[stunt3r]

I am separating some plant extracts using HPLC and GC/MS. I can always observe a particular peak on GC/MS and figured out what compound it is from a library and ms data. I use standards to confirm the identity as well. but I cannot see a such compound in the same sample on HPLC chromatorams. Assuming that the reason for the originating compound decomposes on the GC/MS, is there any way to determine the parent molecule using the GC/MS??

[Arkcon]

Interesting question.  You can start with providing us with the identity of your compounds, and some specifics of your analytical methods.  Briefly, you might want to try less aggressive GC methods.  Or maybe there's another reason it doesn't show up onLC -- maybe that method is too harsh for the compound.

[Prim]

This could be a detector issue. A GC and an LC use different detectors. Detectors are compound specific, if you have a compound without a chromophore you are unlikey to detect it using a UV detector (most HPLC)

What detectors are you employing on the HPLC system? I can see you are using mass spec for the GC. 

[stunt3r]

we tried both diode array and RI detectors. I don't think its a  detector issue because we do see the standard on LC

[WW]

IF you see the standard on the HPLC, it is likely a detection limit issue.  GC/MS will have much higher sensitivity than a UV technique with HPLC.  HPLC can have high background because solvent is constantly flowing through the detector, especially with a solvent like methanol.  in GC the solvent is blown away generally quickly and background is lower.  Also in general MS is just more sensitive