Section: 8 | Common Mass Spectral Fragmentation Patterns of Organic Compound Families |
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John R. Rumble, ed., CRC Handbook of Chemistry and Physics, 103rd Edition (Internet Version 2022), CRC Press/Taylor & Francis, Boca Raton, FL.
If a specific table is cited, use the format: "Physical Constants of Organic Compounds," in CRC Handbook of Chemistry and Physics, 103rd Edition (Internet Version 2022), John R. Rumble, ed., CRC Press/Taylor & Francis, Boca Raton, FL.


Thomas J. Bruno and Paris D. N. Svoronos

The following table provides a guide to the identification and interpretation of commonly observed mass spectral fragmentation patterns for common organic functional groups (Refs. 1–10). It is of course highly desirable to augment mass spectroscopic data with as much other structural information as possible. Especially useful in this regard will be the confirmatory information of infrared and ultraviolet spectrophotometry as well as nuclear magnetic resonance spectrometry.

The reader is referred to other tables in this book for additional information that can be used in assessing or predicting fragmentation patterns, particularly the tables of “Proton Affinities” and “Ionization Energies of Gas-Phase Molecules” in Section 10.


  1. Bowie, J. H., Williams, D. H., Lawesson, S. O., Madsen, J. O., Nolde, C., and Schroll, G., Tetrahedron 22, 3515, 1966. []
  2. Johnstone, R. A. W., and Rose, M. E., Mass Spectrometry for Chemical and Biochemists, Cambridge University Press, New York, 1996. []
  3. Lee, T. A., A Beginner’s Guide to Mass Spectral Interpretation, Wiley, New York, 1998
  4. McLafferty, F. W., and Turecek, F., Interpretation of Mass Spectra, Fourth Edition, University Science Books, Mill Valley, CA, 1993.
  5. Pasto, D. J., and Johnson, C. R., Organic Structure Determination, Prentice Hall, Englewood Cliffs, NJ, 1969.
  6. Silverstein, R. M., Bassler, G. C., and Morrill, T. C., Spectroscopic Identification of Organic Compounds, Sixth Edition, John Wiley and Sons, New York, 1998.
  7. Smakman, R., and deBoer, T. J., Org. Mass Spec. 3, 1561, 1970. []
  8. Smith, R. M., Understanding Mass Spectra: A Basic Approach, John Wiley and Sons, New York, 1999.
  9. Watson, T. J., and Watson, J. T., Introduction to Mass Spectrometry, Lippincott, Williams and Wilkins, Philadelphia, PA, 1997.
  10. Bruno, T. J., and Svoronos, P. D. N., CRC Handbook of Basic Tables for Chemical Analysis – Data-Driven Methods and Interpretation, Fourth Edition, CRC Press/Taylor & Francis, Boca Raton, FL, 2021. []

Mass Spectral Fragmentation Patterns of Organic Compound Families

FamilyMolecular ion peakCommon fragments and characteristic peaks
Continued on next page...
AcetalsCleavage of all C–O, C–H, and C–C bonds around the original aldehydic carbon
AlcoholsWeak for 1° and 2°; not detectable for 3°; strong for benzyl alcoholsLoss of 18 (H2O — usually by cyclic mechanism); loss of H2O and olefin simultaneously with four (or more) carbon-chain alcohols; prominent peak at m/z = 31(CH2ÖH)+ for 1° alcohols; prominent peak at m/z = (RCHÖH)+ for 2° alcohols; and m/z = (R2CÖH)+ for 3° alcohols
AldehydesLow intensityLoss of aldehydic hydrogen (strong M-1 peak, especially with aromatic aldehydes); strong peak at m/z = 29(HC≡O+); loss of chain attached to alpha carbon (beta cleavage); McLafferty rearrangement via beta cleavage if gamma hydrogen is present
(a) ChainLow intensityLoss of 14 mass units (CH2)
(b) BranchedLow intensityCleavage at the point of branch; low intensity ions from random rearrangements
(c) AlicyclicIntenseLoss of 28 mass units (CH2=CH2) and side chains
Alkenes (olefins)Rather high intensity (loss of π-electron) especially in case of cyclic olefinsLoss of units of general formula CnH2n–1; formation of fragments of the composition CnH2n (via McLafferty rearrangement); retro Diels-Alder fragmentation
Alkyl halidesAbundance of molecular ion F<Cl<Br<I; intensity decreases with increase in size and branchingLoss of fragments equal to the mass of the halogen until all halogens are cleaved off
(a) FluoridesVery low intensityLoss of 20 (HF); loss of 26 (C2H2) in case of fluorobenzenes
(b) ChloridesLow intensity; characteristic isotope clusterLoss of 35 (Cl) or 36 (HCl); loss of chain attached to the gamma carbon to the carbon carrying the Cl
(c) BromidesLow intensity; characteristic isotope clusterLoss of 79 (Br); loss of chain attached to the gamma carbon to the carbon carrying the Br
(d) IodidesHigher than other halidesLoss of 127 (I)
AlkynesRather high intensity (loss of π-electron)Fragmentation similar to that of alkenes
AmidesHigh intensityStrong peak at m/z = 44 indicative of a 1° amide (O=C=NH+2); base peak at m/z = 59 (CH2=C(OH)N+H2); possibility of McLafferty rearrangement; loss of 42 (C2H2O) for amides of the form RNHCOCH3 when R is aromatic ring
AminesHardly detectable in case of acyclic aliphatic amines; high intensity for aromatic and cyclic aminesBeta cleavage yielding >C=N+<; base peak for all 1° amines at m/z = 30 (CH2=N+H2); moderate M-1 peak for aromatic amines; loss of 27 (HCN) in aromatic amines; fragmentation at alpha carbons in cyclic amines
Aromatic hydrocarbons (arenes)IntenseLoss of side chain; formation of RCH=CHR’ (via McLafferty rearrangement); cleavage at the bonds beta to the aromatic ring; peaks at m/z = 77 (benzene ring; especially mono-substituted), 91 (tropyllium); the ring position of alkyl substitution has very little effect on the spectrum
Carboxylic acidsWeak for straight-chain monocarboxylic acids; large if aromatic acidsBase peak at m/z = 60 (CH2=C(OH)2) if alpha hydrogen is present; peak at m/z = 45 (COOH); loss of 17 (–OH) in case of aromatic acids or short-chain acids
DisulfidesLow intensityLoss of olefins (m/z equal to R–S–S–H+.); strong peak at m/z = 66 (HSSH+)
  • *The base peak is the most intense peak in the mass spectrum, and is often the molecular ion peak, M+.

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