---

name: interpret-mass-spectrum locale: caveman-ultra source_locale: en source_commit: 82c77053 fence_basis_commit: 82c77053 translator: "Julius Brussee homage — caveman" translation_date: "2026-04-24" description: > Systematic MS interpret → determine mol formula, fragmentation pathways, propose structure. Ionization method, mol ion ID, isotope pattern, common frag losses, purity eval. license: MIT allowed-tools: Read Grep Glob WebFetch WebSearch metadata: author: Philipp Thoss version: "1.0" domain: spectroscopy complexity: advanced language: natural tags: spectroscopy, mass-spectrometry, fragmentation, molecular-ion, isotope

Interpret Mass Spectrum

Analyze MS → mol ion, formula, fragmentation pathways, structural features.

Use When

• MW + formula of unknown
• Confirm synthetic product (mol ion + fragmentation)
• ID impurities / degradation products
• Propose structural features from characteristic frag losses
• Isotope patterns → halogens, S, metals

In

• Req: MS data (m/z + rel int, min full scan)
• Req: Ionization method (EI, ESI, MALDI, CI, APCI, APPI)
• Opt: HRMS exact mass (measured vs calc)
• Opt: Mol formula from other (EA, NMR)
• Opt: MS/MS data (frag of selected precursor)
• Opt: Chrom ctx (LC-MS / GC-MS tR, purity)

Do

Step 1: Ionization Method + Expected Ion Types

Determine what species present before peak assignment:

1. Classify ionization:

Method	Energy	Primary Ion	Fragmentation	Typical Use
EI (70 eV)	Hard	M+. (radical cation)	Extensive	Small volatile molecules, GC-MS
CI	Soft	[M+H]+, [M+NH4]+	Minimal	Molecular weight confirmation
ESI	Soft	[M+H]+, [M+Na]+, [M-H]-	Minimal	Polar, biomolecules, LC-MS
MALDI	Soft	[M+H]+, [M+Na]+, [M+K]+	Minimal	Large molecules, polymers, proteins
APCI	Soft	[M+H]+, [M-H]-	Some	Medium polarity, LC-MS

2. Polarity mode: +ve → cations; -ve → anions. ESI uses both commonly.
3. Adducts + clusters: Soft ionization → [M+Na]+ (M+23), [M+K]+ (M+39), [2M+H]+, [2M+Na]+ besides [M+H]+. ID these before mol ion.
4. Multiply charged: ESI → m/z = (M + nH) / n. Look for fractional m/z spacing (0.5 Da = z=2).

→ Method documented, expected ion types listed, adducts/clusters ID'd → true mol ion determinable.

If err: Method unknown → examine spectrum for clues: extensive frag → EI; adduct patterns → ESI; matrix peaks → MALDI. Check instrument log.

Step 2: Mol Ion + Mol Formula

ID mol ion peak + derive formula:

1. Locate mol ion (M): EI → M+. highest m/z w/ reasonable isotope pattern (may be weak/absent for labile compounds). Soft → ID [M+H]+ / [M+Na]+ + subtract adduct → M.
2. N rule: Odd MW → odd # N. Even MW → 0 or even # N.
3. DBE: DBE = (2C + 2 + N - H - X) / 2, X = halogens. Ring / π bond = 1 DBE. Benzene = 4, carbonyl = 1.
4. HRMS: Exact mass avail → calc formula using mass defect. Compare measured vs candidate formulas in accuracy window (typ < 5 ppm modern instruments).
5. Cross-check isotope pattern: Observed must match proposed formula (Step 3).

→ Mol ion ID'd, MW determined, N rule applied, formula proposed (confirmed by HRMS if avail).

If err: No mol ion in EI (common thermally labile / highly branched) → try softer ionization. Ambiguous mol ion → check loss of common small frags from highest m/z (M-1, M-15, M-18 → help ID M).

Step 3: Isotope Patterns

Use isotopic signatures → detect elements:

1. Monoisotopic elements: H, C, N, O, F, P, I have characteristic abundances. CHNO only → M+1 ≈ 1.1% per C.
2. Halogen patterns:

Element	Isotopes	M : M+2 Ratio	Visual Pattern
35Cl / 37Cl	35, 37	3 : 1	Doublet, 2 Da apart
79Br / 81Br	79, 81	1 : 1	Equal doublet, 2 Da apart
2 Cl	--	9 : 6 : 1	Triplet
2 Br	--	1 : 2 : 1	Triplet
1 Cl + 1 Br	--	3 : 4 : 1	Characteristic quartet-like

3. Sulfur: 34S → 4.4% at M+2. M+2 ≈ 4-5% rel M (after 13C2 correction) → ≈ 1 S.
4. Silicon: 29Si (5.1%) + 30Si (3.4%) → distinctive M+1 + M+2 contributions.
5. Compare calc vs observed: Use proposed formula → theoretical pattern → overlay observed → confirm/refute.

