GC compound responses lower than expected? Maybe this will help.

We occasionally gets calls in tech service from a customer who has been experiencing lower than expected compound responses when analyzing a chemical standard.  In many cases we hear “It worked fine the last time we did it”.  So what could have happened since the last time you successfully did the analysis?  Several of the most common situations (and their potential fixes) are listed below.   The suggestions provided in this post assume you have successfully done this analysis previously, and only recently have experienced lower compound responses/sensitivity.

GC compounds – poor peak shapes and missing peaks

If this is a new analysis for your laboratory, you may need to review our more comprehensive troubleshooting guide (see pages 10-15).

 response_cgram (2)

A.   When only one or a few compounds throughout the chromatogram have a lower response.

 If the compounds are reactive (like many pesticides), system activity may be the cause.  You may find this previous post that I wrote helpful (see Case 3 of Why do only some of my peaks tail (GC)?)   Perform routine GC maintenance like trimming (or replacing) the column, replacing the injection port liner, and replace any other consumable which may contact the sample.   Confirm the chemical standard is OK by analyzing it on different instrument.  You may also want to try analyzing a new chemical standard which has a different lot#, or one from a different manufacturer.

Inject a higher concentration of the problem compound(s) to “prime” the instrument, but don’t forget to run a solvent blank afterward to make sure you do not have carryover.  If you suspect that your injection port may be the source of activity, replace your current inlet liner with a Uniliner® (just don’t forget that Uniliners® are designed to be used in the splitless mode).

Sometimes problematic compounds are listed in the analytical method, along with suggestions for improving their response.  If someone in your lab is familiar with the method, make sure you ask them for troubleshooting advice.

 If the problematic compounds are not reactive and activity isn’t the issue, you may be experiencing compound discrimination in your injection port or contamination somewhere in your system.  If doing split injections, try using splitless mode; but first, dilute the standard so that the on-column concentration is the same as when performing a split injection.  If already using splitless mode, try a different liner style, preferably one with a restriction at the bottom (like a gooseneck liner) to make sure the compounds are efficiently funneled into the column.  If no improvement is observed, the column may have contamination in it; try baking it for 30 minutes at its maximum isothermal temperature (just remember to trim the inlet side of the column first so you don’t drive any contamination deeper into the column).  Finally, make sure you have stored your column properly when it is not in use.  How should I store my GC column?


B.  If you notice that only the early eluting compounds have a lower response, then you should focus on the split ratio, instrument leaks, and/or any standard preparation/dilution which may cause loss of these compounds.

 Just like listed above, if using split mode, analyze the standard in splitless mode (remember to dilute the standard so that the on-column concentration is the same as when performing a split injection).   If response improves, then you need to optimize your split ratio or try a different style injection port liner.

Leaks at the injection port can also discriminate among the lower molecular weight compounds.  Use an electronic leak detector to sniff around the injection port, especially when the column connects to the injection port and around the injection port septa.  Why Leak Check Your GC System?

If analyzing volatile compounds (especially those which are gases at room temperature), make sure that the chemical standard is cold before you open it.  Work quickly to minimize heat transfer from your hands and from the surrounding room.  Only dilute the stock solution into a very cold solvent (never into a solvent which is at room temperature).  Some customers have told me that they even refrigerate their syringe or measuring glassware.  Store your standard solutions in vials which have very little, or no headspace.  Similar advice can be found here:




C.  If only later eluting compounds have a lower response, first review this post When High Boilers Disappear (GC).

If analyzing semi-volatile compounds, make sure that the chemical standard is at least at room temperature, and has been gently sonicated for at least five minutes.  If dilutions are needed of the stock standard, make sure the solvent is at least at room temperature (if cold, you risk higher boiling point compounds precipitating out of solution).

If using a liner packed with wool, check to verify that the position of the wool hasn’t changed.  You may want to review this post Where should the wool plug be positioned in my liner?


D.  When all compounds have a lower response.

If all the compounds have a low response, then instrument sensitivity may be the cause.  Start by trimming and reinstalling the column into both the injection port and detector.  Then, confirm all gas flows (especially for the detector) are at the recommend values.  Next, verify the analytical method hasn’t been accidently changed.  Finally, make sure the autosampler is working properly and the syringe needle is not plugged.  Analyze your standard on another instrument if possible.

In addition, try another lot # of standard, or even another manufacturer’s standard, on the same instrument, back-to-back runs.  If the standard had been diluted from a stock solution, prepare another running standard to confirm no dilution mistakes were made.

Finally, make sure the detector is functioning properly.  You may want to check the troubleshooting section of your instrument manual and/or contact your instrument manufacturer.

 Troubleshooting poster

GC Troubleshooting Tips Poster


Hopefully something here will help you the next time you notice lower compound responses when doing GC analysis.  If none of these suggestions solve your issue, we also have many other blog posts which contain useful information; take a few minutes to review the posts found in these two categories Troubleshooting and Optimizing Applications.  If your problem still persists, email us at support@restek.com.  Thanks for reading.


One Response to “GC compound responses lower than expected? Maybe this will help.”

  1. Matt Clark says:

    Excellent advice Alan,
    It’s also worth taking a second to make sure that the leak check has been done correctly – I’ve had at least one person assure me that they didn’t have a leak, as their 6890 was reporting a flow rate of 5mL / min, exactly what the method called for.

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