Modification Mass Calculator

Each mass shift on this page is derived the same way: write down the atoms the reaction adds or removes, and the delta follows. Acetylation puts a two carbon acetyl group where a hydrogen was, which adds two carbons, two hydrogens and one oxygen and gives 42.010565 Da on the monoisotopic convention. Amidation replaces a terminal hydroxyl with an amine, taking away an oxygen and a hydrogen while adding a nitrogen and two hydrogens, for a net loss of 0.984016 Da. Oxidation is the addition of a single oxygen and nothing else, so its delta is exactly the mass of one oxygen atom. The same balance is worked through with sources in molecular weight and peptide calculations .

The remaining two are one substitution in opposite directions. Phosphorylation adds a phosphate group, which as a monoisotopic addition of one hydrogen, one phosphorus and three oxygens is 79.966331 Da. Deamidation turns an asparagine or glutamine side chain into the corresponding acid by replacing an amide with a hydroxyl, adding an oxygen while removing a nitrogen and two hydrogens, which gives 0.984016 Da. That is the exact negative of the amidation delta, and the pairing is a useful reminder that a substitution close to mass neutral is as likely to move a mass slightly up as slightly down.

Working the deltas out this way rather than looking them up is the part that generalises. The catalogue on this page has five entries and UniMod has hundreds, so anything outside the five has to be derived the same way, and the atom balance is the only method that works without a lookup table. A shift that is not obviously any of these five will still fall out of writing the reactants and products out in full. It is also why the molecular formula calculator is a useful companion: the same delta expressed as a formula difference confirms which atoms are supposed to move.

The propagation is a multiplication, and that is why a count field exists here. One acetylation is 42.010565 Da and two are 84.02113, so a peptide carrying the same modification at more than one site is a base mass plus that product. The multiplication is only correct when every site carries the same thing, which is worth stating plainly because a peptide with one acetylation and one phosphorylation is not two sites of a single modification and cannot be expressed as one delta and one count. It is also why the shift applied is reported alongside the result, so the size of the chemistry stays visible instead of being buried inside a total.

The size of the shift relative to the base matters more than it first appears. Forty two daltons is 11.3 percent of a 373 Da chain and under two percent of a 2300 Da one, so the same chemistry is a far larger perturbation on a short peptide than on a long one, and a tolerance expressed as a percentage therefore means something different in the two cases. A match reported within tolerance is weaker evidence on a short chain than the same tolerance on a long one, which is a good reason to prefer an absolute tolerance when a modified mass is compared against a measured value. The molar mass cross check calculator reports both the absolute and the relative gap for exactly this reason.

Every figure quoted here is taken from UniMod with its accession number attached, and UniMod works in monoisotopic masses. That is the right convention for identifying a modification against a spectrum and the wrong one to mix with an average mass. The average mass delta for acetylation, computed from average atomic weights, is about 42.037 rather than 42.010565, so adding the monoisotopic figure to an average base leaves the total about 0.03 Da above where the chemistry actually puts it. Small, but larger than the four decimal places either calculator displays.

There is an instructive exception to that worry. Amidation looks safe in either convention, because it swaps an oxygen for a nitrogen and the two elements have nearly the same mass, so the net stays under a dalton either way. The pattern is general: the closer a modification is to mass neutral, the less the convention matters, and the further it moves the mass, the more it matters. When a figure that is internally consistent to the last digit is wanted, take the base from the monoisotopic mass calculator rather than the average molecular weight calculator , and stay in that convention through every shift.

The most useful way to run this calculation is in reverse, and the page supports that without saying so. When a specification quotes a modified mass and the unmodified mass is known from the sequence, subtracting one from the other yields the delta the specification implies. Five alanine residues have an average mass of 373.4093, and a specification quoting 415.42 implies a shift of 42.0107, which is an acetylation to within the rounding of the quoted figure. The identification is then confirmed by running the acetylation forward and comparing, which is a measurement the mass difference calculator makes directly.

The honest limit on all of this is scope. The catalogue here is five modifications and the UniMod database contains hundreds, so anything outside the list has to be looked up in UniMod and applied by hand, and this page will not produce that answer. It also does not check the chemistry: whether the sequence contains a lysine that could carry an acetyl group, or a tyrosine that could be phosphorylated, is a separate question about the molecule, and a shift applied to a base with no site for it is arithmetic that means nothing. The two ends of the chain are handled separately, where the terminal modification calculator treats acetylation, amidation and both cyclisation routes as independent states.