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I have two unknown peaks on my GC (both with the same MW or rather highest M/Z ratio peak = 98) and I am trying to confirm their identity.

Unknown-1

Unknown-1

Unknown-2

enter image description here

Based on the expected chemistry I have identified two potential candidate molecules from a library of GCMS spectra (see images below; just click on the images please if you cannot read the smaller font numbers).

Compound-A

enter image description here

Compound-B enter image description here

Is it safe to think these are matches or not really? The MS was run in EI+ mode.

  • Unknown-1 is Compund-B?
  • Unknown-2 is Compound-A?

Both likely? Neither likely? Any one likely?

Is having the same set of M/z fragments good enough (e.g. 98-83-55 similar between Unknown-1 & Compound-B) or ought the abundance ratios also match mostly?

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  • $\begingroup$ Please, do not use external image hostings, since they are not reliable. Prefer the standard Stack Exchange way of uploading images. $\endgroup$ – Wildcat Jul 17 '16 at 8:49
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I would never recommend making an assignment of identity based on Mass Spectrum alone - usually you'd want to get things like IR or NMR Spectra to further corroborate your identification but supposing that the underlying chemistry of the reaction is simple and that all you can do is mass spectroscopy you can use this to identify compounds.

Unknown-1 is Compound B

Plausible, but the base peak of Compound B is 83, but the base peak of Unkonwn-1 is 55. Need more information, but reasonable guess.

Unknown-2 is Compound A

Unlikely as the base peak of Compound A is 69, which is distinctly missing from the spectrum of Unknown-2. Unknown-2 also has significant peaks at 55-57 which are insignificant in Compound A's Spectrum.

Is having the same set of M/Z fragments good enough or ought the abundance ratios also match mostly?

You would have a much stronger case if the abundance ratios also matched. Remember that the peaks are formed by the breaking up of the compound and the relative stability of each fragment. If the compound is the same and run in similar conditions, it should, in principle, break up in the same/similar way.

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  • $\begingroup$ Thanks for your comments IT Tsoi! For NMR as well as IR one needs to isolate pure compounds, correct? Basically this is a GCMS of a byproduct mixture where these two unknowns are most abundant but still at approx. 10% levels. In the absence of a pure isolation of these peaks is there any way to employ NMR / IR? Right now these components are only resolved on the GC column. $\endgroup$ – curious_cat Jul 17 '16 at 16:02
  • $\begingroup$ To clarify, I don't need 100% certainty of identification. Being reasonably sure will do. The underlying goal isn't a novel synthesis merely identifying by-products to enable process improvement. $\endgroup$ – curious_cat Jul 17 '16 at 16:06
  • $\begingroup$ @curious_cat since you just need to be reasonably sure, it may not be necessary to isolate the pure compound - you just need it in reasonable proportions relative to the rest. "Crude NMR" can be used to tell if there is substantial compound to purify from the reaction mixture but since yours is a byproduct this may not work. If you don't need 100% certainty and presumably you know the underlying chemistry quite well, I guess your ID of Unknown-1 as Cpd-B is acceptable but I am not convinced that Unknown-2 is Cpd-A based on the spectra provided. The pattern is just too different. $\endgroup$ – IT Tsoi Jul 17 '16 at 16:26
  • $\begingroup$ Thanks! Is it reasonable to expect that based on the MS whatever Unknown-2 is its molecular weight is also 98? Only C,H,O are expected in there. $\endgroup$ – curious_cat Jul 17 '16 at 16:53
  • $\begingroup$ Yes, it is reasonable to suspect that Unknown-2 has a molecular weight of 98 $\endgroup$ – IT Tsoi Jul 17 '16 at 17:03
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If you plan to publish the results in a pier reviewed journal reviewers would ask to provide three independent characterizations of the compound. 1-H, 13-C NMR and mass spec are typically expected. Based on the molecular weight of the compounds they are small and should be easy enough to synthesize. Or even purify from your reaction mixture, since you are doing it to scale up the process. Once you synthesize them you can TLC pure material and your reaction mixture to see if they have the same Rf value.

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