The horizontal axis of a mass spectrum usually reports mass-to-charge ratio, written m/z. For peptide ions, that number can be much smaller than the neutral molecule's mass because the ion may carry several charges. Reading the axis correctly requires both the charge assignment and the composition of the ion being measured.
Read z as a charge number
IUPAC uses m/z as the conventional mass-spectrometric notation and distinguishes charge number from electric charge expressed in coulombs. In routine peptide interpretation, z tells you how many elementary charges the assigned ion carries. It is not a concentration, residue count or number of peptide molecules.IUPAC Gold Book — Mass-to-charge ratio (opens in a new tab)
For a positive ion written [M+2H]2+, M represents one neutral molecule and two added protons account for the double positive charge in this model. The 2 before H and the 2+ outside the brackets describe different parts of the same assignment: added species and resulting charge.
| Notation | Meaning in this model |
|---|---|
| M | The neutral molecular species being considered |
| [M+H]+ | One molecule with one added proton |
| [M+2H]2+ | One molecule with two added protons |
| [M+3H]3+ | One molecule with three added protons |
Include the added protons before dividing
For an ion formed only by adding z protons, its numerical m/z is (M + z × h) / z when M and the proton mass h are expressed in daltons. Here h is rounded to 1.007276 Da from NIST's constants. This relationship assumes the stated protonated ion, rather than a sodium adduct or a molecular cluster.NIST — 2022 CODATA constants (opens in a new tab)
Use an invented neutral mass of 1,200.000000 Da. The doubly protonated ion gives (1,200.000000 + 2 × 1.007276) / 2 = 601.007276. Simply dividing 1,200 by two gives 600 and leaves out the charge-carrying protons.
The same hypothetical neutral mass would give 1,201.007276 for [M+H]+ and 401.007276 for [M+3H]3+. These are calculated positions, not a claim that all three ions will be observed or have comparable intensities in a real experiment.
Reverse the calculation only after assigning charge
Rearranging the proton-only relationship gives M = z × (m/z − h). Applying z = 2 to 601.007276 returns 1,200.000000 Da. Applying z = 1 would instead return 600.000000 Da. The arithmetic cannot decide which charge assignment is correct without additional spectral evidence.
This is why a peak label must travel with its assigned ion. A spreadsheet column headed observed mass can be ambiguous if some entries are m/z values and others are reconstructed neutral masses. Clarify the quantity before calculating a difference or declaring an identity mismatch.
Compare like quantities at the final step
After accounting for charge, check whether the reference specifies monoisotopic or average mass and whether the terminal groups and modifications match. Correct charge arithmetic does not repair a comparison between different molecular definitions.
For the hypothetical 1,200 Da example, agreement of the assigned ion with its predicted position supports that mass relationship. It does not determine sequence order, distinguish all isomers or measure how many milligrams were in the original vial. Those require other evidence.
- Read m/z separately from neutral mass.
- Record ion composition and charge.
- Include the added or removed species in the calculation.
- Compare equivalent mass conventions and chemical forms.
Sources and further detail
- IUPAC Gold Book — Mass-to-charge ratio (opens in a new tab)
Terminology M03752. Used for conventional m/z and charge-number notation, not as a requirement to round accurate peptide masses to integers.
- NIST — 2022 CODATA constants (opens in a new tab)
Proton mass in unified atomic mass units. Examples round it to 1.007276 Da or 1.0073 Da as stated; exact ion assignments require the appropriate mass convention.
Sources checked 19 September 2026. Worked examples are illustrative unless a supplied report is explicitly identified. This article has not undergone independent scientific peer review.