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Isotope Pattern Calculator (Mass Spectrometry)
In short: Isotope pattern calculator for mass spectrometry: enter a molecular formula or SMILES and an ion type to get every isotope peak with m/z and relative intensity, the monoisotopic, average and nominal mass, a centroid or profile plot, M+1 and M+2 rules of thumb, and a comparison with your observed peaks. It is free, works in your web browser and needs no download.
The pattern is computed exactly from natural isotope abundances of every element, including Cl, Br, S, Si and metals such as Fe, Cu, Zn, Se, Sn, Pt, Ru, Pd, Ag and Hg. Charges and adducts include the electron mass.
Examples
Compare with an observed spectrum
Peak list
How to use the isotope pattern calculator
- Type a Molecular formula such as
C6H5Br,Pt(NH3)2Cl2orCuSO4·5H2O, or switch Input type to SMILES. Use correct capitals (Cl, not CL). - Pick the Ion type: M+• for electron ionisation, [M+H]⁺ or [M+Na]⁺ for positive electrospray, [M−H]⁻ for negative mode. For a charged complex such as
[Pt(NH3)4]2+, choose Ion as written. - Read the monoisotopic, average and nominal mass, then the peak list with m/z, relative intensity and % of M.
- Choose Profile and a Resolving power to see how peaks merge or split on your instrument.
- Open Compare with an observed spectrum and paste your peaks to check the match. Save with Download SVG, Download PNG or Download CSV.
How the isotope pattern is calculated
Most elements have more than one stable isotope. Carbon is 98.93% ¹²C and 1.07% ¹³C; chlorine is 75.76% ³⁵Cl and 24.24% ³⁷Cl. A molecule therefore appears in a mass spectrum as a cluster of peaks: the isotope pattern.
For one element with isotope abundances a and b, n atoms give the terms of (a + b)ⁿ. For a whole formula, the patterns of all elements are multiplied together. This is a polynomial convolution. The calculator does it exactly, with every isotope of every element, and drops only terms below 10⁻¹² of the largest peak.
Cl₂: (0.7576 + 0.2424)² = 0.574 (M) + 0.367 (M+2) + 0.059 (M+4) → 100 : 64 : 10
Three different masses
- Monoisotopic mass: uses the most abundant isotope of each element (¹²C, ¹H, ¹⁴N, ¹⁶O, ³⁵Cl, ⁷⁹Br, ⁵⁶Fe, ¹⁹⁵Pt). Caffeine C₈H₁₀N₄O₂ = 194.0804.
- Average mass: uses standard atomic weights, as in molar mass. Caffeine = 194.19 g/mol.
- Nominal mass: the integer mass from the most abundant isotopes. Caffeine = 194.
For ions, the mass of the electrons removed or added (0.000549 Da each) is included, and m/z is the mass divided by |z|. A profile spectrum draws each isotope peak with a width FWHM = m/R, where R is the resolving power.
Rules of thumb for M+1 and M+2
| Isotope | Effect | Quick rule |
|---|---|---|
| ¹³C (1.07%) | M+1 | about 1.1% of M per carbon atom: C₁₀ gives M+1 ≈ 11% |
| ¹⁵N (0.36%) | M+1 | about 0.37% per nitrogen |
| ¹⁸O (0.20%) | M+2 | about 0.2% per oxygen |
| ³⁴S (4.25%) | M+2 | about 4.4% per sulfur |
| ²⁹Si, ³⁰Si | M+1, M+2 | about 5.1% and 3.4% per silicon |
| ³⁷Cl (24.24%) | M+2 | M : M+2 ≈ 3 : 1 for one Cl |
| ⁸¹Br (49.31%) | M+2 | M : M+2 ≈ 1 : 1 for one Br |
Chlorine and bromine clusters
| Halogens | M : M+2 : M+4 : M+6 |
|---|---|
| Cl | 100 : 32 |
| Cl₂ | 100 : 64 : 10 |
| Cl₃ | 100 : 96 : 31 : 3 |
| Cl₄ | 78 : 100 : 48 : 10 : 1 |
| Br | 100 : 97 |
| Br₂ | 51 : 100 : 49 |
| Br₃ | 34 : 100 : 97 : 32 |
| ClBr | 77 : 100 : 24 |
Worked examples
CH₂Cl₂ (two chlorines)
Ions at m/z 84, 86 and 88 from ³⁵Cl₂, ³⁵Cl³⁷Cl and ³⁷Cl₂.
0.7576² : 2 × 0.7576 × 0.2424 : 0.2424²
M : M+2 : M+4 = 100 : 64 : 10
Bromobenzene C₆H₅Br
⁷⁹Br and ⁸¹Br are almost equal: 50.69% and 49.31%.
