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A mass spectrum is an intensity vs. mass-to-charge ratio plot representing a chemical analysis. Hence, the mass spectrum of a sample is a pattern representing the distribution of components (atoms or molecules) by mass (more correctly: mass-to-charge ratio) in a sample. It is usually acquired using an instrument called a mass spectrometer. Not all mass spectra are the same. For example some mass spectrometers break the analyte molecules into fragments; others observe the intact molecular masses with little fragmentation. A mass spectrum can represent many different types of information based on the type of mass spectrometer and the specific experiment applied; however, all plots of intensity vs. mass-to-charge are referred to as mass spectra.

X-axis: Mass-to-charge ratio

The x-axis of a mass spectrum is a mass-to-charge ratio. The mass-to-charge ratio is most often written as the IUPAC standard m/z to denote the quantity formed by dividing the mass of an ion by the unified atomic mass unit and by its charge number (regardless of sign).

For example, for the ion C₇H₇, ${\displaystyle m/z}$ = 45.5

See IUPAC MS Terms Second Draft. Since a mass spectrum x-axis represents the mass-to-charge ratio it contains mass information that may be extracted by a knowledgable 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".

Alternative x-axis notations

There are several alternatives to the standard m/z notation that appear in the literature. m/e appears in older historical literature. A label more consistent with the SI unit system is m/q where m is the symbol for mass and q the symbol for charge with the units u/e where u is the unit of mass in atomic mass units and e is the unit of charge in elementary charge units. This sometimes appears in units Da/e. It was also suggested to introduce a new unit thomson (Th) for the physical propery m/q, where 1 Th = 1 u/e. According to this convention, mass spectra x axis should be labled m/q (Th).

History of x-axis notation

In 1897 the mass-to-charge ratio ${\displaystyle m/e}$ 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 more physically meaningful mass-to-charge ratio with some early notation as m/e giving way to the current IUPAC 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 were quantized and could be expressed as integers. This may be an origin of the unitlessness of the ${\displaystyle m/z}$ representation of mass-to-charge since both mass and charge were quantized and could be expressed as unitless whole numbers. (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 ${\displaystyle m/z}$ to be more internally consistent and compatible with the broader scientific unit system and other standards (ISO 31, IUPAC green book, IUPAP red book). Currently there is an effort to redefine the standard for x-axis notation.

Y-axis: Signal Intensity

The y-axis of a mass spectrum represents signal intensity of the ions. When using counting detectors the intensity is often measured in counts per second (cps). When using analog detection electronics the intensity is typically measured in Volts. In most forms of mass spectrometry, the intensity of ion current measured by the spectrometer does not accurately represent relative abundance, but correlates loosely with it. Therefore it is common to label the y-axis with "arbitrary units".

Y-axis and relative abundance

Signal intensity may be dependent on many factors, especially the nature of the molecules being analyzed and how they ionize. The efficacy of ionization varies from molecule to molecule and from ion source to ion source. For example, in electrospray sources in positive ion mode a quatenary amine will ionize exceptionally well whereas a large hydrophobic alcohol will most likely not be seen no matter how concentrated. In an EI source these molecules will behave very differently. 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 order to make conclusions about relative intensity a great deal of knowledge and care is required. Additionally there may be factors that affect ion transmission disproportionally between ionization and detection.

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.

See also

• Mass spectrometry for more information on how a mass spectrum is acquired
• Quantities, Units and Symbols in Physical Chemistry (IUPAC green book)
• the Chapter 12: Mass Spectrometry in the IUPAC orange book
• Mass Spectrometry Terms Wiki
• IUPAC definition of mass-to-charge ratio

References

• Recommendations for nomenclature and symbolism for mass spectroscopy, International Journal of Mass Spectrometry and Ion Processes Volume 142, Issue 3 , 25 April 1995, Pages 209-240

• Cooks, R. G. and A. L. Rockwood (1991). "The 'Thomson'. A suggested unit for mass spectroscopists." Rapid Communications in Mass Spectrometry 5(2): 93.

• Spectroscopy
• Mass spectrometry