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Suppose I have a GCMS peak graph for a component, what are possible options to figure out what the molecule may be?

Any tips about good software that will do this? I do know that for many compounds there is a hit in the NIST library, but how does one go about automatically checking the library?

Google came up with OpenChrom. Has anyone used this? The peak library in it is unfortunately not accessible in the free version.

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    $\begingroup$ This is what I use. For a formula, at least. Other methods then allow me to deduce structure. MS can give you many structural clues, depending on the ionization method. $\endgroup$ – SendersReagent Mar 21 '16 at 7:20
  • $\begingroup$ @DGS Thanks. Correct me if I am wrong, but that tool only seems to use the MW based on the top peak, right? Isn't there a way to use the other lower peaks as well? $\endgroup$ – curious_cat Mar 21 '16 at 14:27
  • $\begingroup$ Type in the mass of a lower peak? $\endgroup$ – SendersReagent Mar 21 '16 at 15:18
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    $\begingroup$ That's right. Maybe I wasn't completely clear on your intension. I don't think there is a library for MS data like that. I could be wrong. ChemDraw includes a MS prediction program, but not the other way around, as far as I know. $\endgroup$ – SendersReagent Mar 21 '16 at 16:10
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    $\begingroup$ Not exactly what you are looking for but a good resource for spectroscopic identification is sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_list.cgi $\endgroup$ – StevieD Mar 22 '16 at 19:29
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Have you tried the Golm Metabolome Database? It is a collection of GCMS mass spectra. The focus is on metabolites.

However, on their webpage is the entry "Decision Trees". If you follow the link, there is the option to enter your own mass spectra information and receive a prediction of functional groups in the measured substance. This might be of help to identify your molecule. There are more details in the Wikipedia entry.

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  • $\begingroup$ This answer would be much more useful if you elaborate on the good and bad sides of "Golm Metabolome Database". $\endgroup$ – M.A.R. Mar 23 '16 at 9:03
  • $\begingroup$ Thanks for the hint, @IͶΔ. I have extended the answer. Is that more helpful? $\endgroup$ – Arsak Mar 23 '16 at 11:10
  • $\begingroup$ Yes, much better. Thank you and welcome to the site! $\endgroup$ – M.A.R. Mar 23 '16 at 11:31
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OpenChrom is free of charge, but the NIST db is not. That is why you need to have the NIST db already installed on your system.

Have a look at this tutorial.

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