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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. $\endgroup$ Mar 21, 2016 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? $\endgroup$ Mar 21, 2016 at 14:27
  • $\begingroup$ Type in the mass of a lower peak? $\endgroup$ Mar 21, 2016 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. $\endgroup$ Mar 21, 2016 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, 2016 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, 2016 at 9:03
  • $\begingroup$ Thanks for the hint, @IͶΔ. I have extended the answer. Is that more helpful? $\endgroup$
    – Arsak
    Mar 23, 2016 at 11:10
  • $\begingroup$ Yes, much better. Thank you and welcome to the site! $\endgroup$
    – M.A.R.
    Mar 23, 2016 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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