GC-MS quantification question

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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I'm relatively new to GC-MS and hoping to get some clarification on different methods of quantification in GC-MS.

In the software there is the ability to extract ion chromatograms and select quantifier and qualifier ions. I understand that this is useful if analytes are not fully resolved chromatographically, they can still be resolved by mass if unique ions can be identified. However, if analytes are fully resolved (no coelution), is TIC then used for quantification or would you still use XIC with quantifier and qualifier ions?

What is the difference between using full scan mode and then selecting quantifier/qualifier ions, versus using SIM mode? They seem the same, only that SIM mode selects the ion(s) prior to the run as opposed to scanning the full range and allow for selecting the ion post run. So after the ions are identified, knowing that SIM is able to achieve better detection limits as well as resolve coeluting peaks, what is the advantage to using full scan mode instead of SIM mode?

Thanks!
crong wrote:
I'm relatively new to GC-MS and hoping to get some clarification on different methods of quantification in GC-MS.

In the software there is the ability to extract ion chromatograms and select quantifier and qualifier ions. I understand that this is useful if analytes are not fully resolved chromatographically, they can still be resolved by mass if unique ions can be identified. However, if analytes are fully resolved (no coelution), is TIC then used for quantification or would you still use XIC with quantifier and qualifier ions?

What is the difference between using full scan mode and then selecting quantifier/qualifier ions, versus using SIM mode? They seem the same, only that SIM mode selects the ion(s) prior to the run as opposed to scanning the full range and allow for selecting the ion post run. So after the ions are identified, knowing that SIM is able to achieve better detection limits as well as resolve coeluting peaks, what is the advantage to using full scan mode instead of SIM mode?

Thanks!


The software on most instruments will allow for all three methods above, even TIC. TIC is ok if you have very clean samples and you know exactly what should be there, just like using an FID or ECD or other general detector. Most quantification is done using XIC where you look at a prominent ion for the selected analyte that has as little interference in the analyzed samples as possible, then you add to the selectivity of the analysis by using the qualifier ions to confirm that you are seeing the analyte you are actually looking for. This is similar to using a dual column confirmation using normal detectors so that you eliminate as many false positives as possible. This approach is used with both full scan and SIM acquisition methods.

The choice between full scan and SIM can be because of the need to have definite identification of the analyte for which full scan is best. With full scan you have a lot more information to determine if you have the analyte you are really looking for, or if it is an interfering peak. Samples from clean to mildly contaminated work well in full scan. SIM will give you less interference from background contamination and greater sensitivity because you are filtering out more of the garbage that may be present in highly contaminated samples and even for clean samples the ability to focus on only a few specific masses gives the instrument the ability to pull out more signal for analytes with low response. If you are scanning from 35-500m/z three times per second you are only looking at a single mass(assuming a resolution of 0.1 amu) for 7.17^-5 seconds per scan. Using SIM you can have a dwell up to 1^-3 seconds per mass depending on the number of masses per segment with no problem. Collecting data for 100x longer at the mass of interest can help with sensitivity, but you lose a lot of data that can be used in identification of the analyte you would have in full scan. So each method has its benefits and shortcomings. You just have to decide which will give the best performance for your specific analytical needs.
The past is there to guide us into the future, not to dwell in.
James_Ball wrote:
The software on most instruments will allow for all three methods above, even TIC. TIC is ok if you have very clean samples and you know exactly what should be there, just like using an FID or ECD or other general detector. Most quantification is done using XIC where you look at a prominent ion for the selected analyte that has as little interference in the analyzed samples as possible, then you add to the selectivity of the analysis by using the qualifier ions to confirm that you are seeing the analyte you are actually looking for. This is similar to using a dual column confirmation using normal detectors so that you eliminate as many false positives as possible. This approach is used with both full scan and SIM acquisition methods.

The choice between full scan and SIM can be because of the need to have definite identification of the analyte for which full scan is best. With full scan you have a lot more information to determine if you have the analyte you are really looking for, or if it is an interfering peak. Samples from clean to mildly contaminated work well in full scan. SIM will give you less interference from background contamination and greater sensitivity because you are filtering out more of the garbage that may be present in highly contaminated samples and even for clean samples the ability to focus on only a few specific masses gives the instrument the ability to pull out more signal for analytes with low response. If you are scanning from 35-500m/z three times per second you are only looking at a single mass(assuming a resolution of 0.1 amu) for 7.17^-5 seconds per scan. Using SIM you can have a dwell up to 1^-3 seconds per mass depending on the number of masses per segment with no problem. Collecting data for 100x longer at the mass of interest can help with sensitivity, but you lose a lot of data that can be used in identification of the analyte you would have in full scan. So each method has its benefits and shortcomings. You just have to decide which will give the best performance for your specific analytical needs.


Thank you so much for the informative explanation!

When you say that full scan may be better for definite identification, that means we are able to compare the mass spectra of the analyte peak to a standard (or library) with all fragments, as opposed to just the selected ions in SIM mode?

In other words, in SIM mode it might be possible for a compound to elute at the same time as the analyte, produce the same ions, in the same ratios, but not actually be the analyte? Because there could be differences in other fragments that would only have showed up if a full scan was done?
That is correct. It is normally best to start in full scan when developing a method so you know if you are getting the correct peak identified. Once you know how your method performs chromatographically you can then move to SIM if real samples cause problems with high inteferences or you need more sensitivity. Something like Ethylbenzene versus p-Xylene is an example, they both have 91 as the main ion, along with 105 and 106 as qualifiers, but the ration of 105 to 106 helps identify which is which analyte. If you do SIM and look only for 91, or 91 with 105 as qualifier then it is difficult to distinguish between the two analytes, but full scan will show it easily. Also other substituted benzenes can have 91 along with 105 and 106, but they may also have a major ion of higher mass which would not be seen with SIM but would be seen with full scan, so those could also be mistaken for the analyte of interest.

Once you are certain about the retention time of the analyte then SIM becomes more accurate. It all depends on what information you want from your analysis.
The past is there to guide us into the future, not to dwell in.
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