Mass spectrometry can reveal the mass of an entire molecule, not just its fragments. For this topic, the essential skill is identifying the molecular ion peak and using its $m/z$ value correctly.

The molecular ion

In a mass spectrometer, molecules are ionized so that positive ions can be detected. If a molecule loses one electron but does not break apart, it forms the molecular ion. This ion represents the whole molecule, so it is the peak that gives information about the mass of the complete molecule rather than the mass of a fragment.

The molecular ion is often written as M+. Because only an electron has been removed, the mass of the ion is almost the same as the mass of the original molecule. The lost electron has such a small mass that, at this level, it is ignored when interpreting the spectrum.

Mass spectrometers detect ions according to their $m/z$ values. For the molecular ion in typical A-Level questions, the charge is usually $+1$, so the $m/z$ value is numerically the same as the mass of that ion.

This is why the molecular ion is so useful.

Mass spectrum of hexane with key peaks annotated, including the molecular ion at $M^{+}=86$ and prominent fragment ions at lower $m/z$. The plot reinforces that, for a singly charged molecular ion, the molecular ion’s $m/z$ value equals the molecule’s relative molecular mass. Source

Once the correct M+ peak has been identified, its $m/z$ value can be used directly to find the molecule's relative molecular mass.

Using the M+ peak to find relative molecular mass

The relative molecular mass tells you how heavy a molecule is on the carbon-12 scale. In a mass spectrum, the M+ peak is the key signal because it comes from the unfragmented molecule. For a singly charged molecular ion, the numerical value of $m/z$ is the same as the value of $M_r$.

When reading a spectrum, do not assume that the tallest peak is the molecular ion.

Electron-impact mass spectrum of benzene from the NIST Chemistry WebBook, showing relative intensity versus $m/z$. The molecular ion peak for benzene appears at high $m/z$ (near 78), illustrating how $m/z$ for $M^{+}$ is used to infer molecular mass while other peaks correspond to fragments.

The tallest peak is the base peak, but it may be a fragment ion. Instead, focus on the peak that corresponds to the whole molecule and is usually found at a relatively high $m/z$ value.

How to identify the correct peak

• Look for a peak from the unfragmented molecule.

• Expect the M+ peak to appear at a higher $m/z$ than fragment peaks.

• Remember that fragment ions come from the molecule breaking apart, so they have smaller masses.

• Be aware that the molecular ion peak may be small if the molecule fragments easily.

• If several nearby peaks appear in the molecular ion region, think about isotopes before deciding which peak represents the main molecular ion.

A correct interpretation depends on linking the peak to the whole molecule, not just choosing the highest or tallest signal. Once the M+ peak has been identified, its $m/z$ value gives the relative molecular mass directly in the common case where the charge is $+1$.

Why fragment peaks do not give relative molecular mass

Many peaks in a mass spectrum come from fragment ions.

Fragmentation map for hexane showing formation of the molecular ion ($M^{+}$ at $m/z=86$) and several common fragment ions at lower $m/z$. The diagram emphasizes that the base peak can be a fragment (here at $m/z=57$) and therefore should not be used to determine $M_r$. Source

These are formed when the molecular ion breaks into smaller positive ions. Fragment peaks are valuable because they can provide structural clues, but they do not represent the complete molecule. Using a fragment peak to find $M_r$ would therefore give a value that is too low.

This distinction is central to exam questions on mass spectrometry. You must identify whether a peak comes from the whole molecule or from part of it. Only the molecular ion peak should be used to determine relative molecular mass.

Common mistakes to avoid

• Confusing the base peak with the molecular ion peak.

• Choosing the highest-intensity peak instead of the correct M+ peak.

• Using a fragment ion peak to calculate $M_r$.

• Forgetting that $m/z$ depends on charge as well as mass.

What the notation M+ tells you

The notation M+ is a reminder that the ion comes from the original molecule, represented by M, and carries a single positive charge. In most introductory mass spectra used at this level, this single charge is why the molecular ion peak can be read so directly. If the ion has charge $+1$, then the number shown on the spectrum is effectively the relative molecular mass of the molecule.

This makes the molecular ion peak one of the fastest ways to obtain basic information about an unknown molecular substance. Before using any value, however, always check that the peak really is the molecular ion and not a fragment or a nearby isotopic peak.