Methods and apparatus are provided for separating compounds from natural and synthetic feedstocks using reverse phase liquid chromatography. Reverse phase separation is conducted on short media beds in a multi-stage process. The present technology relates separating compounds from natural and synthetic feedstocks using reverse phase liquid chromatography, that can be done on a commercial scale. Most commercial scale chromatographic separation of natural and synthetic oils uses normal phase media with highly flammable and toxic solvents. The present technology uses primarily alcohols and water as solvents, which help provide a safer workplace, safer products and reduced environmental impact.