I am currently trying to validate VOCs that are not present in the SIFT-MS compound library. The commercially available standard only exists as a mixture of stereo isomers (cis/trans). Before we try to isolate the isomers, which is time-consuming and still in need of a lot of experimentation, I was wondering if the different isomers can have different product ions or if it will just be the same product ions with different branching ratios?
I am sure there should be a difference - after all, cis/trans isomers may behave differently in chemical reactions (and chemical ionization is a chemical reaction !). One can speculate that certain cyclization or fragmentation reaction would be possible for only one of cis/trans isomers. However I cannot give examples; also I don't know how big could be the difference and under which conditions it would be really noticeable. It would be good to hear the opinion of experts in mass-spectrometry.
I think I roughly agree with Khlebnikov & Pach. But the differences could be subtle. For example see the EI MS of geraniol and nerol.. (very little difference in EI fragmentation despite the stereochemical difference ..although GCMS can give differentation). I think you have to give us the structures you are considering before we can help.
I would be very cautious in assigning structure to two different diastereomers based on any differences in fragmentation pattern.
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