Protein Molecular Weight Calculator

Background.

Ordering a synthetic peptide, making up a 1 mM stock, or working out which band on a gel is your protein all start from one number: the molecular weight of the chain. Paste the sequence in one-letter code and you get its average mass in daltons, with the number of residues counted.

The sum is simple but has one catch. When two amino acids join, the peptide bond forms by giving off a molecule of water, so inside a chain each amino acid counts as a residue 18.015 Da lighter than the free amino acid on the reagent bottle. Glycine weighs 75.07 Da as a free amino acid and 57.05 Da as a residue. Add up the residue masses, put back one water for the free amino and carboxyl ends, and you have the mass of the intact, uncharged chain. The residue values are ExPASy ProtParam's averages, from glycine at 57.0519 Da to tryptophan at 186.2132 Da.

Average means the atomic masses are weighted by natural isotope abundance, which is the right basis for weighing, molar arithmetic and the deconvoluted mass of a whole protein. High-resolution mass spectrometry of peptides reports monoisotopic masses instead, built only from the lightest isotope of each element, and those come out lower by roughly 0.6 to 0.7 Da per 1,000 Da.

The figure describes the bare chain of the 20 standard amino acids exactly as typed. Disulfide bonds, phosphates, sugars, a trimmed starting methionine or a fusion tag all change the real molecule, and the common corrections are set out in the questions below.

What is protein molecular weight calculator?

A protein's average molecular weight is the mass of one molecule of its neutral covalent chain, using atomic masses averaged over natural isotope abundance, in daltons (1 Da corresponds to 1 g/mol). For a chain of n residues it is the sum of the n residue masses plus one water, 18.01528 Da. Because daltons and grams per mole are numerically equal, the result converts straight into bench quantities: a peptide of 1,019.14 Da weighs 1.0191 mg per micromole. The residue count gives the mean residue mass, close to 110 Da for most proteins, which makes a quick check on a pasted sequence.

How to use this calculator.

1. 01Paste the sequence in one-letter code. Capitals, lower case and spaces are all accepted, but remove FASTA header lines, position numbers and stop asterisks first.
2. 02Use only the 20 standard codes. Ambiguity codes such as B, Z and X, and the rarer U (selenocysteine) and O (pyrrolysine), have no mass here and are refused.
3. 03Enter exactly the chain you have: include any tag, linker or leftover cloning residues, and leave out a signal peptide or initiator methionine you know is removed.
4. 04Read the mass in daltons and divide by 1,000 for kilodaltons. Divide it by the residue count for the mean residue mass, which normally lands somewhere near 110 Da.
5. 05Correct for modifications before comparing with an experiment, and compare like with like: average masses with gels and whole-protein spectra, monoisotopic ones with high-resolution peptide spectra.

The formula.

Joining n amino acids into a linear chain makes n − 1 peptide bonds and releases n − 1 waters. Rather than track that directly, the calculation works with residue masses, each amino acid minus one water, and adds a single water back: M = Σ residue masses + 18.01528 Da. That extra water is the H on the free N-terminal amino group and the OH on the free C-terminal carboxyl. The residue values are ExPASy ProtParam's average masses, for example alanine 71.0788, cysteine 103.1388, lysine 128.1741 and tryptophan 186.2132 Da. Leucine and isoleucine are isomers and share 113.1594 Da, so mass alone can never tell them apart.

Composition matters as much as length. Tryptophan weighs more than three times as much as glycine, so a glycine–serine linker averages well under 110 Da per residue while an aromatic-rich stretch runs above it. The result is the neutral molecule, not the m/z value a mass spectrometer shows; with n added protons a peak appears at (M + n × 1.00728) ⁄ n. Nothing else is modelled: no disulfide oxidation, post-translational modification, isotope labelling or processing of the chain.

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.
2. [2]IUPAC. Gold Book current 2026. Relative molecular mass terminology. Retrieved 2026-08-06.
3. [3]OpenStax, Rice University. University Physics, 2016. Volume 1 mechanics and Volume 2 thermodynamics. Retrieved 2026-08-06.