Full scan
Electron ionization creates a great deal of mass spectral information due to the high energy fragmentation produced. If the operator selects a range of ions to be analyzed (say from m/z 35 to m/z 450), we call this full scan analysis. The molecular ion in a full scan analysis will be the highest m/z in the spectrum besides isotope ions. It will probably be of low intensity, or it may not be visible at all because of the high energy fragmentation that leaves only a small amount of molecular ion. The fragmented ions can be viewed in the mass spectrum as a pattern of high intensity m/z ions. The analytes can be identified based on their fragmentation patterns and the identity of the molecular ion, if detected.
Selected ion monitoring (SIM)
SIM is the most common method for quantitation of analytes by GC/MS. In contrast to full scan analysis where a range of ions are scanned, in SIM, specific ions are selected to be scanned. These are usually the most intense ions in the full scan mass spectrum of the analyte. For example, the most intense ions in the full scan mass spectrum of morphine that was derivatized with MSTFA is 45, 73, 75, 146, 196, 220, 234, 236, 401, 414, and 429. It is preferable not to use lower m/z ions because there is more of a probability that they will be mases that are common to other compounds. M/z 429, 414, and 401 would be good choices. M/z 429, the most intense ion of the three, would be a good choice to use as the quantitative ion and 414 and 401 as qualifier ions in SIM mode.
SIM mode gives much better sensitivity over scan mode because the analyzer can spend more time scanning the ions of interest, rather than scanning background ions and other interfering ions.
