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Mass spectrometry separates gaseous ions by their mass-to-charge ratio (m/z), producing a spectrum that reveals molecular mass and structural information through fragmentation patterns. Ionization methods — electron ionization (EI), electrospray (ESI), matrix-assisted laser desorption (MALDI) — determine which analytes are accessible and how much fragmentation occurs. The molecular ion peak (M⁺) gives the nominal molecular mass; high-resolution MS provides exact mass for molecular formula determination. Tandem MS (MS/MS) isolates and fragments selected ions for greater structural specificity and is widely used in metabolomics, proteomics, and environmental analysis.
Interpret EI spectra of small organic molecules by identifying M⁺, M+1, and M+2 isotope patterns (for heteroatom detection) and predicting major fragmentation pathways using McLafferty rearrangement and alpha-cleavage rules. Connecting fragmentation to structural features is more instructive than memorizing masses.
Mass spectrometry works by converting analyte molecules into gas-phase ions, separating those ions by their mass-to-charge ratio (m/z), and counting them to produce a spectrum. The horizontal axis is m/z and the vertical axis is relative abundance — the result is a bar chart of fragment masses that acts like a molecular fingerprint.
The ionization step determines what kind of information you get. Electron ionization (EI) fires high-energy electrons at the molecule, ripping off an electron to produce a radical cation M⁺, then typically shattering it into smaller fragments. EI spectra are rich in structural information because each bond has a characteristic probability of breaking — recognizing patterns like alpha-cleavage (breaking adjacent to a heteroatom) or McLafferty rearrangement (involving a gamma-hydrogen) lets you read the connectivity of the molecule. However, EI is hard on fragile molecules. Electrospray ionization (ESI) and MALDI are "soft" methods that deposit much less energy: they produce intact charged molecules, ideal for proteins and nucleic acids, but provide less fragmentation for structural diagnosis.
The molecular ion peak (M⁺) in an EI spectrum is the highest m/z peak from the intact molecule — it tells you the nominal molecular mass. A critical distinction: the molecular ion is not necessarily the base peak (the tallest bar). Base peak just means most abundant ion at the time of detection, which is often a stable fragment. If M⁺ is weak or absent, chemists can switch to a softer ionization technique or use the fragmentation pattern itself to work backward to the molecular mass.
High-resolution mass spectrometry (HRMS) adds a precision layer. Because different elements have slightly different exact atomic masses (C = 12.000, H = 1.00783, N = 14.003, O = 15.995…), measuring m/z to four or five decimal places lets you calculate the molecular formula directly from the exact mass — a technique called elemental composition determination. Tandem MS (MS/MS) adds another dimension: a selected ion is isolated and deliberately fragmented a second time, giving structural information specific to that precursor mass. This is the backbone of proteomics and metabolomics, where thousands of compounds must be identified in a single run.
When interpreting a spectrum, start at the high m/z end: find M⁺ (or [M+H]⁺ in ESI), then look at isotope patterns — the M+2 peak is enhanced by chlorine or bromine (distinctive 3:1 or 1:1 ratios), and the M+1 peak scales with carbon count. Then work down through the major fragments, asking which bonds broke and what structural features they reveal. Connecting fragmentation to molecular structure, rather than memorizing masses, is what makes mass spectrometry interpretable across novel compounds.