added CO2).
  2. Use a 5-mL syringe without a needle to smoothly draw up ~2mL of water.
  3. Attach the needle to the syringe.
  4. Depress syringe to allow excess sample water to stream out, bringing the syringe volume to the desired sample volume (2mL).
  5. Inject the sample (2mL) into the exetainer.
  6. Repeat steps 1-5 for each replicate.
  7. After collecting all replicates, apply a small amount of Apiezon grease to the top of the exetainer to cover the septum, preventing further gas exchange.
  8. Store samples in cardboard exetainer box in the fridge until analysis.
  9. Optional: Weigh samples before and after measurement on GC-FID for added precision. Be sure to weigh samples without grease added to the tops (to prevent gas exchange).


Before you begin running samples on the gas chromatograph, it is important to have a basic understanding of how this machine is configured.

This machine uses a dual direction systemto inject and analyze gas samples.  Samples are injected into a sample loop; you need to inject 2x the sample loop volume (a defined, known volume) into the machine. When initiated, N2carrier gas flushes a known volume (sample loop capacity) of sample from the sample loop into the column – towards the FID detector. Excess sample is vented through the FID vent before entering the column.

Once the sample has left the sample loop, it goes through two columns: 1) a column to catch water and hydrocarbons, and 2) the CO2detector column. CO2concentration is detected by an FID detector.

Partway through the sample run, the machine switches direction of the carrier gas – away from the FID detector. This allows you to pre-emptively load the next sample into the sample loop while waiting for the previous sample to complete its run time.


  • Remove samples from fridge and allow to come to room temperature. We can assume headspace equilibration in the time between sample collection and analysis.
  • Remove Apiezon grease from septa. Use a micro-spatula for higher efficiency in this endeavor. Then wipe top off with a Kim wipe.


  1. Create a new folder in the C: drive with your run date or other unique sequence identifier.
  2. Copy a Results file template into that folder from previously run sequences. You will be copying and pasting your sequence data into this spreadsheet periodically throughout your run.
  3. Open the software. You will see that you are not yet connected to the GC.
  4. Open the CO2-only.CON control file. This will initiate a connection between the computer and Louie. You should now be able to see the FID mV signal.
  5. Set the Default Data File Path. Click on Edit > Overall > Default Data File Path. Navigate to the run folder that you created in step #1.
  6. Reset the Increment. Click on Edit > Channels > Channel 2 > Post Run. Reset the increment to 0 at the top of the window. This will reset the enumeration of your sequence.
  7. Select your “method.” Click on Edit > Channels > Channel 2 > Component. Load the CO2 method file (or desired method file).
  8. Clear previously stored data (if any). Click on View > Results > Clear Results Log.
  9. Replace the (green) septa on the GC by unscrewing the end cap on the injector. Use forceps to remove the old septa and insert the new one. Replace the injector end cap.


  1. Inject your sample into the sample loop. Remember to inject at least 2x your sample loop volume.
  2. You need to have the software window highlighted on the computer (software window is the active window) to initiate the sample. Click on the window if the software is not currently your active window.
  3. With your sample loaded into the sample loop, press the space bar on the computer. This pushes your sample into the column and tells the machine to start the run time.
  4. Wait until you hear the machine click, indicating that the carrier gas has changed direction awayfrom the FID detector. Once this has happened, you are free to pre-load your next sample into the sample loop. It will remain there until you depress the space bar again.
  5. Continue steps 1-4 for all samples in your sequence.


  1. The software collates sample peak areas and retention times in a single table. You may view this table by clicking View > Results > Show Results Log.
  2. Periodically, you will need to copy and paste the Results log into your results Excel sheet.


After your samples have been run, they need to be disposed of as chemical waste. Exetainer caps may be thrown away; they are not reused. Collect all liquid waste in a hazardous waste container (label suggestion below). Exetainers should be cleaned according to the “Exetainer Cleaning” protocol.

Chemical Composition %
Water 99
H3PO4 <1

Download a printable version of this protocol.

Author: Julia Hart

Revision Date: 10 October 2018

Based on memory…