Dear Syadza Firdausiah,

I think that for GC-MS analysis, the retention time (RT) is only a partially good diagnosctic information. As you mentioned, the compounds were in different compositions, and this may have the influence on the RT.

Furthermore, the MS spectra is a good diagnostic information, however numerous compunds (for instance sesquiterpenes) may have even identical MS spectra. So there again may be some misinterpretations.

In my lab practis, I do not look at all at RT (of course if the difference is not too big) and for identfication I use MS spectra and linerar retention indices (LRI). It is much more reliable than RT.

Kind regards, Jacek Łyczko

You may try to make as exactly the same condition as possible but two chromatographic runs may differ from each other in numerous ways. Just like any experiment, we need to do several measurements and run statistics to report average retention values. The difference could be variations in the solvent system, the column condition including change in temperature and residual effect from the previous run, variation in time of injection and injection volume, etc. This happens even if you have then most up-to-date instrumentation. For this reason, we often use internal standard to show by how much the identified compounds vary from the standard in question. The use of MS as a qualitative measure that you mentioned is another useful tool. So, experiments vary and hence you expect to get a drift in retention time even with the same instrument and analyst. Intra and inter-days variation, different instrument and analyst, etc. are parameters that we assess in chromatographic analysis.

Have you changed your column recently? The column gets shorter each time you change it.

If your RT change is within a window of 1 second, that's normal. If you are working in a testing laboratory like myself and you are running hundreds of injections weekly, you'll get used to this slight shift.

You don't need to investigate the cause if the change is so little that your software can still pick up the peak of interest without manually integrating it. Just get used to it. But if you are in a research institution, your supervisor or reviewer may not accept this change even if it is small, in this case you'll need more elaboration in your report or manuscript on the technical inconsistencies in analytical instruments.

Bottom line, ignore that RT shift if it is so small.

Some variation in retention time is normal. There are many reasons for retention time variations: any changes to the column, whether pressure and flow are well regulated, matrix effects, etc. That is why retention time standards, chromatographic alignment software and/or Kovats retention indices are used together with MS data to ensure correct identification.

Any change in the operating conditions of the GC-MS can cause the rt of the compounds to change. Instead of avoiding these changes, the Kovats index of the compounds can be calculated. Thus, the compounds have an index that is more independent of ambient conditions. You can use the papers below.

https://doi.org/10.1002/ffj.3574

https://doi.org/10.18596/jotcsa.350370