Organic Chemistry Structure Determination

Mass Spectrometry

Topic overview

Start with the big picture

Reading a mass spectrum begins with identifying the molecular ion, when present, and comparing its m/z with the expected molecular weight. The base peak marks the most intense ion, while other fragment peaks reveal how the molecule breaks apart. Ionization methods vary in softness, so they can differ in how much fragmentation occurs and whether an intact molecular ion is observed. Isotope clusters, the nitrogen rule, and degree of unsaturation add complementary evidence about composition and structure. In electron-impact spectra, characteristic cleavages and neutral losses can point toward particular structural features. These clues are interpreted together rather than in isolation; the full lesson organizes them across spectrum interpretation, fragmentation pathways, functional-group patterns, and advanced techniques.

Learning objectives

What you'll learn

  • Explain what m/z, the molecular ion, and the base peak indicate.
  • Relate ionization method and softness to fragmentation and molecular-ion visibility.
  • Recognize diagnostic isotope patterns and apply the nitrogen rule.
  • Describe how DBE and common EI fragmentations support structural interpretation.
  • Connect characteristic neutral losses and fragment ions with structural clues.
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