Improving minipurification
To get the best signal to noise ratio -
Use young tissue showing good symptoms and as early as possible in the infection cycle
Avoid plants that are rich in gums
Use fresh tissue; if this isn't practical store tissue in an ultracold freezer
Use high salt concentration buffers (0.4M citrate)
Heat crude extract (ten minutes in hot tap water works well)
If the virus(es) in question is acid stable consider using pH 4.5
For SDS PAGE, make sure proteins are fully reduced (and alkylated if you're silver staining)
Experiment with variables, but always use a series so that the trend is apparent
Remember that specific cases may go against the general rule