M (m/z 156) and M+2 (m/z 158) also carry a ¹³C share.
M : M+2 = 100 : 97.5, M+1 = 6.5%
CHBr₃ (bromoform)
Three Br atoms give the (1 + 1)³ pattern.
Peaks at m/z 250, 252, 254 and 256.
34 : 100 : 97 : 32 (close to 1 : 3 : 3 : 1)
C₆₀ (buckminsterfullerene)
60 carbons: M+1 ≈ 60 × 1.08% of M.
Monoisotopic mass is exactly 720.0000 (¹²C defines the mass unit).
M : M+1 : M+2 = 100 : 65 : 21
Caffeine in positive ESI
C₈H₁₀N₄O₂ + H⁺ = C₈H₁₁N₄O₂⁺.
194.0804 + 1.00728 (proton) = 195.0877.
[M+H]⁺ m/z 195.0877, M+1 = 10.3%
Vancomycin [M+H]⁺
C₆₆H₇₅Cl₂N₉O₂₄: 66 carbons and 2 chlorines.
¹³C makes M+1 ≈ 77%, and two Cl make M+2 almost as tall as M.
m/z 1448.4375; M : M+1 : M+2 = 100 : 77 : 98
Cisplatin Pt(NH₃)₂Cl₂
Platinum has ¹⁹⁴Pt 32.9%, ¹⁹⁵Pt 33.8%, ¹⁹⁶Pt 25.2% and ¹⁹⁸Pt 7.4%, mixed with the Cl₂ pattern.
Broad cluster from m/z 296 to 306, tallest at 300
Common mistakes
- Mixing monoisotopic and average mass. High-resolution MS measures the monoisotopic m/z; molar mass uses average atomic weights.
- Expecting the monoisotopic peak to be the tallest. Above roughly 90 carbons, or with Br, Pt, Sn or Hg, the most intense peak is often M+1, M+2 or higher.
- Forgetting the adduct. In electrospray you rarely see M itself: look for [M+H]⁺ (+1.00728), [M+Na]⁺ (+22.98922) or [M−H]⁻.
- Reading M+2 as two ¹³C atoms only. A tall M+2 (over 30% of M) points to Cl, Br or S rather than carbon.
- Ignoring the charge state. For a 2+ ion the isotope peaks are 0.5 m/z apart, not 1.
- Wrong capitals. CO is carbon monoxide; Co is cobalt. Write Cl, Br and Si with a lower-case second letter.
Need the structure behind the formula? Draw a molecule in MolDraw, a free online chemical structure editor, and copy its formula or SMILES into the calculator.
Open MolDraw editorFrequently asked questions
What is the M+2 peak and what causes it?
The M+2 peak is 2 mass units above the monoisotopic ion. Large M+2 peaks come from ³⁷Cl (about one third of M per Cl), ⁸¹Br (about equal to M per Br) and ³⁴S (about 4.4% per S). Small M+2 peaks come from two ¹³C atoms or ¹⁸O.
Why does CH₂Cl₂ show peaks in a 100 : 64 : 10 ratio?
Each chlorine is ³⁵Cl (75.76%) or ³⁷Cl (24.24%). For two chlorines the ratio is 0.7576² : 2 × 0.7576 × 0.2424 : 0.2424², which is 100 : 64 : 10 for M, M+2 and M+4.
How do I estimate the number of carbons from the M+1 peak?
Divide the M+1 intensity (as % of M) by 1.1. An M+1 of 11% suggests about 10 carbons. Nitrogen adds about 0.37% per atom, so the estimate is rough for N-rich molecules.
What is the difference between monoisotopic and average mass?
Monoisotopic mass uses the most abundant isotope of each element and is what high-resolution MS measures. Average mass uses standard atomic weights and is used for molar mass. For caffeine they are 194.0804 and 194.19.
Why is the monoisotopic peak not the tallest for large molecules?
Each carbon has a 1.07% chance of being ¹³C. With about 90 or more carbons the chance that a molecule contains at least one ¹³C exceeds the chance it contains none, so M+1 becomes the tallest peak.
How does resolution change the isotope pattern?
At low resolving power, peaks of the same nominal mass merge into one. At high resolving power (above about 50 000 near m/z 500), fine structure appears, for example ¹³C₂ and ³⁴S peaks at M+2 separate by about 0.011 Da.
Which isotope abundances does the calculator use?
It uses IUPAC representative isotopic abundances and atomic masses for all stable isotopes of each element, including the metals Fe, Cu, Zn, Se, Sn, Pt, Ru, Pd, Ag and Hg.
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