Hi there,

I'm working on a purified protein sample which is was expressed in bacteria in C13 and N15 media. I need to assess the incorporation  efficiency by MS as this protein is going to be used later on for NRM experiments. This is an aprox 25KDa protein (The sequence of the protein is known). I'm thinking of doing an intact protein analysis by infusion ESI-MS and compare the spectra of the unlabeled vs labeled protein. Does anyone know any software/algorithm to estimate the incorporation efficiency??? I assume that 100% and 0% incorporation efficiency are easy to observe... but I'm not certain how to handle the in-between situation of what I imagine to be a very complex spectra! 

Alternatively, I was planning to do a trypsin digestion and look at the peptide signals from an LC-MS analysis, which seems to be more simple from the data analysis point of view. Again, none and full incorporation seem straightforward analysis, but I wouldn't be completely convinced on how to analyze the incomplete incorporation scenario.

In both cases, samples would be acquired on a high res Velos-Pro Orbitrap MS system.

Anybody have any ideas on how to approach this type of work? I've gone through the literature, and there doesn't seem too much published for this particular application.

Thanks

Alex