What are you analyzing?

What kind of derivatization and why?

What do you mean by "completely different"?

RTs are obviously different (FID=atm. press., MS=vacuum), GC basics...

Columns of the same type??? 

"Different use" of the columns?

Please study some GC(MS) fundamentals, give us some real info and you'll get real answers...

The cause is that the physical principles of action of FID and MS are totally different. The FID measures the currant in a flame which is based on the ions of the burning organic compounds. The chromatogram of the MS (I think you mean the TIC) is based on the intensity of fragments produced by the ionization. There are some compounds which give a low fragmentation in MS but high signals in FID (e. g. aromatic rings). To compare FID and MS chromatograms you should use some authentic references measured with both detectors.

Because the source is different between these methods

Thank you very much for your answers. 

In any case same columns means that I use two HP-5MS but sinceGC-MS is more utilized and therefore the column is shorter, I was expecting different retention time.

Furthermore, since the detector is different, I also expected different intensity of the peaks. But I could not understand why the profiles of the chromatograms were so different. Indeed, if I just inject 3 simple monoaromatic molecules in a mixture. I can see 3 peaks in both the chromatograms. But as soon as I inject a more complex mixture derived from lignin, the situation change drastically.

This is normal i) because of the different detection principles (see my first answer) and ii) because of possible chromatographic effects. Which carrier gas do you use? Helium for both detectors? We are using always hydrogen for FID and helium for MS. The differences in chromatographic separation are dramatic.

When you say "The same sample (after derivatization) ....", do you mean that you took one sample, derivatized it and then injected the same product on both instruments, or that you took one portion of a sample, derivatized it and analyzed by FID then took another portion of the same sample and derivatized for GC-MS. ?

If you did two derivatizations than the most likely explanation for markedly different chromatograms is that something went wrong with one derivatization.  The most straightforward diagnostic for this is to run the derivatives on the intruments they were not run on before.

Thank you very much for the answers.

We use Helium as carrier-gas for both the GC and I tried to inject the solution in the same vial just shifting it from one to another GC.

Hi Micaela

Check on the labels on the columns, do not rely of what people tell you or have written in log books, they might be different stationary phases.

You say that with a 3-component standard the chromatograms are the same. Are all the peaks in this standard about the same size as one another on each instrument ? If they are you do not know which peak is which on the FID and you could have a change in peak elution order that is not detectable, and this will certainly make chromatograms form samples look completely different. Run the three components one or two at a time, or spike the mix with more of one of the components so that you can tell the difference between the peaks on the FID.

What is the phase thickness, column internal diameter and column length in each instrument ?

It is clear that every aromatic compound have only one retention time. So it obviously the reason is the detectors. Is this standard sample or just sample? I think to have full overview you should try 2 samples one for standard and one for solvent alone and inject it and see the choromatogramm 

Regards

I'm not sure about how can you have totally different chromatograms from similar column and method. If you injecting same sample on GC-FID and GC-MS (full scan mode) assuming all method parameters are the same except column length, you should get similar pattern of peak separation. In addition, you'll get mass spectra from MS data that you can use to identify your sample. Please check your MS operation mode if you have missing peaks or low response. Make sure that you run in full scan mode and put appropriate scan mass range for your target compounds i.e. 35-350 for VOCs.

The difference is as a result of column difference.

An FID, or Flame Ionization Detector, is the most common detector paired with gas chromatography instruments for analytical applications.

But how does an FID work?

An FID uses a flame to ionize organic compounds containing carbon. Following

separation of the sample in the GC column, each analyte passes through a flame, fueled by hydrogen and zero air, which ionizes the carbon atoms.

Once formed, the ions are collected and measured as they create a current at the detector’s electrodes. The current is produced as the detector collects the charged ions. The current is then converted to an electrical signal in picoamperes (pA) or millivolts (mV).

however GC works on the principle that a mixture will separate into individual substances when heated. The heated gases are carried through a column with an inert gas (such as helium). As the separated substances emerge from the column opening, they flow into the MS. there in MS compound breaks into parts, and the parts will be separated by weight and charge then you can compare this spectrum with a bank of spectra to find compound