EICs - how many ions to select

[bethlynn]

Hi all,
What criteria do you use to determine how many ions to include in your extracted ion chromatogram? It was suggested by another just to use compare the signal to noise ratio of each scenario and use the ions that give you the highest snr - but actually when i tried this out on a few peaks, the TIC gave me the highest snr.

What are some general rules behind the selection criteria behind using EICs and the number of ions to include?
Please and thanks.

[Don_Hilton]

If you are doing selected ion acquisition, the TIC will only include the ions you collect - and noise contrribution for masses you don't collect will not be there. If you are doing a scan across a mass range, the masses that don't give peaks for your compund will contribute to noise. I've seen cases where adding signals of similar intensity gave an improvement in the signal to noise - and cases where of signals from different masses gave no improvement or degraded the signal to noise measurement. When you sum signals, the signal tends to sum and noise begins to average out - if the noise is truly random. If the noise is the rise and fall of interfering compunds - it is acutally signal - just not the signal you want.

Uou need to look at sampling rate and dwell times - get 8 to 12 points across the peak baeline to baseline If you undersample a peak, you get poor representation of areas. If you oversample a peak,you increase the noise in your measurement. If you are doign a full scan acquisition, look at the possiblity of doing SIM mode acquistion.

A small set of rules is kind of hard to come up with. There are many options in what you might want to accomplish in the chromatographic run and how you might set up the run to get there. How to handle the data is determined by the first two.

[James_Ball]

Hi all,
What criteria do you use to determine how many ions to include in your extracted ion chromatogram? It was suggested by another just to use compare the signal to noise ratio of each scenario and use the ions that give you the highest snr - but actually when i tried this out on a few peaks, the TIC gave me the highest snr.

What are some general rules behind the selection criteria behind using EICs and the number of ions to include?
Please and thanks.

If you are looking for quantitation and qualifier ions to process full scan data, I usually use one for quantitation and two others for qualifiers. I try to choose the mass with largest signal for quant and the two qualifiers at 20% or more compared to the signal of the quant mass. You also want to make sure what you choose is unique to your target so that peaks that elute near your target do not interfere, wither with quant or qualifier masses.

[bethlynn]

Thank you Don and James,

In this case I am processing data to which I no longer have the original retention samples - results are full scan mode and sampling rate/dwell times seem good. However I can adapt for next trials using SIM and this will certainly help my sensitivity.

I was not looking at quantification at this point, just comparison between treatments. Group is terpenes so ions are common but there are a few that are unique. I ended up extracting peak with varying ions and then looking at my library hit level. I chose the group of ions that gave me the large library hit with a decent area count. Does this make good sense?

[James_Ball]

Thank you Don and James,

In this case I am processing data to which I no longer have the original retention samples - results are full scan mode and sampling rate/dwell times seem good. However I can adapt for next trials using SIM and this will certainly help my sensitivity.

I was not looking at quantification at this point, just comparison between treatments. Group is terpenes so ions are common but there are a few that are unique. I ended up extracting peak with varying ions and then looking at my library hit level. I chose the group of ions that gave me the large library hit with a decent area count. Does this make good sense?

I would say that is very sound logic for what you are trying to do.

When not in a regulated situation, use the technique that gives you the best results with the least interference possible.

[carlo.annaratone]

Normally for each compound I select three ions:

strongest one for quantification and other two strong ones for qualification. However I do not only check on the library, but I make sure that those ions are unique to the compound of interest in my matrix. This is especially true in cases like yours when you have many similar molecules with similar fragmentation.