Troubleshooting GC Syringe Issues – Part 2

In an earlier post titled Troubleshooting GC Syringe Issues, I discussed several things to try if sticking plungers are the problem.  In this post, I’ll discuss what to do if the syringe is not pulling up the sample properly (or at all).



So what can cause a syringe to have problems pulling up a sample?


The sample is too viscous.

If your sample is viscous, slow the plunger draw speed.  Many autosamplers have this functionality.

If this still doesn’t solve the issue, you may need to dilute your sample.


The syringe needle is plugged, or partially plugged.

Find out what is plugging your syringe needle.  Is it the sample or septa?

If it is particles in your sample, you may need to add a filtering step before injecting.  Sample Filtration

If you discover it is a piece of septum plugging your needle, try a different needle point style (Pt style #5 with side-hole are the least likely to plug).  Syringe Basics.

Pt Style 5




The plunger is not making a good seal with the syringe barrel.

How worn is the syringe?

Eventually the plunger to barrel sealing performance of syringes degrades as it gets older and worn-out.  This is especially true when using Gas-Tight syringes which have PTFE-tipped plungers.

Most syringe manufacturers recommend that you do not use a plunger from one syringe in another (unless using Gas-Tight syringes where plungers are usually interchangeable).


There is a leak between the needle and barrel.

If using a removable needle syringe, make sure the PTFE seal between the needle and barrel is installed properly and not worn out.

If using a fixed needle syringe, verify that the cement holding the needle to the barrel hasn’t degraded.


The autosampler is not working properly.

Watch the autosampler as it tries to inject the sample.  Is the autosampler programmed properly?  Does it actually penetrate the sample vial deep enough to withdraw an aliquot?  Does the autosampler actually lift the plunger?


Hopefully one of these suggestions will help you out the next time your syringe is not pulling up a sample.  Thanks for reading.

6 Responses to “Troubleshooting GC Syringe Issues – Part 2”

  1. Tom Kergil says:

    WE handle cryogenic fluids at dry ice temps with gas tight liquid syringes.
    The thermal expansion coefficient difference between Teflon and glass make this difficult.
    I think a plunger in needle syringe may be better or could be worse.
    What do you suggest?

    Tom Kergil

  2. Alan Sensue says:

    Hi Tom:

    First, thank you for reading my post. Second, what an interesting question. Because I have never tried using a syringe with cryogenic fluids, I visited the Hamilton website ( to attempt to find an answer for you. Unfortunately, it does not appear they sell any specific syringes for use with cryogenic fluids, and the instruction sheet I found for their Gas-Tight syringes specifically states “For best results, Gastight syringes are intended for use above 10 ºC (50 ºF).”

    For metal plunger syringes, I was only able to find references to using at room temperature and maximum temperature, but nothing concerning minimum temperatures.

    I also visited the SGE website (, and once again, I only found references to using syringes at room temperature and maximum temperature.

    In summary, I do not know the answer to your question. I suggest contacting the company who manufactured your syringe and ask if they have any data showing the minimum temperature which their syringe will perform adequately. I am sorry I was not able to help you with your request.

  3. Suppose the syringe is partially plugged, such that the injection of the test sample is not uni-directional as it exits the tip of the syringe (but more of spray). Would this affect the peak shape of the analytes?
    The instrument being used is an Agilent 6850, cool On-column Injection, constant pressure, isothermal elution at 55 C. The analytes being separated are acetone and ethanol in water. Our contractor for some reason does not stock, replacement syringes. The acetone elutes but just before it reaches baseline a second broad peak elute. The same for the ethanol peak. The method has worked flawlessly for months.

  4. Alan Sensue says:

    Hi Eric: Thank you for reading my post. If I had to guess, I do believe that “spraying” a sample into a column may affect peak shapes. What I can tell you is that many of our customers have issues when doing on-column water injections, which I discussed in my post (Capillary GC Column Killers – Part 4) So in all honesty, I am surprised you have been successfully doing this analysis problem-free for so long. If you can provide me the details of your syringe, I can check to see if we have a replacement syringe and/or needle which will work for you.

  5. Ziad Ali says:

    I have a problem in my syringe auto-sampler in my GC 6890 which is automatically clean the syringe multiple time with solvent like methanol and then goes to the sample and stop there not moving to inject my sample in the GC. I hope some one can help me because its very tough to do the injection manual since you have a lot of sample to be analyzed.

    Thank you.

  6. Alan Sensue says:

    Hello: My question to you is, why does it stop? Is it mechanical/electronic or something else (like a sticking plunger). If mechanical/electrical, I suggest contacting the instrument manufacturer for advice. You may need to return the unit to them for repair. Regards, Alan

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