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Organic Chemistry 2 · Spectroscopy

Mass Spectrometry

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On this page 7 sections
  1. In 30 seconds
  2. Why this matters
  3. The college version
  4. Eli explains
  5. Worked example
  6. Key takeaway
  7. Study tools

In 30 seconds

ionizes molecules, sorts the ions by their mass-to-charge ratio (m/z), and records abundance at each ratio. The gives molecular mass; its isotope satellites (M+1, M+2) reveal carbon count and halogens (Cl, Br). into predictable cations produces the lower-mass peaks, and the tallest peak is the . High-resolution instruments measure , often pinning down the formula uniquely.

Why this matters

Clinical labs use mass spectrometry for newborn screening (exact masses of acylcarnitines and amino acids detect inborn errors of metabolism), therapeutic drug monitoring, and toxicology screens. A drug's spectrum and exact mass act as an identity fingerprint in pharmaceutical quality control, and tandem MS/MS quantifies drugs and metabolites at trace levels in blood and urine.

The college version

1. Ionization and the molecular ion

In electron-impact (EI) MS, a ~70 eV electron beam strikes vaporized molecules and ejects an electron, forming a radical cation M+•. This has essentially the same mass as the neutral molecule, so its m/z gives directly. If it survives to the detector, it appears as the molecular-ion peak at the highest m/z of the isotopic cluster.

2. Mass-to-charge ratio and the base peak

The instrument measures the mass-to-charge ratio (m/z); since most ions carry one charge, m/z is read as the ion's mass in atomic mass units. The base peak is the tallest peak, set to 100%, with others reported relative to it. It is usually the most stable fragment, not the molecular ion.

3. Isotopes and the M+1/M+2 peaks

For n carbons, the is about 1.1% × n of M (¹³C is 1.1% abundant); the flags heavier isotopes. Chlorine (³⁵Cl:³⁷Cl ≈ 3:1) gives M+2 about one-third of M; bromine (⁷⁹Br:⁸¹Br ≈ 1:1) gives nearly equal M and M+2, and two bromines give a 1:2:1 M : M+2 : M+4 pattern. These are the fastest way to spot halogens.

How it works

  1. The sample is vaporized into a high-vacuum chamber.
  2. A 70 eV electron beam ejects an electron, forming radical cations.
  3. Ions are accelerated into a magnetic or time-of-flight analyzer.
  4. The analyzer separates ions by m/z.
  5. The detector counts arrivals and plots relative intensity vs. m/z.
  6. The chemist reads molecular ion, isotopes, and fragments to deduce mass and formula.

Common confusions

Do not confuseWithDifference
Molecular ion (M+•)Base peakIntact-minus-electron vs. tallest (fragment) peak
M+1 peakM+2 peakM+1 = ¹³C; M+2 = Cl/Br/S isotopes
m/zNeutral molecular massIons only; neutral molecules are invisible
Exact massNominal massExact uses precise masses to split ties
Fragmentation peakA real stable moleculeFragments are transient charged species

Memory aids

"M-I-B-D: Mass, Isotopes, Base, Degree." Read top-down: Molecular ion gives mass, Isotope peaks give atoms (C, Cl, Br), the Base peak is just the tallest, and Degree of unsaturation turns the formula into rings + π bonds.

Quick review

Topic Recap

Mass spectrometry weighs charged fragments of a molecule. The molecular-ion peak gives molecular mass; isotope peaks (M+1, M+2) reveal carbon count and halogens; fragmentation ( and neutral losses) hints at structure. Combining nominal mass, isotope patterns, the nitrogen rule, , and exact mass yields a molecular formula — the quantitative first step in structure determination.

Knowledge Check

  1. A compound shows M⁺ at m/z = 122 with an M+2 peak of nearly equal height. Which halogen is present?
  2. An M+1 peak is 6.6% of M. What does that tell you?
  3. An ion at m/z = 43 (base peak) forms by alpha cleavage of 2-butanone. What is the fragment?
  4. A hydrocarbon has molecular ion m/z = 84. Give its formula and degree of unsaturation.
  5. Why can two molecules share a nominal mass, and how is the ambiguity resolved?

