Standard Operating Procedures

Ion Chromatography


This document describes loading and running samples through Yertle, a Dionex Ion Chromatography system. This version was most recently modified by Qianjie Chen and has had many previous contributors (Lei Geng, Ben Johnson, Eric Sofen, Joesph Erbland, Shelly Kunasek). Samples are loaded onto a guard column. Then, sample anions are separated in an analytical column, the fractions of sulfate and/or nitrate are automatically collected in one or more test tubes in a sample fraction collector. 



Listed in order from sample input to sample collection 

  1. Loading line (clear tubing attached to screw-cap right of Yertle)
  2. Loading pump (black box with loading line going in and green line coming out)
  3. Guard Column (small, black cylinder on yertle, connected to Injection Valve)
  4. Analytical Column (long, black cylinder contained within glass coveringm right of guard column)
  5. Fraction Collector (aka Foxy, with red valve) 

Keyboard Shortcuts


Starting up Yertle 

Fill both eluent bottle (front bottle on top of Yertle) and H2O regenerant bottle (the large bottle in the right side of yertle) with fresh water. Full bottles should easily last for a full day of running, but keep an eye on them to make sure. Make sure lids are on flush and snug.  

Attach gas tubing at H2O regenerant bottle (small hose connection), and turn on N2 tank (green tank by the window) by turning the top gray knob ~1/2 turn. Check pressure levels. On the N2 tank, the left hand gauge should be at ~90 psi marked by a blue line.  The right hand gauge indicates the amount of N2 in the tank. If pressure drops below 100 psi a new tank is needed. There are two pressure gauges on Yertle. The eluent gauge should read 3 psi and the H2O gauge should read 12 psi (the new suppressor requires a pressure of 10 to 15 psi to maintain the flow). Keep an eye on these during the day, and adjust with knobs on gauges if needed. 

Turn on Yertle with black switch on the back right hand side of the machine.  

Software startup 

From start menu on Yertle computer (Dell on desk), start Chromeleon software. In the top toolbar, click on “Default Panel Tabset” (5th icon from the right). Choose My Computer and Chromeleon Server.

Maximize new window. In the ICS-2000 System box, click “Connected”, then click “Startup”. The eluent generation and pump will start automatically. EG cartridge should read 10.00 mM (can be adjusted) and Suppressor should read 25 mA. Adjust the current of suppressor according to the following equation:  

where A is the current (in mA), R is flow rate (ml/min), and C is eluent concentration in mM. 

Immediately switch ICS-2000 Injector to “Inject” position by clicking “Inject”. The Label will say “InjectPosition” and turn green.  

Monitor system parameters by clicking the blue circle icon in the top control line. Select “Channel_Pressure” and “ECD_1” and click OK. Right click in the blue signal screen, select signals, click on Channel_Pressure, click ADD>>, and then OK. This will display the signal of what is being washed off the column (ECD_1 in yellow) and the pressure in the column (Channel_Pressure in red). Monitor pressure, if it levels off at around 1700-2100 psi, let the system run in this setup for about an hour. You will see 1-3 peaks in the yellow signal as the column is flushed. If the pressure does not level off or rises in spurts, you need to prime the pump (see below). It is recommended to prime the pump every day when the IC is turned on. 

Priming pump

If the pressure does not level off between 1700-2100 psi, you will need to prime the system pump. First click “Shutdown”. All eluent generation and suppressor activity will stop. 

In the ICS-2000 Pump box (upper left corner), click on “Pump Settings…”, then click “Prime”. A window will pop up and ask you to open the waste valve. When facing the IC, there are two black pumps with knobs in the lower portion of the machine. The waste valve is the left one. Open this valve ~1 full turn (max), then click OK. 

Let the pump prime for 10 minutes. After 10 minutes, you will want to simultaneously click “Off” with your left hand and close the waste valve with your right hand. DO NOT OVERTIGHTEN THE WASTE VALVE! This will cause pressure to be too high and the system will shut down. Immediately close the pump settings window and click “Startup”. 

Monitor pressure again and make sure it levels off. If pressure is too high, you can loosen the waste valve A LITTLE BIT; if pressure is too low, you can tighten waste valve A LITTLE BIT. Small movements on this valve make a big difference, so be careful and only touch it if the signal is out of whack. 

As described above, let the system flush for about an hour. 

Additional flushing

During the last 10-20 minutes of the column flush, you can also flush the Sample collection valve.  

For the sample collection valve, Switch to the Foxy Jr Panel (Crtl-Tab). If the Foxy panel is not open, click in it (FOXYJR.pan) in the program panel (top right) in the Browser Window.  

In the Foxy Panel, click the box next to “Valve”. You will hear a click from the red valve on the fraction arm, and see liquid and perhaps some gas bubbles moving through the line as water moves to waste. 

Flush both for 10-20 minutes, and make sure to UNCLICK the Foxy panel Valve box. In a run, the program will open this valve when a peak is determined and the fraction will be collected. 

Measuring Samples

Making a Sequence

First, you will need to create a sequence. Toggle to the white Browser screen. In the left hand panel, make sure you are in the folder YERTLETHETURTLE_1. You can create a new folder either with your name or project name if one does not exist.  

There is a template for a sample sequence named YYMMDD_SAMPLERUN_TEMPLATE. Open this, then Save As in the file menu, and rename it with the date in the format shown and your run name. Make sure to save it in the appropriate folder. 