→ Pattern analyzed, Cl/Br/S/Si presence determined, consistent w/ proposed formula.

If err: Isotope res insufficient (low-res instrument) → M+2 unresolvable. Note limitation, rely on exact mass + other spectra for elemental comp.

Step 4: Fragmentation Losses + Key Frag Ions

Map pathways → structural info:

1. Catalog major frags: All peaks > 5-10% rel int w/ m/z.
2. Neutral losses from mol ion:

Loss (Da)	Neutral Lost	Structural Implication
1	H.	Labile hydrogen
15	CH3.	Methyl group
17	OH.	Hydroxyl
18	H2O	Alcohol, carboxylic acid
27	HCN	Nitrogen heterocycle, amine
28	CO or C2H4	Carbonyl or ethyl
29	CHO. or C2H5.	Aldehyde or ethyl
31	OCH3. or CH2OH.	Methoxy or hydroxymethyl
32	CH3OH	Methyl ester
35/36	Cl./HCl	Chlorinated compound
44	CO2	Carboxylic acid, ester
45	OC2H5.	Ethoxy
46	NO2.	Nitro compound

3. Characteristic frag ions:

m/z	Ion	Origin
77	C6H5+	Phenyl cation
91	C7H7+	Tropylium (benzyl rearrangement)
105	C6H5CO+	Benzoyl cation
43	CH3CO+ or C3H7+	Acetyl or propyl
57	C4H9+ or C3H5O+	tert-Butyl or acrolein
149	Phthalate fragment	Plasticizer contaminant

4. Map frag pathways: Connect frag ions by successive losses → frag tree from M down to low mass.
5. Rearrangement ions: McLafferty (γ-H transfer + β-cleavage) → even-electron ions from carbonyl compounds. Retro-Diels-Alder → characteristic cyclohexene.

→ All major frag ions assigned, neutral losses calc + correlated w/ structure, frag tree built.

If err: Frags don't correspond to simple losses → consider rearrangement. Unassigned frags → unexpected groups, impurities, matrix/BG peaks.

Step 5: Purity + Structure

Evaluate spectrum for purity + assemble proposal:

1. Purity check: GC-MS / LC-MS → examine chrom for add'l peaks. Direct-infusion → look for unexpected ions not frags/adducts of analyte.
2. BG + contaminant peaks: Common: phthalate plasticizers (m/z 149, 167, 279), column bleed (siloxanes 207, 281, 355, 429 in GC-MS), solvent clusters.
3. Structure proposal: Combine formula (Step 2) + isotope (Step 3) + frag (Step 4) → structure / candidate set.
4. Rank candidates: Frag tree → rank. Best = explains most frag ions w/ fewest ad hoc.
5. Cross-validate: Compare vs NMR, IR, UV-Vis. MS alone rarely unambiguous for novel compounds.

→ Purity assessed, contaminants ID'd if present, structural proposal / ranked candidates consistent w/ all MS + cross-validated where poss.

If err: Multiple components w/o chrom sep → flag mixture, recommend LC-MS / GC-MS reanalysis. No satisfactory proposal → ID which add'l data (HRMS, MS/MS, NMR) would resolve.

Check

• Ionization method ID'd + expected ion types documented
• Mol ion located + distinguished from adducts, frags, clusters
• N rule applied + consistent w/ proposed formula
• DBE calc + accounted for in structure
• Isotope pattern matches formula
• Major frag ions assigned w/ neutral losses + structural rationale
• Frag tree built M → low mass
• Contaminant + BG peaks ID'd + excluded
• Proposal cross-validated w/ other spectra

Traps

• Mis-ID mol ion: EI → base peak often frag, not M. M = highest m/z w/ reasonable isotope pattern. ESI adducts ([M+Na]+, [2M+H]+) → mistaken for M.
• Ignore N rule: Odd-mass M → odd # N. Forget → impossible formulas.
• Confuse isobaric losses: Loss 28 = CO or C2H4; loss 29 = CHO or C2H5. HRMS / add'l frag → distinguish.
• Neglect multiply charged: ESI → 2+/3+ at half/third expected m/z. Non-integer spacing between isotope peaks → multi charge diagnostic.
• Over-interpret low-abundance: Peaks < 1-2% rel int → noise, isotope contribs, minor contaminants, not real frags.
• Assume pure: Many real spectra = mixtures. Check chrom purity + look for ions inconsistent w/ proposed structure.

→

• interpret-nmr-spectrum — connectivity + H environments → structural confirm
• interpret-ir-spectrum — func groups explaining observed frag
• interpret-uv-vis-spectrum — chromophores in analyte
• interpret-raman-spectrum — complementary vibrational
• plan-spectroscopic-analysis — select + sequence techniques pre-acquisition
• interpret-chromatogram — GC/LC chrom data coupled w/ MS