by
JMcK » Fri Jan 18, 2013 9:16 pm
Since no one else has responded, I'll take a stab at this.
1) In LC/MS, the effluent from the LC is ionized, and the ions are directed into a mass spectrometer. The spectrometer generally records all ions within the set range. You can collect all ions within the working range and plot the total ion chromatograph (TIC). If the analyte that you are observing has a unique mass, you can get better resolution of that analyte by performing SIM, single ion monitoring, where you only monitor the specific ion.
You would use MS/MS if you need to confirm that the mass you are monitoring belongs to the analyte of interest. You could for instance monitor anisole at m/z 108. You would detect all ions at this m/z ratio, including other ions of other molecules such as benzyl alcohol, or fragments formed from degradation of larger molecules. You can perform MS/MS however. With the first mass separation, collect only m/z 108 ions. Then you would allow this ion to fragment and perform mass separation and look for a fragment with m/z 65 (C5H5+). That will give you further confirmation of the analyte's structure.
2)Some molecules form anions easier than cations, and vice versa. Sometimes you get more structural information using positive mode than negative mode, etc. Use the mode that is better suited for your analyte and your separation conditions.
