We thought we could get away with it, as us GC-MS folks have always called those interfering and non-analyte peaks our ghost peaks. They come in various shapes and sizes and can be cumbersome for the analyst who wants to screen the sample. Sometimes one wonders if peaks that are found and identified are really part of the content of the sample or if they are introduced somehow.
Please bear in mind that when analyzing with GC, typically quite strong extraction solvents are being used. These strong solvents… well, they extract! So surface material can also be extracted. Even contaminants from the laboratory air can be extracted into the solvent. When injecting the sample one hopes it is only the sample, when in fact one most likely also injects all the other stuff extracted along with it.
These interferences can reach enormous concentrations and interfere with results. Sometimes the interferences are not seen when analyzing in the targeted approach of SIM or MS/MS mode. But sometimes they do create issues or even hide potential issues of contamination.
Common Causes of Interference
- Contaminated carrier gas
Please ensure that when installing a new system in the lab the lines, filters and connections are clean and flushed. If installing the first GC ever in the lab or in a certain room of the lab please make sure to use a certified installer. If the lines have never been used, flush them for 15 minutes. Normally gas lines are clean upon delivery. Please check the specifications, and finally when ordering a new GC or GC-MS system let the manufacturer specify for you the desired gas quality. Replace the filters regularly and watch the color changes on the indicators.
- Column bleed
Most definitely column bleed is a common sight in GC and GC-MS. Most of the time it is seen as a rise in the baseline at the end of the temperature programme. When analyzing with MS one typically sees m/z 207 and 281 for an apolar type column. It is crucial to condition a column according to the guidelines.
See this video for more information on GC column conditioning.
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- Septum bleed
Another very common cause is septum bleed. This can result in a typical pattern of repeating peaks, and are easily identified with MS as they all have m/z 221, m/z 355 and m/z 429. Septum bleed can occur in the septum of the injector port, and can also occur in the septum of the vial, especially when storing a vial of which the septum is already pierced. Tiny septum particles will be extracted and cause repeating peaks.
- Injector issues
Contaminants can possibly deteriorate inside the heated injector. Please make sure you are using the best possible conditions and consumables for injecting samples. In fact, choosing the right injector settings and liners is quite cumbersome, as there are so many parameters and choices to make. Also the lines, like the split lines, can be contaminated and cause ghost peaks.
For these matters please reach out to your local support team for advice on choosing the best liner and parameters, or go to our Apps Lab Library for looking up the parameters and the consumables and a direct download of the complete method into the system.
Feel free to reach out to me in case of questions or comments.