There are two ways a mass spectrometer can be used. It can be used to look for all the ion fragments of a single molecule, or it can be used to look for only a few specific ions that the user has specifically targeted.
Full scan:
Electron ionization creates a great deal of mass spectral information. If the operator selects a range of ions to be analyzed (say from m/z 35 to m/z 450), we call this a full scan analysis. Although the interpretation of such an analysis is outside the scope of this course, a full scan analysis can be used to identify an unknown molecule and determine the molecular weight of the molecule. This method is used commonly in analytical chemistry settings to identify unknown molecules. A full scan can be done to help identify a molecule without needing to know specifically what you're looking for.
Selected ion monitoring (SIM)
A SIM method is a method to look for (or confirm) the presence or absence of a specific molecule that one is interested in. SIM is used when you know what you are looking for. In contrast to full scan analysis, where a range of ions is scanned, in SIM, only 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 are 45, 73, 75, 146, 196, 220, 234, 236, 401, 414, and 429. Labs can use these specific ions to qualify (prove) the identity of the molecule. Labs will establish rules that specific ratios of ions be detected in order to positively identify a compound. A well-designed SIM method will be able to positively identify the presence of a compound with a specificity of greater than 99.999%. This is far superior to the specificity achieved with an immunoassay. Multiple reaction monitoring (MRM) is even more common than SIM and is discussed later.
