Troubleshooting Injection Port Septa

Gas Chromatograph (GC) injection port septa are a critical item in your GC system, but many of the associated problems are often misunderstood. This article will focus on different injection port septa, potential problems, and common fixes.


Probably the number one problem with GC injection port septa is coring, which is when a hole is produced in the septum when it is punctured by a syringe needle. In addition to causing poor chromatography, or loss of sample from the injection port, coring can cause unwanted and unknown (ghost) peaks in the chromatogram. When septa are cored, small septum particles are introduced into the injection port, where the volatile components vaporize and are chromatographed by the GC system. Many analysts believe that these “ghost” peaks are caused by a capillary column because the mass spectral library identifies these peaks as siloxanes (a common capillary column polymer phase). It is important to note that a GC column will not chromatograph itself (it will only produce baseline), and these peaks may be caused by injection port septa, autosampler vial septa (when they contain silicone), or the deactivation layer on an injection port liner (when the layer has become damaged).


To correct issues with coring, the following should be considered:

1. Old septa will become dry and brittle over time as they lose their volatile components. To maximize the useful lifetime of septa, always keep them away from heat and in their sealed container.

2. Smaller OD (outside diameter) syringe needles (26g) will typically core a septum much less than a larger OD needle (22g).

3. Over-tightening the septum nut will increase the risk of coring septa.

4. Softer, more pliable septa are less likely to core than firmer septa (such as BTO®). Please remember, however, that softer septa usually have a lower maximum operating temperature than firmer septa, so use caution if you decide to switch brands.

5. Point-style #2 (beveled needle point) are much more susceptible to coring septa (especially when the tip has become bent or dull) than either a point-style #1 (conical needle) or point-style #5 (conical needle with side-port).

6. Switching to a Merlin Microseal™ which eliminates the potential for coring.

Merlin Microseal™

Another potential issue is when septa melt while in the injection port. The published maximum septa temperatures are the temperatures the injection port can be heated to without melting septa, and not the true melting point of the septum material. This is especially important to know if the septa are to be used for other purposes outside of a GC injection port. In addition, injection ports from certain instrument manufactures may expose septa to higher temperatures than expected, causing them to melt. This is especially true while using 17mm septa. However, simply choosing septa with the highest maximum temperature may not be the best approach. As mentioned in #4 above, these septa tend to be much harder, which not only may lead to coring, but also bent syringe needles when using an autosampler (if your injection port isn’t hot enough to soften the septum).

A third potential issue is extraneous peaks in the GC chromatogram, but without any signs of septum coring. As mentioned earlier, septa contain volatile components which, if introduced into the injection port, will be chromatographed by the GC column. Most modern GC systems have a “septum-purge”, which is designed to “sweep” septa’s volatile components away. If this purge is not functioning properly, these components will eventually be introduced into the injection port and chromatographed as ghost peaks. Please review your instrument manual for setting the proper septum-purge flow.

If your septum-purge is functioning properly, and your chromatogram still has extraneous peaks, try using a new syringe, new rinse vials, and a different bottle of rinse solvent. If your samples/standards are in a high boiling-point solvent, a highly-viscous solvent, or water, try using a gas-tight syringe.

One last comment on minimizing extraneous peaks, never touch anything associated with the injection port (including liners, o-rings, septum, etc.) with your bare hands, or even most gloves, as finger oils or other contaminants may be deposited on the item. Instead, use clean metal tweezers or clean, all-cotton gloves.

As a final note, if you are experiencing any of the above problems, and a permanent fix is not readily available, you may want to try wrapping the septum in a thin layer of aluminum foil. This has been shown to minimize the amount of septum off-gassing and prevent melted septa from sticking to the injection port.

Below are related links that you may find informative.

Handy Septum Size Chart

Preventing Septum Problems

Merlin microseal or Septa… should they really “SEAL” ?..

Septum particles in my insert.. Good, Bad or Ugly?

If you experience these or any other septa issues, please contact Restek Technical Service at 1-800-356-1688 ext. 4, for assistance. Thank you.

2 Responses to “Troubleshooting Injection Port Septa”

  1. Alan says:

    Could you clarify: Your the above section says: 5. Point-style #2 (beveled needle point) are much more susceptible to coring septa (especially when the tip has become bent or dull) than either a point-style #1 (conical needle) or point-style #5 (conical needle with side-port). Do you mean LESS susceptible, because the point literature on a different web page of yours indicates that the Beveled Point#2 is LESS susceptible to coring ????

  2. Alan Sensue says:

    Hi Alan. When I write my posts (or communicate with customers) I ignore marketing literature and share my personal experiences with customers. Based upon my experiences, point style #2 syringe needles were far more prone to coring septa than either a point style #1 or point style #5 needle. For full disclosure, when I am unfamiliar with a certain product, I will rely on marketing literature because I have no other frame of reference. Having said this, based upon your experiences, have you had more or less coring with a specific needle style? Thank you. Alan

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