It seems like you should be able to separate them chromatographically, and then it won't matter whether their fragmentation patterns are similar or not, you just have to match up the retention times. Here's a different derivatization method (methanol and trifluoroacetic acid) for them that has been shown to work, too: http://www.pnas.org/content/90/16/7749.full.pdf

Thanks a lot for the reference....I haven't tried this derivative for citrulline before.

Are you using GC-MS because it is what you have available? This is a tailor-made LC-MS application.