Ion mobility separation

Recently we purchase an Ion mobility QTOF (IMMS) and run simple
application with small molecules that shows 3 peaks for our marker.

A question raised from our colleagues about the possibility that IMMS can separate
the same molecule that protonated on different spot of the molecule.

Does anyone can answer this question? Did IMMS separate between same
molecule with different protonated site (e.g. NH2+ vs. OH2+)?

  • It is hard to tell experimentally if the multiple peaks observed are due to multiple conformations or localization of where the molecule is protonated. There are two ways to go about determining this. The first is to synthesize the small molecule and sequentially replace one at a time the amino acid(s) that are likely to be protonated, and observe the resulting number of peaks. The other option is to perform theoretical modeling and determine if the multiple peaks observed are from multiple conformations or differentiation of where the protonation site is.

  • Charged different functional group and sepaaration of them is very common phenomena. They are usually very close to each other - CCS is changed a little. There might be another reason - different adducts (M+H, M+NH4) and fragmentation after IM separation of the heavire adduct - NH4 - back to M+H. These peaks are quite separated. If there are real isomers, they would be at least a little separated in LC. If all three peaks are absolutely coeluted, they are probably only one compound. Here is an example of both - two different charged OH and M+NH4, which fragment to M+H:

  • This question has been marked as assumed answered.

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