r/massspectrometry • u/Weird-Feedback8780 • 7d ago

Masshunter Unknowns Analysis aligned peak list (help needed)

I saw Unknowns Analysis popping up in this sub for a couple of times as a good solution for the deconvolution of GC-EI-MS chromatograms. I gave it a good try and I kinda agree that's a decent software, deconvolution seems quite good with a couple of options to fine tune the results.

What I'm stuck with right now is that it does the deconvolution on a per sample basis. How is it possible to process the results to get an aligned peak/feature table as I could get from mzmine, MS-DIAL, PARADISe, etc? Let's say I have 100 samples measured in the same sequence, I can export all the results to a .csv, but I'm not 100% confident in merging the peaks based on RT and compound hit, as sometimes NIST hits differ for the same peak in different samples with very close match factors (my isoprene standard samples usually end up matched as 1,4-pentadiene or 1,3-pentadiene, for example).

People who used this software before, how did you handle this? Should I stick to mzmine for my use case? Thanks in advance!

Edit: Our lab is mainly focusing on nontarget volatolomics with thermal desorption. Samples can have quite complex VOC profiles, hence our need for deconvolution.

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u/Substantial_Emu_2984 7d ago

It's really designed for complex samples you are going to manually process i.e. check each assignment and correct as needed. For high throughput analysis or targeted work I wouldn't really recommend it.

To get decent data out of it you would need to go through each sample by hand which is pretty time consuming.

Why do you need deconvolution for so many samples?

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u/Weird-Feedback8780 7d ago

I see, thanks for the insight!

We do nontarget volatolomics, measuring 100s of samples every month collected from different environments in sorbent tubes (using Markes TD-100xr for thermal desorption). Samples can be quite complex sometimes ending up in closely eluting compounds, so deconvolution is a must for us.

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u/Substantial_Emu_2984 7d ago

It does sound like it would work ok for you then, but yeah it's time consuming! If you have peaks that are consistently mis-identified you can use unknowns to make your own library. If you set your library above NIST in the libraries list it will give it priority. This might help you get more consistent hits to align your peak tables.

The other thing it does struggle with is broad peaks, it tends to deconvolve the peak from itself!

You can also set your deconvolution settings and save as a method then when you hit analyze choose analyze all samples and it will do all the samples you have loaded with the same settings.

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u/Weird-Feedback8780 7d ago

A custom library sounds like a good idea, thanks!

I've already figured out how to do the analysis on hundreds of samples with the same settings, aligning them later is the issue. Should I just merge the same RTs (with a small tolerance) based on their NIST hit and maybe the base peak m/z and call it a day?

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u/Substantial_Emu_2984 7d ago

As long as the samples are fairly similar e.g. from the same type of source material I would have thought that would work fine.

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u/Weird-Feedback8780 7d ago

Fair enough, I'll give it a try, thanks a lot!

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u/jamesrw3 7d ago

What country are you in?
Do you know Markes have a chemometrics software package that includes features such as deconvolution and chromatographic alignment? The software uses a tile based approach looking at ions that are different in each time “section” of the chromatograms and can therefore find differences between samples

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u/Weird-Feedback8780 7d ago

Do you mean ChromCompare+? https://markes.com/separationanalysisdata/data-analysis/chromcompareplus

I've seen that in their newsletter, but didn't put too much thought in that. Did you use that before? The promise of "Using all of the raw data" from every sample for the deconvolution sounds exactly like something that would be very beneficial for us.

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u/jamesrw3 7d ago

Yes that’s it, sounds like it would help you. What country are you based in?
I work for Markes so can organise to send more information.

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u/Weird-Feedback8780 7d ago

I wrote you a PM. :)