Accuracy, precision and the tolerance nobody states

The single hardest discrimination in routine peptide identity work is glutamine against lysine. The two residues differ in elemental composition by one carbon-hydrogen-hydrogen group swapped for one nitrogen-hydrogen, and the resulting mass difference is thirty-six thousandths of a dalton. On a peptide of four thousand daltons that is nine parts per million. An orbital trap or Fourier-transform instrument will separate it without difficulty. A quadrupole will not see it at all, and neither will most of the identity confirmations sold in this market.

The isotope pattern, and how it declares the charge

Because carbon-13 is present at roughly 1.1% natural abundance, a peptide containing one hundred and ninety carbon atoms will exist substantially as molecules containing one, two or three carbon-13 atoms. In a spectrum this appears as a series of peaks above the monoisotopic peak, separated in mass by approximately 1.00336 daltons and distributed in intensity according to the binomial statistics of the composition.

Two things follow, and both are practically useful. First, the spacing between adjacent isotope peaks in a charge-state cluster is one over the charge: a spacing of 0.5 on the m/z axis means the ion is doubly charged, 0.333 means triply, 0.25 means quadruply. This is the simplest charge assignment available and it requires no assumptions about the sample at all. Second, the relative intensities of the isotope peaks are predictable from the elemental composition, so a cluster whose shape departs markedly from the calculated envelope is evidence that two species are overlapping.

Both observations require an instrument capable of resolving the isotope peaks at the relevant m/z, which is where resolving power stops being a specification-sheet number and becomes the thing that determines whether a spectrum can be interpreted at all. Below roughly ten thousand resolving power, a multiply charged peptide envelope collapses into a single broad hump that carries neither the spacing nor the shape information.

Resolving power, defined and then converted

Resolving power is conventionally defined as m divided by Δm, where Δm is the width of the peak at half its maximum height. An instrument quoted at 30,000 resolving power at m/z 1000 produces peaks roughly 0.033 wide at that position, which is sufficient to separate the isotope peaks of a triply charged ion. The same instrument at m/z 4000 may deliver rather less, because resolving power is not constant across the mass range and the figure on a specification sheet is quoted at whichever mass flatters it.

The number that matters for identity work is whether the instrument can separate two species whose masses differ by the amount you care about. To distinguish a deamidated peptide from its parent at four thousand daltons requires separating peaks 0.98 apart, which is a resolving power of roughly four thousand — modest. To distinguish a glutamine-for-lysine substitution requires separating peaks 0.036 apart at the same mass, which is a resolving power above one hundred thousand. Those two requirements differ by a factor of twenty-five and both are described in the trade by the same phrase, high resolution.

The Journal’s practice, adopted after an exchange with a laboratory that pointed out we had been sloppy about it, is to state the discrimination rather than the specification: not “high-resolution MS”, but “sufficient to resolve a 0.98-dalton shift at the parent mass”. It is longer and it says something.¹

The instrument classes, and what each can support

A single quadrupole mass filter provides unit resolution and mass accuracy of a few tenths of a dalton. It is entirely adequate to confirm that a sample is broadly the compound expected and to detect large modifications, and it is the analyser in most low-cost LC-MS systems. It cannot resolve an isotopic envelope at peptide molecular weights and therefore cannot assign charge from spacing.

Time-of-flight analysers separate ions by the time they take to traverse a flight tube. A linear tube gives modest resolving power; adding a reflectron and delayed extraction raises it into the tens of thousands, and modern quadrupole time-of-flight hybrids achieve low single-figure parts-per-million accuracy with routine calibration. Orbital trapping instruments measure the frequency of ion oscillation in an electrostatic field and convert it by Fourier transform, delivering resolving powers from sixty thousand to several hundred thousand and sub-part-per-million accuracy with internal calibration. Fourier-transform ion cyclotron resonance remains the highest-performing class and the least common outside academic facilities.

What this hierarchy means for a reader of certificates is that the instrument named on the document sets a ceiling on what the document can claim, independent of the laboratory’s competence. An unnamed instrument leaves that ceiling unknown, which is why the Journal now treats the absence of an instrument name as a material omission rather than a stylistic one.

Calibration, drift, and the internal standard

Every mass spectrometer is calibrated against a mixture of compounds of known exact mass, and every mass spectrometer drifts away from that calibration afterwards. The rate depends on the analyser type, on ambient temperature stability, and in trapping instruments on the number of ions in the trap: space-charge effects shift apparent masses in a manner that depends on how much sample was injected.

External calibration means the calibrant was run separately, before or after the samples. It is simple, it is what most routine work uses, and it is vulnerable to everything that happens between the calibration and the sample. Internal calibration means a compound of known mass was present in the same spectrum as the analyte, so the correction is applied to the measurement rather than to the instrument. Internal calibration is the reason sub-part-per-million figures are achievable at all, and it is the difference between a stated accuracy and a demonstrated one.

None of this is exotic or contested; it is ordinary laboratory practice, described in accreditation requirements as part of metrological traceability and in the pharmacopoeial chapters as part of system suitability.² The reason it belongs in an article aimed at buyers is that it explains why two competent laboratories analysing the same vial on the same class of instrument can differ by tens of parts per million, and why the honest response to such a difference is to ask about calibration rather than about honesty.

A short glossary, because the terms are used loosely

m/z — mass-to-charge ratio, the quantity a mass spectrometer actually measures. Monoisotopic mass — mass calculated using the lightest stable isotope of each element. Average mass — mass calculated using standard atomic weights. Nominal mass — the integer sum of integer isotope masses; adequate for small molecules, useless here.

Resolving power — m divided by peak width at half height; the ability to separate nearby masses. Mass accuracy — deviation of a measurement from the true value, in parts per million. Mass defect — the difference between an exact mass and its nominal value, and the property that makes near-isobars separable.

Adduct — an ion formed by association with something other than a proton, commonly sodium or potassium. Charge-state envelope — the family of differently charged ions from one compound. Isobaric — of identical mass at the achieved precision. Isomeric — of identical composition and different structure. b and y ions — the complementary fragment series produced by amide-bond cleavage.

Precision in these terms is not decoration. Several disputes this department has been asked to adjudicate turned out, on inspection, to be disagreements about whether the word mass meant monoisotopic or average.

What remains genuinely open is stereochemistry. Racemisation during synthesis is a well-described chemical risk, it is invisible to every routine test sold to private buyers in this market, and the Journal has no basis for estimating how common it is. We would rather say that plainly than fill the gap with an inference. If any of the four independent services begins offering chiral amino-acid analysis at a price a private buyer would pay, this department will report the results.