What is a neutral loss in mass spectrometry?

A neutral loss is a small molecule or radical (H2O = 18.0106 Da, CO2 = 43.9898 Da, CH3• = 15.0235 Da) that leaves the ion during fragmentation and is not detected. The fragment ion appears at the parent m/z minus the loss. In ESI MS/MS, characteristic losses point to functional groups: −18 hydroxyl, −17 amine, −44 carboxylic acid, −46 formic acid, −80 sulfate, −98 phosphate, −162 hexose.

How do chlorine and bromine show up in a mass spectrum?

Chlorine is 75.76% 35Cl and 24.24% 37Cl, so one Cl gives an M+2 peak about one third (32%) of M. Bromine is 50.69% 79Br and 49.31% 81Br, so one Br gives M and M+2 of almost equal height. Two Cl give about 100:64:10 (M:M+2:M+4), two Br about 51:100:49, and one Cl plus one Br about 77:100:24. The table on this page lists the patterns for 1 to 3 halogens.

What is the nitrogen rule?

A molecule made of C, H, N, O, S, P, Si and halogens has an odd nominal mass only if it contains an odd number of nitrogen atoms. So an EI molecular ion at odd m/z (for example 59 for trimethylamine) has 1, 3, 5 … nitrogens, and an even M•+ has zero or an even number. For protonated molecules [M+H]+ the parity flips: an even m/z means an odd number of N.

How do I estimate the number of carbons from the M+1 peak?

Each carbon adds about 1.1% (13C abundance 1.07%) to the M+1 peak. Take the M+1 intensity as a percentage of M and divide by 1.1: an M+1 of 8.8% suggests about 8 carbons. Nitrogen (0.36% each) and sulfur (0.75% 33S) add a little; the formula panel computes the full envelope.

What is the difference between EI and ESI fragmentation?

EI (70 eV electron ionization) makes a radical cation M•+ that fragments extensively by alpha-cleavage, inductive cleavage and rearrangements such as the McLafferty rearrangement; radical losses (CH3•, C2H5•, Cl•) are common. ESI makes even-electron ions ([M+H]+, [M+Na]+, [M−H]−) that fragment in MS/MS mainly by losing stable neutral molecules (H2O, NH3, CO2, sugars). The tool hides radical losses in ESI mode.

How are adduct m/z values calculated?

From the neutral monoisotopic mass M: [M+H]+ = M + 1.007276, [M+NH4]+ = M + 18.033826, [M+Na]+ = M + 22.989221, [M−H]− = M − 1.007276 and M•+ = M − 0.000549. These include the mass of the electron removed or added, which matters at ppm accuracy. Example: sucrose C12H22O11, M = 342.1162, [M+Na]+ = 365.1054.

What ppm tolerance should I use for peak matching?

About 5 ppm for Orbitrap and modern Q-TOF data, 10–20 ppm for older TOF instruments, and 0.3–0.5 Da for unit-resolution quadrupole or ion-trap EI spectra. Mass error (ppm) = (observed − calculated) ÷ calculated × 10⁶.

Mass Spec Fragment Helper

Enter a parent m/z to list fragment ions for common neutral losses (H2O 18.0106, CO 27.9949, CO2 43.9898 …), paste observed peaks to match them, or enter a formula to get the exact mass, [M+H]+ / [M+Na]+ / [M−H]− m/z, rings plus double bonds, nitrogen rule and the M+1 / M+2 isotope pattern.

Parent Ion m/z

Precursor m/z (Da)

Ionization Mode

EI ESI

Loss Category

Min fragment m/z

Observed fragment peaks (optional)

Quick examples

Enter a parent m/z and click Calculate to see fragment ions.

Observed Peak Matches

Observed	Loss	Calculated	Error

Fragment Ions

Fragment m/z	Loss (Da)	Formula	Interpretation

All masses are monoisotopic. Fragments below the minimum m/z threshold are excluded.

Formula → exact mass & isotope pattern

Elements C H N O S P F Cl Br I Si Na K; parentheses allowed, e.g. C6H5(CH2)2Cl.

Molecular formula (neutral)

Monoisotopic mass
Nominal mass
Average MW
Rings + double bonds

Ion m/z click a row to use it as the parent

Isotope pattern (nominal)

Chlorine and Bromine Isotope Patterns

Relative heights, tallest peak = 100. Abundances: 35Cl 75.76%, 37Cl 24.24%, 79Br 50.69%, 81Br 49.31% (NIST).

