A concept I was introduced to at ASMS is isotope envelope fingerprinting. Some research on this topic revealed that the idea isn't exactly new (just another new one to me!). The idea is that under certain conditions the number of charges that a protein accepts as well as the masses within the "convoluted" isotope envelope would be enough for a protein ID.
It makes sense on some level, right? I've ran the Waters IGg standard dozens (hundreds?) of times in my life, and it pretty much always looks the same. The fans of isotope envelope fingerprinting want to exploit this and leave MS/MS for other assays (or for confirmation). My guess is that it would be fine unless we are looking at complex things. I can easily pull the 5 proteins in my normal intact/top down mix apart by just their envelope, but I would love to see data on complex runs.
Protein Goggle is a program that can be used to compared IEFs (not to be confused with IEF...sigh....). If you're an academic researcher, you can get Protein Goggle for free to check it out. If you're me, you probably wouldn't have time to try it out anyway!
The interface looks pretty straight-forward.
You can read more about this concept and the software you'd need for doing this type of analysis here.
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