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I'm trying to get a better understanding of how mass spectrometry works, and how to read the results. I feel that I currently have a good grasp of how the process works, and now I'm looking at data collected from mass spectrometry (EI specifically) and trying to understand how to identify molecules from those results. What I noticed is that examples online tended to not display the amount of hydrogen hitting the detector. For an example in this case, I'm using results from the NIST data base for methane but I've had similar questions with other molecules. (https://webbook.nist.gov/cgi/cbook.cgi?ID=C74828&Mask=200)

Why are there no peaks shown for the hydrogen atoms being knocked free from the methane or other molecules that I've looked at? Is it just not displayed by the NIST graph? Do the hydrogen atoms that get knocked pick up an electron to become neutral, and hence fly right through? What's going on?

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It is due to two factors mainly though there are others influencing -

  1. Hydrogen atoms (mass:1 amu) have a very low mass-to-charge ratio. In many cases, mass spectrometer may not be optimized to detect such small m/z values effectively, or these values may be less distinguishable from noise.

  2. The ionization efficiency for hydrogen atoms or very small fragments can be relatively low. This means that even if hydrogen atoms are formed, they might not be efficiently ionized

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    $\begingroup$ Concerning the ionization step, it may be helpful to consider the ionization energy of hydrogen compared to the other radicals. To ionize hydrogen you would need high kinetic energy electrons, and these would likely generate larger molecular fragmentation or secondary ionization that would alter the mass-spectrum. $\endgroup$
    – PAEP
    Commented Aug 2 at 16:42

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