What happens to the "leftover" Ions in the Mass Analyzer I am very intrigued by what happens to the ions which do not make it to the detector in mass spectrometers, do they just pile up? I have never seen anyone clean our quadrupole, is this done? or do they just stay there indefinitely? I am talking of a triple quadrupole detector in a GC instrument, which deals with very small quantities, but after thousands of injections there must be a considerable mass of analyte on the analyzer. Even more so considering that most ions which go through the quadrupole do not make it to the detector.
 Thanks.
Most would end up being sucked out though the vacuum pump with the other residual gases. I assume that a lot of them collide with the sides of the vacuum chamber and are neutralized before sublimating in the vacuum.

The quads can become contaminated and require cleaning after several years of heavy use. Because there are such small quantities at that stage of the process, it's not uncommon for an MS to reach the end of it's service life before the quads need to be cleaned.