In a system and method for feature alignment in chromatographic systems, the system runs a first sample through a first separation column. The system determines a first set of features for the first sample run. The system runs a second sample through a second separation column and detects a second set of features for the second sample run. The system estimates a systematic shift in features between the first sample run through the first separation column and the second sample run through the second separation column. The system adjusts the second set of features detected for the second sample run through the second separation column based on the estimated systematic shift to obtain a third set of adjusted features.