by
crong » Wed Feb 06, 2019 11:56 pm
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?