Halogens	M	M+2	M+4	M+6
Cl	100.0	32.0	—	—
Cl₂	100.0	64.0	10.2	—
Cl₃	100.0	96.0	30.7	3.3
Br	100.0	97.3	—	—
Br₂	51.4	100.0	48.6	—
Br₃	34.3	100.0	97.3	31.5
ClBr	77.4	100.0	24.1	—
Cl₂Br	62.0	100.0	44.9	6.2
ClBr₂	44.1	100.0	69.2	13.4

Common EI Fragment Ions

Diagnostic low-mass ions in 70 eV EI spectra.

m/z	Ion	Suggests
30	CH2=NH2+	primary amine (alpha-cleavage)
31	CH2=OH+	primary alcohol or methyl ether
43	CH3CO+ / C3H7+	methyl ketone, acetate, or propyl
44	C2H4O•+	McLafferty ion of an aldehyde
45	COOH+ / C2H5O+	carboxylic acid or ethyl ether
57	C4H9+	tert-butyl or butyl chain
58	C3H6O•+	McLafferty ion of a methyl ketone
60	C2H4O2•+	McLafferty ion of a carboxylic acid
74	C3H6O2•+	McLafferty ion of a methyl ester
77	C6H5+	phenyl (monosubstituted benzene)
91	C7H7+	tropylium: benzyl or alkylbenzene
105	C6H5CO+	benzoyl: aryl ketone or benzoate
149	C8H5O3+	phthalate ester (common contaminant)

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Summary

The Mass Spec Fragment Helper subtracts well-known neutral losses (water 18.0106, ammonia 17.0265, CO 27.9949, ethylene 28.0313, CO2 43.9898, hexose 162.0528 and about 40 more) from a parent ion and lists the expected fragment m/z with an interpretation. Paste the peaks you actually observed and it matches them to losses within a tolerance in Da or ppm. A formula panel computes the monoisotopic mass from NIST atomic masses, the m/z of M•+, [M+H]+, [M+NH4]+, [M+Na]+ and [M−H]− (electron mass included), rings plus double bonds, the nitrogen rule, and the isotope envelope, so you can recognise the 3:1 M+2 pattern of one chlorine or the 1:1 pattern of one bromine. Everything runs in your browser.

How it works

Enter the precursor m/z and choose EI (radical cation M•+) or ESI (even-electron ions such as [M+H]+). The mode hides losses typical of the other technique.
Each fragment m/z = parent m/z − neutral loss mass, using monoisotopic masses (C 12.000000, H 1.007825, N 14.003074, O 15.994915, S 31.972071).
Optionally paste observed fragment peaks and a tolerance. Each peak is matched to the closest calculated fragment and the error is shown in mDa and ppm: error = (observed − calculated) ÷ calculated × 10⁶.
In the formula panel the exact mass sums the most abundant isotope of each element. Ion m/z adds or removes a proton (1.007276), NH4+ (18.033826), Na+ (22.989221) or one electron (0.000549).
Rings plus double bonds = C − H/2 + N/2 + 1, counting halogens as H, Si as C and P as N. A whole number fits a neutral molecule or odd-electron ion, a value ending in .5 an even-electron ion.
The isotope pattern convolves NIST natural abundances: 13C 1.07%, 15N 0.364%, 18O 0.205%, 34S 4.25%, 37Cl 24.24%, 81Br 49.31%.

Use cases

Shortlist likely fragments when interpreting an unknown EI mass spectrum.
Assign MS/MS product ions to neutral losses (−18 water, −44 CO2, −162 hexose) with a ppm error.
Check whether a peak cluster shows the 3:1 (Cl) or 1:1 (Br) M+2 pattern.
Estimate the number of carbons from the M+1 peak (about 1.1% per carbon).
Apply the nitrogen rule to an EI molecular ion.
Compute [M+H]+, [M+Na]+ and [M−H]− for a candidate formula before searching a high-resolution spectrum.
Teach common fragmentation: alpha-cleavage, McLafferty rearrangement, tropylium at m/z 91.

Frequently Asked Questions

Last updated: 2026-10-10 · Reviewed by Nham Vu