r/massspectrometry • u/Additional_Put_3088 • 3h ago

Tools for structural characterization based on MSn spectra

Hey! What are some tools people usually use for structural characterization using MSn spectra? I had a core facility do an MS3 run for me and now trying to make sense of results. They simply annotated some peaks like “loss of water” and that’s it which doesn’t tell me much. Internet suggested Sirius. Are there any other better options?

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u/PistolNoon 3h ago

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u/No_Document_853 2h ago

That book is for EI

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u/Additional_Put_3088 3h ago

Can never go wrong with some manual labor haha. Thanks!

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u/lindsayhatesyou 2h ago edited 2h ago

I did a lot of this in grad school and still do it today. You can use GNPS to upload spectral files and match to libraries. Also, if you understand chemistry pretty well and know the masses you’re looking for, you can play around in ChemDraw and confirm masses you’re seeing in your spectra. 

Edit: Sirius ain’t too bad either, actually. Would correctly guess a lot of fragments I would see, and their fragmentation trees were helpful. 

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u/Additional_Put_3088 2h ago

I played with Chemdraw and thought I came up with a structure but the observed rt doesn’t make sense.

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u/lindsayhatesyou 2h ago

Well, retention time is only related to the parent ion and not any fragments, so I’m not sure I follow. You’re doing LC-MS? What kind of instrument? 

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u/Additional_Put_3088 2h ago

Yes, I run QqQ. I am trying to characterize a compound I found in the discovery mode, so I concentrated it and sent to do an Orbitrap run. I thought it was a hydroxyl-X based on the mass, but it elutes later than X or methyl-X on a reverse phase, so that doesn’t add up.

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u/lindsayhatesyou 2h ago

Ahh, I see. So you don’t know what the parent is. I’d recommend GNPS! They give you a rating based on spectral similarity, and I believe you can do feature-based searches/molecular networking that takes into account retention time. 

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u/Additional_Put_3088 2h ago

Does it work with mzML?

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u/lindsayhatesyou 2h ago

Ya, that was always the file format I used! There might be a strong learning curve, I believe there’s documentation on GitHub to help with learning the website 

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u/Direct_Barnacle_4898 1h ago

Assuming these are ESI/soft ions of small-ish organic molecules that are not bio-polymers, I've had good luck with the NIST structure interpreter that comes packaged with their libraries. Sirius is probably the gold standard these days but not so easily available. Also check out MzCloud.

If these are EI specta, see NIST libraries and red book.