Is tandem mass spectra a good approach to analyse complex peptide mixtures?
Haven't done that myself, but have read of it. Check out for example
Please check Agilent Catalog 2005 page 640-655. It shows example of LC/MS for peptide analysis and characterization.
Provided you can get clean parent ion spectra the instrument can produce CID (Collision Induced Dissociation) spectra which may allow an identification of the parent ion to be made. If the original mixture is very complex then separation by an orthogonal front end technique is necessary (on or off-line). LC-MS. Liquid chromatography followed by MS. The reason that this separation needs to be accomplished is that to many closely related ions in terms of m/z (mass/charge) produces 'space charge' effects in the instrument which severly limits its analytical utility.
sample preparation is a key step before mass analyze