TargetLynx / QuanLynx integration issues

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

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Dear colleagues
I don't understand the logic behind Quan/TargetLynx integration parameters. I am struggling for years and get more or less acceptable results, but I hate not having full control over the integration especially of small peaks.
Please have a look at the attached chromatogram to see what I mean.

Problem 1: Fictional baseline
Image
https://ibb.co/B4c2rRW

Problem 2: Baseline separation or not?
Image
https://ibb.co/hspGJjw

How can I tell the algorithms to draw the baseline of the peak not from a fictional baseline but from the actual measured data points? How to discriminate what is baseline separated and what not?
The same issues appear using "traditional" and "apex track" integration.
Many thanks in advance,
Jörg
Those peak boundaries - are they manually set or automatically detected? Let's start with automatically detected boundaries. I don't know which options your software exposes so my answer is based on general understanding of ApexTrack. It's easier to see with the 2nd chromatogram that you have a cluster of 2 peaks (they meet at p2):
ImageBecause these peaks are not baseline-resolved ApexTrack determines a shared baseline for the whole cluster between p1 and p3. Hence your Peak1 baseline is below p2 - it's where the shared baseline is located.

If you want the baseline to touch p2 you need to ensure the peaks don't form a cluster:
1. Either Peak1 needs to end earlier (increase Touchdown threshold)
2. Or Peak2 needs to start later (increase Liftoff threshold)
3. Or both of the above.

Alternatively you may try to make the software ignore Peak2:
1. Increase Curvature threshold (Peak2 isn't sharp, so it will be ignored if the threshold is high enough)
2. Or increase the smoothing (increase window size).

But. If the peak boundaries are not autodetected (if you set them manually) then there's yet another possibility - both Peak1 and Peak2 are considered as one peak. Which means too much smoothing is happening and you need to decrease window size. Increasing Touchdown/Liftoff thresholds also may help.
Product Manager at https://elsci.io
sbashkyrtsev wrote:
If you want the baseline to touch p2 you need to ensure the peaks don't form a cluster:
1. Either Peak1 needs to end earlier (increase Touchdown threshold)
2. Or Peak2 needs to start later (increase Liftoff threshold)
3. Or both of the above.

Alternatively you may try to make the software ignore Peak2:
1. Increase Curvature threshold (Peak2 isn't sharp, so it will be ignored if the threshold is high enough)
2. Or increase the smoothing (increase window size).

But. If the peak boundaries are not autodetected (if you set them manually) then there's yet another possibility - both Peak1 and Peak2 are considered as one peak. Which means too much smoothing is happening and you need to decrease window size. Increasing Touchdown/Liftoff thresholds also may help.

The Apex track parameters offered by Waters are VERY limited, see screenshot:
Image

The traditional algorithm offers some more parameters:
Image


The best peak detection control is offered by Chromeleon, by the way...
Your first situation has arisen because of the dip at 0.32min. The software has taken this as base-line and assumed that your peak is actually part of a string of improperly separated things from 0.32min onwards. The truth of the matter is that if you have a very wobbly baseline, then the result is liable to error no matter how sophisticated the integration algorithm.
If the dip at 0.32min is repeatable, you might just be able to deal with it by setting the integration extent in TargetLynx so that it only starts integrating after the 0.32min problem. This is an additional parameter in a TargetLynx method that is not found on the integrator settings part of chromatogram processing (in fact it usually causes trouble, because people get their integration looking good outside TargetLynx, then they process everything, and it's different. The reason is that TargetLynx didn't integrate the entire chromatogram, instead for economy it did only the region around the expected retention time, but if this began half way through a spurious peak, it can get confused).

Your second situation is a matter of personal choice. The integrator believes that there is a second peak (so do I) and if it drew a baseline to touch the data curve, it would be throwing away a genuine, wedge-shaped piece of real peak. The option is there, to make it ignore the drop-line (it's the join-valleys setting). But again, you might end up with a less accurate result than the one that looks strange.

On the whole, there are two things worth remembering about integrators: (1) how good they are is not proportional to how many settings they have; (2) most of us work best with familiar tools; the better we know an integrator, the better they are. I couldn't say what the best integrator is. I've used quite a few, and find that each has its own characteristics. On the whole, when they don't do a good job, it's because there is something a bit wrong with the chromatogram; quite often, this means there is no definitive 'right' behavior. All one can aim for is consistency (assuming the problem can't be solved by changing method/samples etc.)
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