This is a common GC troubleshooting question. Since determining the source of the ghost (contamination) peaks can be difficult, I decided to write this post to (hopefully) help our customers.
GC column carryover
When I operated an instrument on a daily basis, it was only a matter of time before something caused ghost peaks in my chromatogram. So how did I narrow down the source of the ghost peaks? First, I would cool the injection port. Then, I would program the GC so that I could simply press the Start Button to acquire data for an analytical analysis without injecting any sample, standard, solvent blank, etc. In other words, with a cold injection port, and without injecting anything, I would acquire some data while heating the GC oven. In most cases, there were no ghost peaks in my chromatogram, or if there was, they were much, much smaller. This told me that the ghost peaks were not a result of my GC column. However, if the ghost peaks remained, I would trim 1-loop (approximately 0.5-meters) from the inlet side of my capillary column and perform a 10 minute bake-out by setting the GC oven to 20°C less than the column’s maximum isothermal temperature.
Injection port septa
If the GC column is not causing ghost peaks, where should you look next? One of the most common sources is injection port septa. I wrote the following post to help identify and fix this issue.
To test, replace the injection port liner after thoroughly cleaning the injection port. Then replace your injection port septa and make sure your septum purge is working properly (by measuring the septum purge flow with a flow meter). Keep the injection port cool and without injecting anything, obtain some data like described in the GC column carryover paragraph above. This same test can also identify potential off-gassing contamination from the injection port O-ring (if applicable to your instrument).
If the baseline does not contain ghost peaks, heat the injection port and acquire an analytical analysis without injecting anything. If the baseline still does not contain ghost peaks, inject a solvent blank into a heated injection port. If you observe peaks, your syringe, blank solvent, and/or rinse vial solvent may be the problem, and you should review the posts below. Or, your injection port may not be as clean as you think it is.
Another potential source of ghost peaks is from your sample/standard vial septa. So how do you test for this? I used to remove the septa from the vial cap and make an injection (manually or using an autosampler). Do you still see peaks? If not, these septa are likely the cause. If you do, then switch to a septa made from different material and repeat the experiment. Remember to only inject once from a vial, as piercing the septa multiple times may lead to ghost peaks.
If nothing listed above helps you determine the source of the ghost peaks, take a closer look at your instrument and/or carrier gas. Testing carrier gas is relatively easy; cool your injection port and GC oven temperature to 35°C while letting the carrier gas flow for several hours (do not cool the detector). With the GC oven and injection port still at 35°C, start acquiring data with the instrument. Then, increase the injection port and oven temperatures. If you notice ghost peaks, then suspect the carrier gas. (Example of a carrier gas filter trap shown below.)
Split Vent line and trap
If you normally operate the GC in splitless mode, you need to check one more thing. The ghost peaks may actually be coming from the split vent line and/or split vent trap. Remember that the split vent line is seldom heated, so material (compounds) introduced into it may be condensing out, and vapors may be working their way back into the injection port. To test, set the injection mode to split (2:1 split should be fine). Inject a few solvent blanks. Without letting the instrument switch to splitless mode, acquire data for a sample, standard, or solvent blank. If the ghost peaks disappear while in the split mode, then the split vent line and/or trap are likely the problem, and both should be replaced. (Example of a split vent trap shown below.)
I hope something here has helped you identify and fix the source of your ghost peaks. For additional information on troubleshooting ghost peaks, I suggest you read Jaap de Zeeuw’s blog post Poster on sources for “Ghost-Peaks” in Gas Chromatography which contains links to five articles he has written about ghost peaks.