See IUPAC definition (1997) Since a mass spectrum x-axis represents a relationship between the ion mass and the number of elementary charges that a given ion carries it contains mass information that may be extracted by a knowledgeable mass spectrometrist. Once this is done many mass spectrometrists use dalton (Da) as the unit of mass in order to avoid the clumsy "atomic mass units".
In 1897 the mass-to-charge ratio of the electron was first measured by J. J. Thomson By doing this he showed that the electron, which was postulated before in order to explain electricity, was in fact a particle with a mass and a charge and that its mass-to-charge ratio was much smaller than the one for the hydrogen ion H+. In 1913 he measured the mass-to-charge ratio of ions with an instrument he called a parabola spectrograph Although this data was not represented as a modern mass spectrum, it was similar in meaning. Eventually there was a change to the notation as m/e giving way to the current standard of m/z.
Early in mass spectrometry research the resolution of mass spectrometers did not allow for accurate mass determination. Francis William Aston won the Nobel prize in Chemistry in 1922 "For his discovery, by means of his mass spectrograph, of isotopes, in a large number of non-radioactive elements, and for his enunciation of the Whole Number Rule." In which he stated that all atoms (including isotopes) follow a whole-number rule This implied that the masses of atoms were not on a scale but could be expressed as integers. (In fact multiply charged ions were rare, so for the most part the ratio was whole as well.) Today we know this to be not true; however for the most part the nomenclature convention has held while the whole-number rule has disappeared. There have been several suggestions (e.g. the unit thomson) to change the official mass spectrometry nomenclature to be more internally consistent and compatible with the broader scientific unit system and other standards (ISO 31, IUPAC green book, IUPAC red book).
On the detection side there are many factors that can also affect signal intensity in a non-proportional way. The size of the ion will affect the velocity of impact and with certain detectors the velocity is proportional to the signal output. In other detection systems, such as FTICR, the number of charges on the ion are more important to signal intensity. In Fourier transform ion cyclotron resonance and Orbitrap type mass spectrometers the signal intensity (Y-axis) is related to the amplitude of the free induction decay signal. This is fundamentally a power relationship (amplitude squared) but often computed as an [rms]. For decaying signals the rms is not equal to the average amplitude. Additionally the damping constant (decay rate of the signal in the fid) is not the same for all ions. In order to make conclusions about relative intensity a great deal of knowledge and care is required.
A common way to get more quantitative information out of a mass spectrum is to create a standard curve to compare the sample to. This requires knowing what is to be quantitated ahead of time, having a standard available and designing the experiment specifically for this purpose. A more advanced variation on this the use of an internal standard which behaves very similarly to the analyte. This is often an isotopically labeled version of the analyte. There are forms of mass spectrometry, such as accelerator mass spectrometry that are designed from the bottom up to be quantitative.
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