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From Chemistry LibreTexts — 4.11: Mass Spectrometry:

Limitations of MS generally stem from compounds that are not easily ionizable, or which decompose upon ionization. Geometric isomers can generally be distinguished easily, but differences in chirality are not easily resolved. Complications can also arise from samples which are not easily dissolved in common solvents.

Does anyone have any examples of such compounds (either of both emphasized qualities)? I think possible compounds that are difficult to ionise are those with many valence electrons since it is more energetically favourable to attract, rather than to donate electrons, like chlorine.

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    $\begingroup$ Any large molecule. $\endgroup$ Apr 22 at 10:42
  • $\begingroup$ The statement quoted is a bit narrow. A technique like MALDI used e.g., to characterize proteins and peptides typically is set up to be very gentle (even more than CI/chemical ionization, which already is considerably softer than hard electron ionization EI). And since MALDI-MS (often MALDI-TOF MS) desorbs molecules out of a solid matrix, solubility of an analyte in a liquid solvent is a lesser problem, than a MS used as a detector at the exit of a GC or LC. $\endgroup$
    – Buttonwood
    Apr 22 at 12:56

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In a sense, everything you put into a mass spectrometer decomposes; the (mass/charge ratio of the) fragments arecactually valuable in distinguishing different isomers.

That being so, extensive decomposition can conceal the full molecular weight of a compound and thus make it hard to distinguish from simpler molecules. A good example is provided by 2,2,3,3-tetramethylbutane, $\ce{(CH3)3C — C(CH3)3}$. The central carbon-carbon bond breaks easily leading to formation of (two copies of) the very stable tert-butyl cation, so that the apparent base peak shows only half the true molecular weight (really, only half the true molecule).

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