Protein Molecular Weight Calculator

Background.

Type a protein or peptide sequence in one-letter code and this page returns its average molecular weight in daltons — the number you need to plan an SDS-PAGE gel, convert between milligrams and moles, sanity-check a mass-spectrometry readout, or design a synthetic peptide order.

The arithmetic is a sum with one twist. Each amino acid in a chain contributes its residue mass — the free amino acid minus one water — because forming every peptide bond condenses out H₂O. Summing residue masses over the sequence and adding back a single water for the intact chain's free N- and C-termini gives the neutral average mass. Residue masses run from glycine's 57.05 Da to tryptophan's 186.21 Da, with the often-quoted ‘average residue’ near 110 Da — a useful mental shortcut (a 300-residue protein weighs roughly 33 kDa) that this page replaces with the exact sum.

‘Average’ is a specific technical choice: masses are computed from natural isotope abundances, matching what a gel, an analytical balance, or a deconvoluted ESI spectrum of a large protein reports. High-resolution mass spectrometry of peptides instead resolves monoisotopic masses — lightest-isotope-only values that sit measurably below average ones (about 0.6 Da per kDa) — and the two must never be mixed in one comparison.

The model is the bare, unmodified chain of the 20 standard residues: no disulfide oxidation (subtract 2.016 Da per bridge formed), no phosphorylation (+79.97 each), no glycosylation, no N-terminal methionine trimming. Real mature proteins carry such differences routinely, which is why a measured mass rarely matches the sequence mass exactly — and why the gap between the two is itself diagnostic information.

What is protein molecular weight calculator?

A protein's average molecular weight is the mass of its neutral covalent chain computed with natural-isotope-abundance atomic masses: the sum of the residue masses of its amino acids (each residue being the amino acid less the water lost in peptide-bond formation) plus one H₂O (18.015 Da) for the chain's termini. It is expressed in daltons (g/mol). The companion output, residue count, is simply the sequence length — together they give the mean residue mass, a quick check that a sequence was typed correctly (values far from ≈110 Da suggest a problem).

How to use this calculator.

1. 01Paste or type the sequence in standard one-letter code (ACDEFGHIKLMNPQRSTVWY) — the 20 canonical residues; ambiguity codes like B, Z, or X have no defined mass and are rejected.
2. 02Read the average molecular weight in daltons; divide by 1,000 for the kDa figure gel markers use.
3. 03Use the residue count to compute the mean residue mass as a typo check — a run of accidental glycines drags it far below the usual ≈105–115 Da band.
4. 04Convert to molar terms directly: the example's 1,019.14 Da means 1.019 mg of pure peptide is 1 µmol — the arithmetic behind every stock-solution recipe.
5. 05Adjust for known chemistry before comparing to an experiment: −2.016 Da per disulfide bridge, +79.97 per phosphate, +42.01 per acetylation, and expect monoisotopic — not average — values from high-resolution MS of peptides.

The formula.

Peptide-bond formation is a condensation: joining two amino acids expels one water, so a chain of n residues contains n amino acids minus (n − 1) waters. Bookkeeping is cleanest with residue masses — each amino acid's mass less 18.015 — summed over the chain, plus one water restored for the free α-amino and α-carboxyl ends of the intact molecule. The masses are averages over natural isotopic abundance (carbon 12.011, not 12.000), which is what distinguishes this figure from the monoisotopic mass of high-resolution MS; the gap grows with size, reaching about 9 Da for a 15 kDa protein, entirely from heavy-isotope statistics. The heaviest residue is tryptophan (186.21), the lightest glycine (57.05), so sequences of equal length can differ in mass by a factor of three in principle. The engine sums per-residue Decimal values in one pass and rounds once at the output — identical letter-by-letter arithmetic to doing it by hand from a residue-mass table, with no accumulation error.

A worked example.

Frequently asked questions.

References& sources.

1. [1]ExPASy, Swiss Institute of Bioinformatics. ProtParam documentation current 2026. Average amino-acid masses and molecular-weight calculation. Retrieved 2026-08-06. independence: primary; access: open.
2. [2]IUPAC. Gold Book current 2026. Relative molecular mass terminology. Retrieved 2026-08-06. independence: secondary-check; access: open.
3. [3]OpenStax, Rice University. University Physics, 2016. Volume 1 mechanics and Volume 2 thermodynamics. Retrieved 2026-08-06. independence: primary; access: open.