One consideration that you seem to have left out of the sample prep phase is the need for sample clean-up. Many of the separation steps and characterization steps are going to be completely reliant on sample clean-up, especially anything that is mass spec related. Clean-up would include precipitations, various types of chromatography - especially Reverse Phase HPLC (it is the most mass spec compatible), ultra centrifugal filtration, dialysis, and plenty of others. You could also include protein enrichment (e.g. titanium dioxide, lectins) or depletion methods (e.g. albumin/IgG depletion)here.
Also for protein separation and characterization don't forget HPLC, this is a huge one in pharmaceutical research. RP-HPLC is a tool that can be used to fractionate complex samples as well as provide information for characterization when used in conjunction with either UV diode array or multiple UV wavelength detectors.
Another thing, I'm not sure if this is really in the scope of what you are doing, but I feel like digestion (e.g tryptic digestion) needs to be mentioned somewhere since it is such an important technique in regards to characterization with Mass Spectrometry. You can also include things like iTraq as a subset of digestion for quantitation.
If you want to include something that is on the leading edge of proteomic mass spec, that would be multiple-reaction monitoring (MRM) which would be used for protein characterization (especially quantitation).
Don't forget Western Blotting, this is heavily used.
Edited by proteaMatt, 11 June 2012 - 01:39 PM.
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