Hi all,
This question may solicit some practical ways of analyzing MS/MS data. I am performing collision induced dissociation to fragment my protein. The goal of my experiment is to observe the fragmentation patterns of my protein. Since I am doing ESI-MS, my precursor ion is multiply charged. This may complicate the identification of the fragment peaks. Is there an automated way to interpret CID fragments from multiply charged precursor protein ions?
Thanks!
perform charge state deconvolution. I assume you are using thermo instrument, then read this
https://tools.thermofisher.com/content/sfs/manuals/Man-XCALI-97576-Protein-Deconvolution-30-User-ManXCALI97576-A-EN.pdf
Hi Nav..
If you are trying to just Deconvolute the multiply charged intact mass spectra of the protein molecules then you may try the Protein Deconvolution software (Thermo Fisher)..
But if you are trying to predict the fragmentation pattern of Intact protein attained using CID/ETD (Top Down approach), you may consider using Prosight Lite...
http://prosightlite.northwestern.edu/
Article ProSight Lite: Graphical software to analyze top-down mass s...
Perhaps the analysis of intensity ratio can help you as in my old work:
Separation of mass spectra of binary salt systems: calculations of mass spectra of pure system components from binary data
Mar 1991. International Journal of Mass Spectrometry and Ion Processes
Jan Kapala
If the amount od data is big enough, there the another method can help you:
The interpretation of mass spectra of inorganic molecules
Mar 2006
International Journal of Mass Spectrometry
Jan Kapala
Charge states can be resolved by two methods (and preferably both):
1) If the isotopic series is resolved, for a given charge state, then the mass difference between the isotopes should = 1/charge state on average. Mo is the monoisotopic uncharged parent mass, which can be determined from the monoisotopic (or average mass of the isotopic series) = (Mmeasured - charge state) * charge state.
2) If there are other charge states of the same species in the spectrum, then you can determine the spacing between the apex of each series. This mass spacing should widen by (Mo + charge state)/charge state for each charge state of the protein. This method works whether or not you can resolve the isotopes of any given charge state, but can give you harmonics of the true Mo as a result, Hence confirmation by (1) above is helpful.
Don't just trust the software, it can and does go awry from time to time. These methods can give you a close-enough answer to double check the software.
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