A peptide’s molecular weight equals the sum of its residue masses plus one water molecule: molecular weight = sum(residue mass for each residue) + 18.02 Da. This post explains why exactly one water gets added back for the whole chain, and how the result feeds into mass, mole and concentration calculations elsewhere on this site.
A sequence is a chain, not a pile of loose amino acids
Write out a sequence like GHK and it is tempting to add up the molecular weight of glycine, histidine and lysine as free amino acids and call it done. That overcounts. When two amino acids join in a peptide bond, they lose a water molecule: the carboxyl group of one and the amino group of the next condense into an amide bond, releasing H2O.
For a chain of n residues there are n-1 peptide bonds, so n-1 water molecules are lost relative to n separate free amino acids. Reference tables sidestep having to redo that subtraction every time by publishing residue masses directly, which are already the free amino acid mass minus one water. Summing residue masses and adding back exactly one water for the whole chain gives the same answer with less bookkeeping.
How do you calculate peptide molecular weight from a sequence?
molecular weight = sum(residue mass for each residue in the sequence) + one waterTwo versions of “residue mass” exist depending on what you are computing:
average molecular weight = sum(average residue masses) + 18.01528 Da
monoisotopic mass = sum(monoisotopic residue masses) + 18.010565 DaAverage residue masses use each element’s naturally occurring isotopic abundance, which is what a benchtop balance effectively measures. Monoisotopic masses use only the most abundant isotope of each element, which is what a mass spectrometer typically resolves as the base peak. The two numbers are close but not identical, and which one a source is quoting matters; that distinction gets its own explanation in monoisotopic mass vs. average molecular weight.
This site’s average molecular weight calculator and monoisotopic mass calculator both run exactly this sum, reading residue masses from one reference table so the two methods stay consistent with each other.
Molecular formula is the same idea, one level lower
Instead of summing masses, you can sum atoms. Each free amino acid has a known formula (carbon, hydrogen, nitrogen, oxygen and sulfur counts). Add up the formulas for every residue in the sequence, then subtract n-1 waters (two hydrogens and one oxygen per peptide bond) the same way. The molecular formula calculator does this and reports the resulting elemental composition, which is the more granular version of the same mass-minus-water logic.
From molecular weight to moles
A molecular weight by itself is a mass-per-mole figure, not a mass and not a mole count. To go from a mass of peptide to how many moles that represents, you need to divide by the molecular weight:
moles = mass / molecular weightThe mass to moles calculator does that conversion once you have a molecular weight, whether it came from a sequence-based calculation here or from a vial label. This is also the point where unit families start to matter: mass can be grams, milligrams or micrograms, and moles can be moles, millimoles or micromoles, so getting the scale right before dividing is worth a pass through the unit conversion guide if the numbers look off by a factor of a thousand.
Sanity checking a published molecular weight
Sequence-derived arithmetic is exact given a correct sequence, but sequences get mistyped and published values sometimes come from a different source than the one you are working from. If you already have a molecular weight from a certificate of analysis or a supplier’s page, the molar mass cross-check calculator compares that supplied value against the value computed from the sequence you enter and reports the difference, so a transposed residue or an extra glycine does not go unnoticed.
What this does not cover
None of these calculators infer a sequence from a mass, model a peptide’s three-dimensional structure, or account for post-translational modifications unless a modification mass is entered separately (the terminal modification calculator handles common N- and C-terminal changes). They also do not tell you what to do with a synthesized peptide; they compute a number from a sequence, nothing more.
In short: peptide molecular weight = sum(residue masses) + one water molecule, using average residue masses for average molecular weight or monoisotopic residue masses for monoisotopic mass.