Tryptophan normally oxidize during the dryness of TFA in the conversion
flask. That's probably the reason you aren't seeing it. The two
unexpected peaks you see in the chromatogram are probably byproducts of
the tryptophan degradation. There are two things to do in order to solve
the problem: reduce the conversion flask dry-down time and/or add DTT to
the solvents, that prevents tryptophan degradation. I hope this help.
Good luck!
Abbracci,
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Ricardo Bastos Cunha
Centro Brasileiro de Sequenciamento de Proteinas - UnB
mailto:rbcunha@guarany.cpd.unb.br
http://www.unb.br/cbsp/CBSP.html
http://www.geocities.com/Athens/Acropolis/5221
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