Provided are methods and apparatus for determining conditions for performing chromatography, particularly flash chromatography. The methods may be utilized for separating compounds in a sample in a column chromatography system. The method includes determining at least two retention factors corresponding to the TLC performance of a target compound and an adjacent compound and defining a sample loading amount and a solvent gradient profile using at least two solvents that will result in differential elution of the target and adjacent compounds from a chromatography column. The chromatography system and loading parameters may be selected to provide satisfactory separation of the target compound from adjacent compounds.