I have taken the GC-MS of methanolic extract of few plant samples. I need to compare the compounds abundance and concentration in same samples, prior to and after some processing. Can i justify the concentration based on abundance /intensity of peaks?
If you are just comparing the compound abundance then use area normalization procedure rather than peak intensity. For determining the exact concentration you have to take into consideration that MS is using high energy i.e. 70 eV at which you will not observe any molecular ion but fragment ion.
You can go for GC Fid for this purpose and identify the desirable compound's retention time before and after the treatment.Form the Fid Peak area (before and after the treatment) and using of internal standard you can quantify the amount of the compound .
Mole % does not denote the exact concentration it denotes only % of the total moles
To quantify properly each compound you need to calibrate any instrumental analysis using standards at known concentration of the compound you want to quantify to obtain the "response farctor". That is (area standard/amount of compound)/(area compound/amount of standard). This generally works also if you use heights instead of areas. In complex mixture like methabolic extracts from plants probably this approach is very difficult to apply then you could use % heigth or % area just to see the differences before and after the process not pretending to compare real concentrations.
Regards,
Micaela
I have hard copy of GC results, How can I calculate peak area % and concentration of a peak. can anybody help me
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