Here is situation: Compound is run on GCMS give a mass spectrum. Old standards are used from a library. The identification is made by observing with eye that the two OVERALL patterns are SImiliar. No comparison of ion fragment intensities are used. My position is that the scientific protocols require the comparison of ion fragment ratios and that small and large fragment ions are equally informative. Am I right or wrong on this? The time to maximum peak height is not used for comparison of known and unknown samples but are necessarily consistent with the library standard, if that is known. Sometimes only the library standard mass spectra are compared. Base Peaks mass may vary between Known and Unknown spectra.
Correction: the TIC times to maximum peak heights may be different if known for standard sample run. But in any case they are ignored in identification.
You are right. The comparison of ion fragment ratios and that small and large fragment ions are both informative.
However, the mass spectra of compounds on GC-MS are very dependent on experimental conditions. For example, the ionization voltage, at highionization voltage, it is often difficult to get the maximum mass (the molecule it self) especially if this substance is easily decomposed.
For example, at such conditions, the dimer and monomer are hard to distinguish because the distribution of small fragments are very similar. But, if you lower the voltage, you may distinguish dimer and monomer by the maximum mass peak.
So, if the GC-MS conditions are different, it is possible there would be some differences from data from a library.
You may compare your compound with the standard compound in a same equipment with the same conditions. You can try other auxiliary means such as NMR, FTIR at the same time or properties like boiling/melting point.
I am not doing the comparisons. I am reviewing work done by others and I am seeing more and more comparisons being made ONLY on the overall comparison of the mass spectra, while totally ignoring quality of match (which is not done), the use of library standards run of unknown instruments or dated over 6 months before the analysis being done on the same instruments that have been retuned many times between the two runs, and ignoring the fragment ratios. I was looking for any consensus of opinions and if any one had an opinion different from mine on the lack of quality of those analyses. Thank you for your replies.
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