What is a neutral loss in mass spectrometry?

A neutral loss is a small molecule (e.g. H2O = 18 Da, CO2 = 44 Da) that leaves the parent ion during fragmentation. The fragment ion that remains has the parent m/z minus the neutral loss mass. Identifying these losses is a primary strategy for deducing functional groups.

What is the difference between EI and ESI fragmentation?

EI (electron ionization) creates a radical cation M•+ that often fragments extensively via alpha-cleavage and rearrangements. ESI creates a protonated molecule [M+H]+ (or multiply charged ions) that fragments more gently in MS/MS, primarily by charge-directed mechanisms. This tool handles both modes but applies mode-appropriate neutral losses.

Does this tool account for isotope peaks?

No — all m/z values are monoisotopic. For Cl/Br-containing compounds, you would observe a characteristic isotope pattern (+2 peak), but this tool operates on the monoisotopic parent mass only.

Why are some calculated fragment m/z values not shown?

Fragments with a calculated m/z below 10 or above the parent m/z are automatically excluded as they are not physically meaningful. Only positive, sub-parent values appear in the results table.

Can I use this for high-resolution (exact mass) data?

The tool uses accurate monoisotopic masses for all neutral losses (e.g. H2O = 18.0106 Da) so the fragment m/z values are suitable for comparing against high-resolution data within typical instrument mass accuracy.

Mass Spec Fragment Helper

Name: Mass Spec Fragment Helper
Availability: InStock
Author: Nham Vu

Enter a parent m/z and find all common neutral losses and fragment ions to interpret EI or ESI mass spectra.

Parent Ion m/z

Precursor m/z (Da)

Ionization Mode

EI ESI

Loss Category

Min fragment m/z

Quick examples

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

Fragment Ions

Fragment m/z	Loss (Da)	Formula	Interpretation

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

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Summary

Enter a parent m/z and find all common neutral losses and fragment ions to interpret EI or ESI mass spectra.

How it works

Enter the parent or precursor ion m/z value (integer or decimal).
Select the ionization mode — EI (electron ionization, radical cation M+) or ESI (electrospray, protonated [M+H]+).
Optionally filter by loss category: all, small molecules, functional groups, or alkyl chains.
The tool subtracts each neutral loss mass from the parent m/z and displays all positive fragment m/z values.
Each row shows the fragment m/z, neutral loss mass, loss formula, and a chemical interpretation.
Click any row to highlight it, or use Copy Table to export the results.

Use cases

Quickly shortlist likely fragments when interpreting an unknown EI mass spectrum.
Identify characteristic neutral losses (e.g. -18 water, -44 CO2) in ESI-MS/MS data.
Cross-check observed fragment peaks against the calculated list during de novo structure elucidation.
Teach students common fragmentation rules by showing which losses apply to a given precursor.
Screen a series of m/z values rapidly during metabolomics or natural product dereplication.
Verify that a proposed molecular formula produces fragments consistent with the spectrum.

Frequently Asked Questions

Last updated: 2026-07-24 · Reviewed by Nham Vu