Could the proteome of E. coli be fluorescently labelled?
One at a time, you could potentially label all of them. 

If you're asking how many proteins you could label at once, your biggest limitation is probably your microscope. In order to distinguish between different types of proteins you need different color fluorescent labels (dyes, fluorescent proteins, etc). Even the fanciest fluorescent microscopes tend to be set up to excite/record labels in &lt;10 distinct wavelengths.

In practice I've only seen experiments where there were tracking 3 distinct types of proteins at one time.