Answers and Rationales

  1. Bromine. A 1:1 M : M+2 pattern is the Br hallmark (⁷⁹Br:⁸¹Br ≈ 1:1); chlorine would give ~3:1.
  2. About 6 carbons. M+1/M ≈ 1.1% per carbon, so 6.6/1.1 ≈ 6.
  3. The acylium ion CH₃C≡O⁺ (m/z = 43). Alpha cleavage on the ethyl side of the carbonyl gives the resonance-stabilized acetyl cation.
  4. C₆H₁₂, DoU = 1. C₆H₁₂ = 84; DoU = (2×6+2−12)/2 = 1 (one ring or π bond).
  5. Different exact masses. N₂, CO, and C₂H₄ are all nominal 28 but have distinct exact masses; high-resolution MS resolves them.
Eli, the EliExplains learning guide

Eli explains

The same idea, in plain words

Explain it like I’m 10

Imagine throwing a LEGO spaceship at a wall: some copies survive intact, others shatter into wings and engines. A mass spectrometer does the same to molecules — it knocks an electron off (so pieces carry charge) and bends the charged pieces through a curved track, where light pieces curve a lot and heavy pieces curve a little. A detector counts how many of each weight arrives, giving a bar graph of "weight vs. how many."

It is like a scale that weighs ions, not neutral molecules. The comparison "where it stops being exact" is that the "weight" we read is really mass divided by charge (m/z), and many peaks are transient charged fragments that exist only inside the machine for microseconds — not isolable molecules. A fragile molecular ion may never appear, so a missing peak never proves the molecule was absent.

Simple Example

Methane (CH₄) gives a molecular ion at m/z = 16. Fragmentation knocks off hydrogens one at a time, producing a "comb" of peaks at m/z = 15, 14, 13, 12.

Worked example

Interpreting a mass spectrum:

  1. Read the molecular-ion region. The highest m/z cluster gives the nominal molecular mass.
  2. Read the isotope pattern. Large M+2 → Cl (3:1) or Br (1:1); visible M+1 estimates carbon count via (M+1)/M × 100 ≈ 1.1n.
  3. Compute the degree of unsaturation: DoU = 2C + 2 + N - H - X2 where halogens X count like hydrogen and each N adds one; DoU = rings + π bonds (degree of unsaturation from formula).
  4. Apply the nitrogen rule. Odd nominal mass (for CHNO/halogen molecules) implies an odd number of nitrogens.
  5. Read fragmentation. Look for losses of stable neutrals (−15 CH₃, −18 H₂O, −29 C₂H₅) and for alpha cleavage pieces.
  6. Confirm with exact mass. In high-resolution MS, the exact mass distinguishes same-nominal-mass formulas (e.g., CO = 27.9949 vs. C₂H₄ = 28.0313), completing molecular formula determination.

Key takeaways

  • High yield: Molecular-ion peak → molecular mass; M+1/M+2 → composition.
  • High yield: Cl ≈ 3:1 (M : M+2); Br ≈ 1:1; two Br → 1:2:1.
  • High yield: The base peak is the most abundant fragment, not necessarily the molecular ion.
  • High yield: Alpha cleavage breaks the bond next to a heteroatom or carbonyl, giving resonance-stabilized cations.
  • High yield: Alkanes fragment by C–C cleavage into carbocation/radical combos, giving clusters spaced by 14 (CH₂).
  • High yield: Nitrogen rule: odd nominal mass ⇒ odd number of N (CHNO/halogen molecules).
  • The molecular ion may be absent for fragile, highly branched molecules — its absence is information, not failure. MS proves mass and formula, not full connectivity.

Keep learning

Ready to build on this? Continue to the next lesson.

Study tools & related lessonsYou’ll learn to · Key vocabulary · Related

You’ll learn to

  • Explain what mass spectrometry measures and how a molecule becomes a detectable ion.
  • Interpret the molecular-ion peak, isotope peaks (M+1, M+2), and the chlorine/bromine patterns to find molecular mass and formula.
  • Describe common fragmentation pathways (alpha cleavage; alkanes, alcohols, amines, carbonyls) and identify the base peak.
  • Use high-resolution (exact-mass) data with the degree of unsaturation to assign a molecular formula.

Key vocabulary

Mass spectrometry
Weighs charged fragments of a molecule
Electron-impact MS
Ionization by knocking out one electron
Molecular ion
Intact molecule minus one electron (M+•)
Molecular-ion peak
Highest m/z peak of the cluster
Mass-to-charge ratio (m/z)
Mass ÷ ionic charge
Molecular mass determination
Reading mass from the molecular ion
Isotope peaks
Satellites from ¹³C, ³⁷Cl, ⁸¹Br
M+1 peak
One unit above M, mostly ¹³C
M+2 peak
Two units above M
Chlorine isotope pattern
3:1 M : M+2
Bromine isotope pattern
1:1 M : M+2
Fragmentation
Molecular ion breaking into cations
Alpha cleavage
Bond break one atom from a heteroatom/π system
Base peak
Tallest peak (100%)
High-resolution MS
Measures mass to several decimals
Exact mass
Mass from the most abundant isotopes
Molecular formula determination
Mass + isotopes + exact mass → CₓHᵧ…
Degree of unsaturation
(2C+2+N-H-X)/2

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