Troubleshooting GC Syringe Issues

I think we all have experienced various syringe issues at one time or another, and of course, problems seem to occur at the worst times. Hopefully this post will help you quickly correct two of the most common issues we get asked about in tech service.

Probably the #1 issue is coring of septa. That problem was covered in a post which I wrote in September (link below).

Troubleshooting Injection Port Septa


The #2 issue is a sticking plunger. This occurs when the sample/solvent dries from inside the syringe and leaves behind sticky residue, which basically “glues” the plunger to the barrel. To fully understand why this happens, think about how a syringe works. For liquid syringes with a bare metal plunger and glass barrel, the liquid works its way between the plunger and the barrel to create a seal. Once the syringe is properly wetted and the seal is formed, it allows the plunger to pull up the liquid sample. Even though the syringe is usually rinsed with clean solvent after a sample injection, if the sample contains “sticky” material, not all of it may get rinsed out. If this happens, and the liquid dries, the remaining residue may bind the plunger to the barrel.

So the obvious question is, how can this issue be prevented? Below are a few suggestions.

1. Try using a Gas-Tight® syringe, which contains a PTFE tip on the bottom of the metal plunger. Unlike a bare-metal plunger, the seal is formed by the tight contact of the PTFE and the syringe barrel. As a result, the sample/solvent is not able to get between the metal plunger and the barrel, so rinsing the syringe after a sample injection seldom leaves behind any residue. However, if you allow the plunger dry while inside the syringe barrel, it may become difficult to remove, and sometimes the PTFE tip will dislocate from the metal plunger and become stuck in the syringe barrel. To prevent this, remove the plunger from the barrel while the PTFE tip is still wet and store the plunger separately from the syringe barrel (if possible).

Please note that PTFE-tipped plungers rarely last as long as bare metal plungers, so replacing every liquid syringe with a Gas-Tight® one may not be economical for your lab.

2.   Substitute a different rinse solvent; one with a higher boiling point. As I mentioned, when the liquid dries inside the syringe, sticky residue may “glue” the plunger to the syringe barrel. Instead of rinsing the syringe with just the same solvent as your sample, use a higher boiling-point solvent for the final rinse (one which will not evaporate out of the syringe between sample injections). For example, let’s say your samples are in methylene chloride (approx boiling point 40°C), and you notice your plunger is drying out between analyses. As your final syringe rinse, try using toluene (approx boiling point 110°C). Just remember to rinse the toluene out of the syringe before injecting your next sample. If your autosampler has two rinse vials, this can easily be done.

3.   If you do end up with a stuck syringe plunger, Hamilton has a few suggestions to try (I pasted this information directly below). However, just in case you are not successful in freeing the plunger, you may want to keep a few extra spare syringes available.

The plunger in my syringe is stuck. What can I do to free it up?

Frozen plungers are caused by improper care of your syringe. Here are a couple of suggestions to save your syringe: Soak the syringe in alcohol, acetone or warm water. Do not soak them for longer than 5 minutes. Sonic cleaners can sometimes help to free up the plunger. If the plunger does not start to move after this, you will need to replace the syringe. Proper cleaning will help prevent frozen plungers. Especially when the syringes are being used for life science applications, where sugary or protein based sample are required. We recommend using a like solvent to dissolves the sample. Rinse the syringe thoroughly and then remove the plunger and allow the syringe and plunger to air dry separately. MICROLITER Syringe Plunger Types Standard Microliter Plunger Stainless steel with a stainless steel button staked to the plunger rod. This type plunger is individually fitted to the syringe barrel. Interchanging plungers between syringes will permanently damage syringes.


Hopefully you have found this information helpful.  If so, you may also want to review Troubleshooting GC Syringe Issues – Part 2.


If interested in learning a little more about syringes, please see the links below. If you have any questions, give us a call.

Syringe Basics

7 Responses to “Troubleshooting GC Syringe Issues”

  1. Andrew says:

    Thanks for your post. I have been dealing with sticking plungers even though I am only using ultrapure water in the syringe barrel. Is there any explanation for why this might occur when no “sticky” material is expect?
    Appreciate any thoughts/tips. Thanks!

  2. Alan Sensue says:

    Hi Andrew. Thanks for reading my post. You may want to send your question to SGE or Hamilton for their explanation, but if I had to guess, there must be something in the water that is left when it dries, perhaps clear crystals of salt, or something similar. Or, could the plunger be developing small rust spots? This is assuming that the plunger is entirely made of metal, and not one which contains a PTFE tip. If it does have a PTFE tip, it is more difficult to move when dry, but most do not refer to this as “sticking”; it is simply a function of a tighter fit.

    My suggestion, if you are using a metal-only plunger syringe and you continue to have these issues, I suggest filling-up a very clean, clear drinking glass or beaker or jar/bottle with the water and letting it evaporate (or at least some of it). Do you see anything left sticking to the clear glass? Also check the plunger using a magnifying glass for any rust or pitting.

    I hope this helps.


  3. D.vijaykumarsarma says:

    My problem is having extra peaks found in one sample run in sequence. Same are not found in repeated analysis. Why it happen?

  4. Alan Sensue says:

    Hello. Thank you for reading my post. Unfortunately, I am not able to provide you an answer based upon the limited information you provided. My advice, read the following post (link below) and if you still have this issue, contact Support ( with additional information. Thank you. Regards, Alan

  5. sandeep says:

    I am using HP9793 auto sampler with HP 5890 series II GC, I never had issues for a year using the auto-injector (non-viscous samples), but recently when I am using it to inject propylene glycol which is viscous compound, there are issues with precision for replicate injections, the areas would differ by 1000’s. what might be the solution for this issue. As I look in to it precisely I see the sample not being picked up to the level given from second injection. It forms air bubbles.

    Do I have to replace the syringe?
    Are there any syringes that are suitable for viscous compounds?

  6. Alan Sensue says:

    Hello: Unfortunately, you did not provide a catalog number for the syringe you are using. As I mentioned in my post, make sure it is a PTFE plunger-tipped Gas-Tight syringe. If it is, I would replace the syringe which is not performing properly because the PTFE-tip may be worn out and not making a good seal. Keep in mind that Gas-Tight syringes usually have shorter lifetimes than liquid-only syringes.

    In addition, for improved reproducibility when analyzing glycols, I suggest the following:

    1) Do not inject water-only samples. Always dilute water samples with an equal amount of methanol so that the sample/standard you inject consists of 50% water/50% methanol.

    2) Never inject splitless or direct mode, only inject split, and never more than 1µL. When using 0.32mmID capillary columns and smaller, injections should be split 10:1. If using a 0.53mmID column, injections should be split 4:1.

    3) Use the proper split liner. Make sure it has an open bottom. You may wish to review this post I wrote.

    I hope something here helps. If you continue to have issues, you may want to contact the syringe manufacturer for additional troubleshooting assistance. Regards, Alan

  7. Moh says:


    I suggest you change the speed of plunger when it is going to pull up the sample to the slowest rate and also put viscosity delay on 7 (Max) , Another thing you may need to do is to adjust your split ratio to let the sample goes to the column as less as possible, I recommend 1: 100,

    Another tip is to add a solvent (Methanol/IPA ) to your sample to make it less viscose and eliminate the solvent peak during the processing .

    The best syringe is 10µL type and inject just 1µL. make sure you rinse the syringe before and after each run to avoid the carry over issues.

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