LC–MS ion assignment: worksheet
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Fictional teaching model. No peptide sequence, measured sample or instrument performance is represented. The ±5 ppm criterion is invented for this exercise.
Four observations, one fictional retention zone
All four rows belong to the invented retention group R1. Their positive charge numbers are supplied. No isotope envelope is provided from which to infer charge; no peak intensities are implied.
Your starting data — use these six-decimal observations as written
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| Row | Synthetic observed m/z | Supplied charge z |
|---|---|---|
| A | 1235.577638 | +1 |
| B | 618.289367 | +2 |
| C | 1257.558369 | +1 |
| D | 1235.589993 | +1 |
The hypotheses and inputs
Use a hypothetical neutral mass M = 1234.567890 Da. This number is an arithmetic model input, not an exact mass calculated from a real peptide formula. Consider only these three positive-ion hypotheses:
Allowed hypotheses; M, p and s are the numerical masses in Da
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| Ion hypothesis | Charge z | Calculation |
|---|---|---|
| [M + H]⁺ | +1 | M + p |
| [M + 2H]²⁺ | +2 | (M + 2p) / 2 |
| [M + Na]⁺ | +1 | M + s |
Set p = 1.0072764665789 Da for the proton and s = 22.989221 Da for the approximate sodium-ion increment. Keep all supplied digits until the final display.
The sodium value is a rounded teaching approximation: the NIST sodium-23 atomic mass, 22.9897692820 u, minus the CODATA electron mass, 0.0005485799090441 u. Ionization energy is neglected in this approximation. The unrounded subtraction is 22.9892207020909559; the exercise fixes s at six decimal places. Da and u name the same mass unit.
NIST CODATA 2022 · NIST: ²³Na · BIPM: Da / u
For this exercise only, a hypothesis is within the criterion when the absolute ppm error is ≤5. A real method needs an appropriate, justified acceptance criterion; this page supplies none for laboratory use.
Calculate, compare, then qualify
- Calculate the expected m/z for each allowed ion. For each observation, compare only hypotheses with its supplied charge number.
- Subtract calculated m/z from observed m/z. Divide that signed difference by the calculated m/z of the same ion, then multiply by one million.
- Keep the sign in your result. Compare the absolute value with 5 ppm and record either “within the fictional criterion” or “outside”. If no allowed hypothesis passes, leave the assignment unresolved.
- Explain why row B needs a different denominator from row A, why row C suggests a sodium-adduct candidate, and what further evidence would be needed for a structural assignment.
Signed error convention used throughout this worksheet
ppm = (observed m/z − calculated m/z) / calculated m/z × 1,000,000
Positive means the observation is higher than the calculation; negative means lower. Do not take an absolute value until you compare with the criterion. This definition fixes the sign convention, which should always be checked when reading another report.
Record your calculations and decision
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| Row | Ion / z | Calculated m/z | Signed difference | Denominator | ppm / decision |
|---|---|---|---|---|---|
| A | |||||
| B | |||||
| C | |||||
| D |
Explain your denominator for B and the evidence still missing after a mass match.