Fragmentation
Definition
Breakdown of the molecular ion into smaller charged and neutral pieces. The fragmentation pattern is the chemical fingerprint that identifies the compound.
- Process
- Breakdown of molecular ion into smaller ions
- Output
- Fragmentation pattern (mass spectrum)
- Use
- Compound identification, chemical fingerprint
- Field
- Mass spectrometry
Common questions
Why is the fragmentation pattern described as a chemical fingerprint rather than just a byproduct of analysis?+
Fragmentation occurs at predictable, structure-dependent bond-breaking points, so the resulting set of fragment masses and their relative abundances is highly specific to a compound's molecular structure, letting analysts match an unknown spectrum against reference library spectra to confirm identity.
What determines where a molecular ion is most likely to break during fragmentation?+
Cleavage tends to occur at the weakest bonds and preferentially forms the most stable resulting fragment ions, such as those stabilised by resonance or a favourable charge distribution, which is why certain functional groups produce characteristic, predictable fragment ions.
Can two structurally different compounds produce very similar fragmentation patterns?+
Yes, isomers or closely related structural analogues can produce overlapping fragmentation patterns, which is why analysts also compare retention time from the preceding chromatographic separation alongside the mass spectrum rather than relying on fragmentation alone.
Related terms
- Base Peak
- The most intense peak in a mass spectrum, normalised to 100 percent relative abundance. All other peaks in the spectrum are reported...
- EI (Electron Ionisation)
- Hard ionisation at 70 eV. Produces extensive fragmentation, ideal for library search. Standard ion source in GC-MS.
- ESI (Electrospray Ionisation)
- Soft ionisation at atmospheric pressure for polar and thermally fragile analytes in solution. Standard source in LC-MS for drugs and biomolecules.
- M/z (Mass-to-Charge Ratio)
- The x-axis of every mass spectrum. Ions are separated by their mass divided by the number of charges they carry. For singly-charged...
- MALDI
- Matrix-Assisted Laser Desorption / Ionisation. A soft method that uses a UV-absorbing matrix to ionise large biomolecules. Almost always paired with a...
- Molecular Ion (M+)
- The intact ionised molecule with no fragmentation, formed by removing a single electron from the parent. Its m/z gives the molecular weight...
- Nitrogen Rule
- An organic molecule with an odd-numbered molecular weight contains an odd number of nitrogen atoms. A staple trick for narrowing down a...
- TOF (Time-of-Flight)
- Mass analyser that separates ions by their flight time down a field-free drift tube. Theoretically unlimited mass range, very high speed.