GC/MS data gets used in a number of ways. For some it is simply a fancy multichanel detector and as long as ion ratios are correct, the operator takes the area and quantifies the chroamtographic peak. For others it is about identifying unknowns. NIST has a program that is available for free form their web site that will deconvolute GC/MS chromatograms. For the more complex chromatograms, something like this can be helpful - but beware. While a deconvolution routine unscambles spectra, the noise goes somewhere - like into the spectra. So be a bit careful if you are depending on the spectrum for M+1 and M+2 ratios.
Interpretation for a very large number of people is a matter of making library searches. While this is helpful, undersand that the search result is a mathematical calculation and may return a result that is in no way related to the compund that you are trying to analyze. There are many spectra that look quite similar to each other - but the compunds are not. There are some simple rules that help you to stay out of trouble - like if there is a major ion shoing in the library spectrum but not in the unknown, it is NOT a good match.
Another problem with library searches is that there are many compunds that are not in the libraries. If you have one of these in your sample, you will not get a good match - but often you will be provided with a library hit, and sometimes even a pretty good match score.
Be sure that you have a way of confirming an ID before you tell others what you found. It is a lot easier to purchase a bottle of something than it is to go down the hall and make sure that everybody who heard from somebody else that you really found something different.
Some knowledge of chemistry - typically organic for GC/MS and some study in one of the good texts in MS is a good idea if you will be trying to identify unknowns. Examination of the molecuar ion can tell you alot. Ion ratios give away some information on elemental composition. For an easy example, chlorinated and brominated compunds have very distinctive molecuar ions.
Understand chromatgraphy. Sometimes you can eliminate suggestions from the library hit list because they do not make sense in th eorder of peaks in the chromatogram.
Do I use statistics? The library search uses simle statisitcs. I use chemistry to pick through the results.
Remeber, if it only took software to do chemical analysis, we would be part of the IT department by now.
