Amino acids can be separated using either a reversed phase column or an ion exchange column. The method almost always requires a gradient, and usually some form of derivatisation to enable detection with a UV or fluorescence detector.

Shodex offer two columns for amino acid analysis. The first is the Shodex CXpak P-421S (4.6mmID*150mm), a cation exchange column, which is suitable for a broad spectrum of amino acids. Under most circumstances, this is the column of choice. Analysis times are around 50 minutes, using a citrate buffer gradient.

There is also RSpak NN-814, a polymer-based reversed phase column packed with polyhydroxymethacrylate bonded with trace amounts of sulfo groups. This gives a mixed mode separation, which can be used to separate certain amino acids which are not easily separable using the CXpak column. The elution order is different. Acidic amino acids, such as aspartic acid, are separated by ion exclusion mode and elute faster. Neutral substances are separated by reversed phase and alkaline amino acids are separated by a mixture of reversed phase (in case of hydrophobic structure) and ion exchange mode. Therefore, amino acids basically elute in the following order: first the acidic amino acids, second the neutral amino acids and finally the alkaline amino acids.

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