Terminal Modification Calculator

A linear peptide has exactly two chemically distinct ends, and each carries a functional group that appears nowhere else in the molecule: a free amine at the N terminus and a free carboxyl at the C terminus. Each can be capped independently, and because the two sites are nowhere near each other, the shifts simply add with no interaction between them. That is why this page takes two selectors and returns two deltas alongside the total rather than offering a single combined option. There is no case in which capping one end obliges a change at the other, which is exactly why the two selectors are independent rather than a pair of mutually exclusive choices.

The second reason to treat the ends on their own is that a terminal modification changes the elemental composition and not only the mass. A cyclised N terminus removes atoms from the formula, and an amidated C terminus does the same, so a molecular formula computed from a bare sequence stops matching the moment either end is capped. The molecular formula calculator will happily produce a formula for the unmodified chain, and that formula is then wrong for the material in a way the mass alone does not reveal, since many different formulas can share a mass while no formula can be half right.

Cyclisation of the N terminus is the case worth working through, because it is chemically interesting and because its mass effect is small enough to hide. A chain beginning with glutamine cyclises by losing ammonia, which is 17.026549 Da on the monoisotopic convention. A chain beginning with glutamate cyclises by losing water instead, which is 18.010565 Da. Two different starting residues give the same named product and two different masses, and the 0.984016 Da separating them is exactly the oxygen against amine difference that also separates amidation from deamidation. Neither loss leaves a free amine at that end, so both routes consume the same reactive group while moving the mass by amounts that differ by less than one dalton.

Seventeen or eighteen daltons is a small fraction of a peptide of any length, and small enough to sit inside the tolerance of a rounded specification. A supplier who quotes a molecular weight to one decimal place has a resolution of 0.05 Da, so a cyclised terminus does not appear as a discrepancy in that figure at all. What it changes is real regardless: the free amine of the N terminus is consumed, which is a difference in the reactive groups of the molecule and not only in its mass, and no calculation from a bare sequence reproduces it. The summation the base mass comes from is set out in molecular weight and peptide calculations .

Amidation replaces a terminal carboxyl with an amide, which removes an oxygen and a hydrogen while adding a nitrogen and two hydrogens, for a net loss of 0.984016 Da. On the 390 Da chain used in the worked example above that is a quarter of one percent, and on a peptide of several thousand daltons it is well under a tenth of one percent. A shift that small is invisible to any specification quoted at low precision, and it is equally invisible to anyone comparing masses by eye. The N terminus option is usually the larger of the two by a wide margin, so on a doubly capped peptide it is the pyroglutamyl state that dominates the total while the amidation hides inside it.

The total is where the two ends become legible. Take five alanine residues, whose unmodified average mass is 373.4093, and apply a cyclised glutamine N terminus together with an amidated C terminus. The two deltas take the mass to 355.3987. Choose the glutamate route for the cyclisation instead and the same chain lands on 354.4147, exactly 0.984016 lower. Seeing the two figures side by side makes plain that a specification sitting near either of them is describing a terminus state rather than a different peptide, and the molar mass cross check calculator reports either gap as a percentage so the two can be told apart at a glance.

Nothing on this page establishes that a given material carries any of these states. Whether a product is acetylated, amidated or cyclised is a property of the sample, and it has to come from the documentation that describes it or from a measurement, never from a calculation. What this page provides is the mass each option implies, so that a quoted figure becomes interpretable once the question is known, and so that a discrepancy comes with a small set of named candidate explanations rather than none at all. The distinction between a calculated mass and an established fact is the one to hold on to when a specification and a sequence are read together.

Two further limits follow from the design. The base mass is typed in by hand, so it can carry the wrong isotope convention, and since every delta here is monoisotopic, the monoisotopic mass calculator is the consistent starting point while the average molecular weight calculator gives an approximation. And the calculator is not given the sequence, so it cannot check that the first residue is a glutamine or a glutamate at all, which is the single precondition that makes either cyclisation option meaningful. In chain modifications belong to the modification mass calculator , and where a quoted mass has to be turned back into a composition, the mass to sequence estimator is the tool that starts from a mass rather than from a sequence.