I think you may be confusing liquid chromatography and gas chromatography, gas chromatography afaik can't distinguish between the left handed and the right handed form of a molecule but liquid chromatography mass spectrometry can (and that's not the most sensitive / efficient way to do it either).
One of the GC columns has a chiral stationary phase. Chromotography works whether the carrier fluid is a liquid or a gas. The real problem with gas chromotography is that amino acids have a low vapor pressure. They seem to be chemically functionalizing them to improve the volatility.
http://en.wikipedia.org/wiki/Chirality