Water Isotope Analysis by CRDS


This document describes how to initiate a sequence of water samples for analysis of oxygen and hydrogen isotopes by cavity ring-down spectroscopy (CRDS).  Also included are instructions to clean the machine’s syringe and change the septum; both tasks should be done at the start of each run. The entire protocol takes place at the machine, located in OSB 446.

Please see separate protocols for more information about collecting water isotope samples in the field and preparing the samples for a run (e.g., loading vials and preparing standards).


The cleaning solution used to clean the syringe is 1-methyl-2-pyrrolidinone, which is toxic. Use nitrile gloves when cleaning the syringe.


  1. Syringe
  2. Septum
  3. Loaded sample vials


  1. Turn on the air tank in the closet to the right of the machine. It may be necessary to open the tank and the line.
  2. Allow air to run for ~1 hour prior to starting your sequence.
  3. Verify that air is flowing to the machine by checking the small, downstream regulator on the wall behind the Picarro. Flow should be 2.5 psi.


*Note: If you are using a brand new syringe, you should still go through the cleaning process.*

  1. Make sure the “CRDS Data Viewer” is open on the computer. If not, double click the icon on the desktop.
  2. Open the Autosampler GUI by double-clicking that “Autosampler Control” icon on the desktop.
  3. Click the “Chg Syringe” button at the top. The autosampler will now move the syringe to a position where the syringe may be removed.
  4. Remove the syringe. There are two “gates” holding the syringe in place: 1) in front of the main barrel of the syringe, 2) positioned over the plunger head.
  5. Manually insert the syringe into the cleaning solution (1-methyl-2-pyrrolidinone) vial (usually located on shelf just above machine) and move the syringe plunger up and down 5-6 times. Work slowly to allow time for the cleaning solution to make its way all the way to the top of the syringe. DO NOT remove the syringe from the cleaning solution while doing this! Only pull the solution up, and flush it back in to the cleaning solution reservoir.
  6. Manually insert the syringe into the Milli-Q water vial (located to the left of the sample tray). Draw up 8 uL, remove syringe from vial, and carefully inject waste into waste vial, located directly adjacent to Milli-Q reservoir. Repeat 5 times.
  7. Replace syringe in autosampler and make sure that both the barrel gate and the plunger head gate are closed. Volume markings on the barrel should be facing outwards, towards the user. Click the “Swap Done” button in the Autosampler GUI to send the autosampler back to its ready position.


  1. In the Autosampler GUI window, choose the injection method suitable for the salinity of your samples. Ensure that your desired method has a check mark next to it on the left-hand side of the window.
  2. Next to your desired injection method, designate the number of samples in your sequence by setting the “End” number.
  3. Next to your desired injection method, designate the number of injections per sample by setting the “#Inj” number.
  4. Load your sample vials into the autosampler tray. This is “Tray 1” and the only tray that we have. It may be necessary to flick or tap your samples to make sure that there are no air bubbles trapped at the bottom of your vials. 


  1. Open the “Coordinator Launcher” by double-clicking the icon on the desktop.
  2. Select “High Precision” from the drop-down menu. This is different from “MPM High Precision”; do NOT select this one.
  3. Click “Launch.”
  4. The machine will perform self-cleaning procedures, ~3 minutes. Wait until it has finished, as indicated by the message “Waiting for injected sample…”
  5. When self-cleaning has finished, return to the Autosampler GUI window.
  6. Click “Run.”
  7. Watch and wait for your first sample to be injected into the vaporizer unit.


  1. After you first sample has been injected into the vaporizer unit, return to the “Coordinator Launcher” window.
  2. Click “Change Septum” in the upper right-hand corner at any time. The machine will tell you to wait until it has finished analyzing the first sample injected.
  3. While you are waiting to change the septum, your first injected sample should reach the analyzer. In the “CRDS Data Viewer” window, [H2O] ppm should reach between 19,000-21,000 ppm if the machine is functioning properly.
  4. When the machine says “Ready to Change Septum” in the “Coordinator Launcher” window, you may proceed.
  5. Remove padded metal cover from injector.
  6. Using a wrench or other appropriate tool if necessary, unscrew the injector nut. CAUTION: The metal will be hot. Handle by the plastic top.
  7. Use forceps to remove old septum. The septum is held inside the injector nut, which you just unscrewed.
  8. Use forceps to place new septum in its place inside the injector nut. Orientation does not matter with these septa.
  9. Replace injector nut by screwing until hand-tight.
  1. Replace padded metal cover.
  2. Click “Septum Changed” in the “Coordinator Launcher” window. Your sequence will resume.
  3. Open the “CRDS Data Viewer” window (it’s always open when the instrument is on, but may be minimized) to verify that the instrument is collecting data.
  4. Completed analyses will show up with one line for each injection in the upper box of the CRDS Coordinator window. This window is updated following each injection.


  1. When your entire sequence is finished, close the CRDS Coordinator window. The instrument will continue to wait for an injection is this window remains open, even though the sequence is finished.
  2. Open the “Shortcut to IsotopeData” folder on the desktop. Copy your datafile to a flash drive (inserted into the USB port on the front of the instrument), or email the data file to yourself through a web browser.Please do not delete any data files from this computer, even your own data! A complete data record for the instrument is essential for diagnosing problems that will inevitably show up in the future.
  3. Remove your vials from the tray!


  1. Throw used vial caps in the trash. We do not reuse these.
  2. Empty vials by flicking contents into a trash can (water only).
  3. Collect used vials in a beaker or other glass container.
  4. Place vials in drying oven at 60 C for 2 hours to dry completely before reusing.


Septa:Septa Thermolite Plus, 9.5mm (3/8”), 50/pk, Restek, Item No: 23877.

Syringe: 10uL SGE Syringe 6-pack, P/N 002972, SK-10F-C/T-GT-5/0.63C, Trajan SciMed.

Download a printable version of this protocol.

Author: Julia Hart

Revision Date: 5 December 2018