Seeni,
As far as picking a method: First look to see if the target market requires a particular method. Or at least what detection limits are required. You may be able to use the method of your choice as long as you can prove performance - and if you use a published standard method, you will still need to prove performance. If you are trying to become an accredited lab, it involves much more work that selecting a method.
In your question about showing all ten compounds in the GC-MS chromatogram. Your instrument should have some kind of reporting software built in. While you can do things like a display of specific ion traces along a chromatogram, pesticides may be the small peaks between all the other stuff extracted from food. You may want to consider a display of the traces of ions used to quantitate and confirm each compound (analytes and internal standards). This type of report should be part of the standard reporting software.
You describe that you use the base peak for identifying each compound -- which, depending on the compounds and the matrix, may be OK. Some pesticides show a base peak that is common to a number of other compounds that will coelute. And these will show up as interferences at the part per million or part per billion levels. Your chromatographic software should provide some kind of automatic peak identification that will use retention time and multiple characteristic ions to help locate analytes for you. In pesticides containing chlorine or bromine, some of the higher mass ions are not as strong as the base peak, but provide much cleaner signals, since all the other stuff eluting at that point in the chromatogram is lower molecular weight, and will give much lower limits of detection. And, in some types of samples, because of coelution of interfering compounds, there may be a peak present for an ion at the base peak, but there is nothing present for the higher weight ions.
Don
