[Poria]

Hello,

I'm doing an study about the chemical composition of birch tree at different temp and holdup-time with MS/GC, FID, TCD.
Unfortunately my background is not chemical engineering but closer to mechanical.
Now i have a problem with duplicates and even triplicates compounds found at different retention time in the same experiment when i analyze the resulting chromatogram.
What i do is to pyrolyse the sample with an pyrolysis unit (Pyrola 2000)  and the pyrolysis gas is then fed to all three detectors simultaneously in the GC.
I use a capillary GC column Length= 30m  I:D= 0.25mm  Film thickness= 0,25µm
When I’m then transfer the peaks >2% from the Chromatogram to Excel i find  duplicate and triplicate molecules in both MS and FID at different retention time with different area% and probability%. Sometimes this are just next to each other in the Chromatogram and sometimes there are other compounds in between them. At some extreme cases I will find one at 5.xx min and the duplicate At 20.xx min.
I use NIST MS search 2.0 library and Thermo Xcalibur qual browser.
I suspect that there might be some contamination in the the system that causes this problem.
From what i understand this should not be happening and I have no idea how to tackle this problem.
An example from an FID reading in the attachment.

i would really appreciate some help. Sorry for the bad spelling and  language I'm from Sweden

[DrCMS]

I'm not sure I understand what your problem is but I think it is because you do not understand what you are actually doing.

You take a sample of birch, pyrolyse it and inject the resulting mixture into a GC that has three different detectors.

The FID and TCD detectors will only tell you something is exiting from the column they can not tell you what it is.
If you or previous experimenters have injected standards and built up a retention time library then the software can tell you if the sample peak has a retention time similar to a particular standard but that does not mean it is the same material.

The MS can compare the fragmentation of a peak to a library of standards and give you the best match but that is only the best match to the library you are using and the lower the probability the less likely is is that that is what the sample actually is. 

Obviously a single compound can not elute at two different times but as the software is taking best guesses, that I think are nowhere close to reality, that is why the same name come up for different peaks at different times.

In your data the matches are all less than 35% so I'd say there is very little chance that any of them are what the software is assigning.

[Poria]

Thank you for your answer,
I do understand how the FID and TCD work and that the software is only guessing by comparing the fragments detected by the MS but my question is can a substance come at 2 different r-times at all? Is this even possible?
And if this is what is getting how can i put the results in a report where i have to show the abundance of a substance as a function of time and temp?
I don't think is as easy just to put the area of the duplicates or the triplicates together and interpolate a new probability.
I have search to see if there is any other reports that tackle this issue but haven't found any. 
Unfortunately the probabilities i get from the most of the substance are very low. I think this is because of the material I'm using (Birch saw dust).
Any suggestions?
   

[curiouscat]

I do understand how the FID and TCD work and that the software is only guessing by comparing the fragments detected by the MS but my question is can a substance come at 2 different r-times at all? Is this even possible?

Those are not the same substance. Your library is mistakenly reporting that they are.

[DrCMS]

my question is can a substance come at 2 different r-times at all? Is this even possible?

No it is not which I what I already told you in my first answer.

Unfortunately the probabilities i get from the most of the substance are very low. I think this is because of the material I'm using (Birch saw dust).

The low probabilities have NOTHING to do with the quality of the material you are using.  It could be you are getting very poor chromatography and are not cleanly separating all the materials from each other so that a single peak is actually made up of multiple compounds or it could be that the library you are checking against does not contain any of the materials you are producing from the samples or that the MS is not working properly.

I do understand how the FID and TCD work

I'm not sure you do because your other statements/questions make no sense if you did.

And if this is what is getting how can i put the results in a report where i have to show the abundance of a substance as a function of time and temp?
I don't think is as easy just to put the area of the duplicates or the triplicates together and interpolate a new probability.

This last line shows you really do not understand what I have been trying to tell you at all.


You can not just blindly take the answers from this machine and assume they are correct.  As I have said before I very much doubt that ANY of the results you have so far are anywhere close to reality. 

Try buying some of the compounds the machine had assigned and inject them individually and see if it gives >90% assignments, if not the MS is not working properly.
Next try mixing them together and injecting the resulting mixture you should get as many individual peaks as materials you mixed and each should give >90% assignments, if not the GC is not working properly.

[WW]

I agree with DrCMS on this one.

My experience with this software is a 35% match means nothing.  And these are the matches you are likely to find with pyrolysis of a sample such as plant tissue.  Certainly not a clean technique!  there may be many smaller coeluting compounds with the major peaks that cause these bad matches.  even if you had a 95% match, do not blindly trust the software!!!!