Best way is probably just column chromotography. Carotenoids are nice and easy to fractionate because they are usually colored, and it's easy to scale because you just run a bigger column if you have more sample to run. If you have an HPLC that can collect fractions that could work to.
A ton of undergrad chemistry courses focus on seperating chlorophyll and beta carotene from Spinach, so there are lots of protocols out there...though those are from plants and I just remembered you are trying to get them out of E.Coli.
Can you see color changes in the colony morphology on agar or in the broth in liquid culture?
A few videos on youtube of the basics of separating cartenoids from plants as well.
I also attached a power point presentation I found on google about caretenoid seperation, not sure how good it is.
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