Each sequence should start and end with a WaterBlank (described later) using the Program noCollect-SulfateTest and an Injection volume of 3.0 mL. Samples are named as you wish, with the volume you inject, and the Program named XXX (will fill this in after resin testing is done). Fill this template out and make sure to save it. You will be able to edit this sequence throughout the day as needed. 

Alternatively, one can always copy and paste a previous sequence from other's directory to his/her own directory. Running program and quantify method will be copied and pasted together with the sequence. In this case, one doesn't need to make his/her own method and program files. 

Loading Samples

This procedure is the same for WaterBlanks and samples. WaterBlanks are run at the beginning and end of each run to make sure there is no contamination in the system. Make sure to load and run a WaterBlank first. 

Note that the maximum sample size that can be run through yertle is 45µeq mol (the capacity of the guard column) . If your sample is larger than this, split into multiple fractions. Note, it is the total amount of anions (e.g., including Cl-, NO3- and SO42-), not only your targeted anion, that should be less than 45 µeq mol. 

First, make sure the load line is clear. Place the loading tube (on right hand side of machine attached to blue cap) in a vial of fresh water. Open command window (F8), click Pump_ECD, LoadingPump, Closed, and Execute. You will hear the loading pump turn on. Let 1 mL pump through. The graduated cylinder on the metal shelves to the right of the computer measures the amount of water being put into the system. Once 1 mL has gone through, click Open and Execute. The line is clear of previous samples. 

Now fill the load line with sample. Put the load tube in your sample vial. Again, start the loading pump as described above. When 1mL has gone through, shut off loading pump.

Now load sample onto the loading/guard column. Switch the ICS-2000 Injector from “Inject” mode to “Load” mode. The panel will turn yellow. Make sure the graduated cylinder has enough volume for the sample to pass through. Start loading pump and load your sample. To ensure loading all of the sample, right as the last of your sample is being pumped up, add >1 mL of water into the sample vial with a squeeze bottle, and pump through an additional 1 mL. This will push any remaining sample in the load line onto the loading column. Be careful to not allow air to be sucked up into the line.

If you are loading a sample/standard for which you only want to load a certain volume, make sure to monitor the graduated cylinder and stop when the target volume is reached.

Repeat this loading procedure for each sample.

Testing the retention time of each targeted anions

In order to collect the fractions of sulfate and/or nitrate, you will need to identify the peaks determined by the IC. Different anions have different retention times, but which have to be determined first (the column introduction shows a sample chromatograph with anion peaks and their respective retention times, but due to system set up and the aging of a column, the real outcome in your run could be very different from the introduction). The recommended procedure of testing the sulfate and/or nitrate peaks are as follows: 

  1. load a very small aliquot (~1 ml, varying with the sample concentrations) of a sample, and run through the IC. Several peaks will be determined, including nitrate and sulfate. 
  2. load the same aliquot of the same sample, and then load ~ x ml of standard solution (the standard solution is a solution with NO3- and SO42- concentrations of 1 mM). The value of x will vary with the absolute amount of nitrate and sulfate in the sample aliquot. The nitrate and sulfate peaks will be easily identified by comparing the chromatograph with that from step 1. 

Note, technically, one can just run the standard solution (with known concentrations of Cl-, NO3-, and SO4-) to determine the retention times of nitrate and sulfate and according those to identify sulfate and nitrate peaks/fractions in a real sample. However, for samples other than polar snow/ice, the sample matrix contains a large amount of other ions in addition to Cl-, NO3- and SO42-, the interference between these ions will cause the retention times of nitrate and sulfate in real samples different from those determined using standard solutions.   

Running samples / blanks

Make sure your sequence is saved. Toggle to the Panel tab screen. Make sure manual acquisition is off (click blue circle again). On the upper menu bar, pull down the menu for “Batch” and click on “Start”. Under “Batch List”, remove any old sequences and Add the sequence file you created. 

Click “Ready Check”. This makes sure everything is ok and ready to run. A two line message will indicate if everything is prepared. 

Click “Start”. The Injector will switch to “Inject” (green), and a chromatogram will start. Runs last 15 minutes for a WaterBlank and XXX for samples. 

After  the run starts, pull down the Batch menu again and click “Stop”.  Select “After Current Sample” and click ok. This will tell the machine to stop after the current sample, since we do not have an autosampler set up. 

Fraction collector notes

Place pre-cleaned plastic test tubes in the plate of the fraction collector. Sample collection valve will be turned on once a peak is determined, and the fraction of that peak will be collected. You can also manually turn on/off the valve to collect only a targeted fraction, or set up the program to open the valve at the time when a targeted peak appears.  

WaterBlank Notes

Make sure the WaterBlank is acceptable before proceeding with samples. A good blank will have no peaks larger in amplitude than 2-5µS. If there is a peak larger than this, it means contaminants exist in the system. Usually running two or three blanks is enough to bring the peak amplitudes down to acceptable levels. If not, let the system flush in Inject mode for another 15 minutes before trying again. 

Additional Samples

Follow this same procedure for additional samples. Make sure to flush the load line in between different samples (i.e. not aliquots of the same sample). Run another WaterBlank at the end of the day.


To shut down at the end of the day, first clear the load line as previously described. In the ICS-2000 System panel, click “Shutdown” then unclick “Connected”. Close the N2 tank (top gray knob), and release the pressure in the system by disconnected the line by the H2O Regenerant bottle. Turn the machine off at the back.