Protein Molecular Weight Calculator
Paste a protein or peptide sequence using standard one-letter amino acid codes to estimate its molecular weight. Whitespace and line breaks are ignored, and case does not matter.
Last updated: September 25, 2026
Frequently asked questions
How is this different from the Molecular Weight Calculator?
The Molecular Weight Calculator works from a chemical formula like H2O or NaCl. This tool works directly from a protein or peptide's amino acid sequence, summing residue masses rather than parsing element counts.
Which amino acid codes are supported?
The 20 standard one-letter codes (A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V). Ambiguity codes like X, B, J, and Z, and non-standard characters, are flagged rather than guessed at.
Why isn't the molecular weight just the sum of the individual amino acids?
Forming each peptide bond releases one water molecule, so residues in a chain weigh slightly less than the free amino acids. This calculator sums residue masses (already accounting for that) and adds back one water molecule for the two ends of the finished chain.
Does this include modifications like glycosylation or disulfide bonds?
No. It calculates an unmodified, sequence-only estimate. Post-translational modifications, glycosylation, disulfide bonds, bound cofactors, and multimer (multi-chain) assembly all change a real protein's mass and are not modeled here.
Can I paste a sequence with line breaks or FASTA formatting?
Line breaks and spaces are removed automatically. Remove any FASTA header line (starting with >) before pasting, since it is not a valid amino acid sequence.
How accurate is this compared to mass spectrometry?
It gives a useful estimate using average residue masses, but it is not a substitute for a measured mass. Real proteins can differ due to modifications this tool does not model, and mass spectrometry measures the actual molecule directly.