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I'm looking for info about what happens to chemical species after undergoing MS. As I understand the process:

  1. We have an high-energy electron beam to ionize our sample. This often leads to fragmentation, yielding things like radical species and cations. At this point, the neutral radicals don't get affected by the EM field and just sort of hang around until they're sucked out by the vacuum. What happens to these radicals after they're no longer in a vacuum environment? I would assume they react with something eventually, but this seems potentially dangerous (admittedly in small quantities, but still).
  2. The ionized species then go through to be detected and then my understanding is that they're vented out of the lab, presumably for safe disposal somehow. What exactly happens to these ionized species once they're out? Again, the species seem like they'd be quite reactive (depending on the particular sample). What happens to these ionized species after we're done analyzing them with the mass spec?

I'm sure it depends on the precise sample, but presumably (hopefully) the waste systems are setup for a wide variety of waste particles, so it would be helpful to have a general answer. Thanks!

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    $\begingroup$ Well, depending on the instrument, molecules you detect may be destroyed. In instruments that don't detect ring current, detection requires the ion of interest slamming into a hard surface and stimulating the emission of photons or electrons and detecting those resultant photons or electrons. But in most mass spec, the molecules you detect are a small fraction of the molecules that go into the ion source. $\endgroup$
    – Curt F.
    Jun 12, 2023 at 23:47
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    $\begingroup$ If you are doing MS on potentially toxic substances, you need to treat what comes out of the pump (e.g. use a burn box). And be careful changing your pump oil. $\endgroup$
    – Jon Custer
    Jun 13, 2023 at 12:37

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The good news is that there is no shortage of electrons in the world. Gas phase radicals at ambient pressure do not survive long (perhaps on the order of femto to nanoseconds), so there is no concern of free radicals leaking from a mass spectrometer into the environment. Also recall, that we are constantly bathed in cosmic rays as well, that can balance any random electron lost from air. Secondly, the actual amount injected in the MS is so small (nanograms/micrograms), that it is not a major issue of environment pollution as well.

There are so many times of MS and ionization strategies but your query indicates standard electron impact MS. It is true that waste from electrospray ionization sources (liquids) is more serious and proper venting is needed (outside to open air).

In general waste from an MS instruments and vacuum pump exhaust should be vented outside the labs. The oil from vacuum pumps has to be replaced periodically to avoid build up of waste products. Finally, the internal components of MS do get dirty with time, and they have to be cleaned periodically by qualified engineers.

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