The analyzers can be run several different ways besides the normal full scan mode, especially scanning tandem mass spectrometers such as triple quadrupoles.

Two of the most common of these are selected ion monitoring and selective reaction monitoring. Selective reaction monitoring is done on a triple quadrupole only, but other analyzers can mimic these methods in post processing.   These methods set up the mass spectrometer to look for a particular compound.  These methods could be done for a couple of compounds during a single chromatography run and is particular useful for quantitation.

Two other methods of using the mass spectrometer are neutral loss and product ion scans. These methods are done on triple quadrupole mass spectrometer, but like selective reaction monitoring, it could be emulated in post processing.  These scans scan the mass spectra looking at the ions that either loses a particular neutral mass or form a particular product ion. These spectra show the ions formed from molecules that belong to a particular class of compounds.

Another very common method, especially in proteomics, is data dependent acquisition. This method takes a full scan, then a computer uses that scan to decide which ions to perform tandem mass spectrometry on based on rules determined by the operator.   This method can be done on any tandem mass spectrometers not just scanning tandem mass spectrometers.