Molar Mass Cross-Check Calculator

This page sets two numbers against each other that were produced by entirely different routes. The derived figure is a weighted sum over a tabulated residue table applied to a sequence that was typed in. The supplied figure came from a synthesis record, a catalogue entry or a certificate of analysis, and it carries whatever convention, rounding and chemical form its author chose. Because the arithmetic is independent, agreement is genuine corroboration rather than a tautology, and disagreement is diagnostic: it establishes that at least one of the two descriptions is wrong, even though it does not say which.

That asymmetry is the point of the tool. The sequence fixes the derived value exactly, within the convention being used, and no amount of care in the supplied figure can move it. So the derived side is the reference and the supplied side is the claim under test. When they differ, the useful question is not whether the calculator is right but what would have to be added to or taken away from the molecule to shift the derived value onto the supplied one, which is a question about chemistry rather than about arithmetic. The average molecular weight calculator is where the reference side comes from if the sequence itself needs recomputing.

Three effects produce a gap of a few tenths of a dalton, and none of them indicates a problem. The first is rounding in the supplied figure: a value quoted to one decimal place can be half a tenth either side of the truth, so anything up to 0.05 Da is arithmetic rather than chemistry. The second is the isotope convention, and it is the one people miss, because the number is labelled molecular weight and carries no hint that a different convention exists. This page derives an average mass, so a specification quoted as monoisotopic will always show a small gap, and closing it means comparing against the monoisotopic mass calculator rather than adjusting the figure by hand.

The third is the residue table itself. Average atomic weights are periodically revised and more than one table is in circulation, so two careful people working from different published sources can differ in the second decimal place with neither of them wrong. Take the four residue chain used in the worked example above, whose derived average mass is 390.35008. A specification quoting 390.4 differs from that by 0.04992, which is 0.013 percent and comfortably inside what rounding alone explains. The same chain quoted as 390.14 differs by 0.21, and that gap is the isotope convention rather than rounding. The two are worth telling apart, because only one of them is a mistake on your part.

Above roughly one dalton the gap stops being a convention and starts being a claim about the molecule, and the sign narrows the possibilities quickly. A supplied figure higher than the derived one means something is present that the sequence does not contain: a cap, an in chain modification, a counter ion or salt, a spacer, or a conjugate. A supplied figure lower means something has been lost: a residue omitted from the sequence that was typed, a cyclised terminus, or a form quoted as the free base when the material is a salt. The magnitude then narrows it further, because the common modifications have distinct masses.

The masses worth recognising on sight are the ones this site carries. About 15.995 is the addition of a single oxygen. About 17.03 and about 18.01 are the two routes to a pyroglutamyl terminus, and they differ from each other by about 0.98. About 42.01 is an acetylation and about 79.97 a phosphorylation. A gap matching one of these to within its rounding is a strong hint rather than a proof, and the modification mass calculator and the terminal modification calculator will show exactly what each one implies for a given base mass.

A gap close to a single residue mass points somewhere else altogether. Residue masses run from about 57 for glycine to about 186 for tryptophan, so a difference of that size is the signature of a missing or an extra residue rather than of a modification, and the first thing to check is the sequence rather than the chemistry. Whichever way the comparison goes, the mass difference calculator quantifies a gap between any pair of numbers once the pair has been chosen, and a gap quoted as a percentage of the derived value rather than of the supplied one keeps the comparison on the same footing every time.

A small percentage establishes consistency between two descriptions and very little else. It does not verify identity, because a molecule of the right mass with the wrong sequence, the wrong stereochemistry or a modification in the wrong place will match perfectly. It does not establish purity, which is a separate measurement with its own uncertainty, so a mass match says nothing about an assay. Nor does it resolve an ambiguity in the source, since this page has no access to the document the supplied figure came from and cannot tell you whether that figure was measured, calculated or conventional.

One direction of inference is out of reach here entirely. When the supplied figure is correct and the sequence is unknown or only partly known, the useful question runs the other way: which composition would produce this mass. The mass to sequence estimator starts from a mass and narrows the possibilities, and it is honest about returning an estimate rather than an identification. Where two independent routes give the same number, that is the strongest statement this kind of arithmetic supports, and where they do not, the disagreement is the finding rather than the failure.