Protein Molecular Weight Calculator
Estimates the molecular weight of a protein from its amino acid count and average residue mass. Use it when designing proteins, interpreting SDS-PAGE results, or planning purification workflows.
Last updated: September 2026
Formula below · 2 sources (genome.gov, Wikipedia) · Updated Sep 2026
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About this calculator
A protein is a chain of amino acids linked by peptide bonds. Each time two amino acids join, a water molecule (18 Da) is released. The total molecular weight therefore equals the sum of the free amino acid masses minus the water lost at each peptide bond: MW = (aminoAcids × averageMW) − ((aminoAcids − 1) × 18). Use the average mass of a free amino acid, about 128 Da for typical protein composition; the often-quoted 110 Da is the average residue mass with the water already removed, so if you only have that figure use MW ≈ aminoAcids × 110 instead (entering 110 here would subtract the water twice and understate the mass by about 14%). For precise work, sum the individual residue masses from a table; this calculator gives a rapid estimate when the exact sequence is unknown.
How to use
Suppose you have a protein of 300 amino acids. Step 1 — Enter 300 in 'Number of Amino Acids'. Step 2 — Enter 128 in 'Average Free Amino Acid MW'. Step 3 — The calculator computes: MW = (300 × 128) − ((300 − 1) × 18) = 38,400 − 5,382 = 33,018 Da (≈ 33 kDa), matching the 300 × 110 Da residue rule of thumb. This estimate helps you predict where the band should appear on a gel or which membrane to choose for a Western blot.
Frequently asked questions
Why do we subtract 18 Da for each peptide bond in the molecular weight formula?
When two amino acids form a peptide bond, a molecule of water (H₂O, 18 Da) is released through a condensation reaction. A chain of N amino acids forms N−1 peptide bonds, so N−1 water molecules are lost in total. Failing to subtract this water would overestimate the protein's mass. This correction is why the formula uses (aminoAcids − 1) × 18 rather than N × 18.
What average molecular weight should I use for a typical amino acid?
The commonly accepted average is approximately 110 Da per residue, which reflects the natural abundance of all 20 standard amino acids in most proteins. However, if your protein is unusually rich in large residues like tryptophan (186 Da) or small ones like glycine (57 Da), the average will shift accordingly. For the most accurate result, use the known sequence and sum individual residue masses from an amino acid table. This calculator is best for quick estimates when the full sequence is unavailable.
How does protein molecular weight affect SDS-PAGE band migration?
In SDS-PAGE, proteins are denatured and coated with the detergent SDS, giving them a uniform negative charge proportional to their mass. Smaller proteins migrate faster through the polyacrylamide gel, while larger ones move more slowly. By knowing your protein's estimated molecular weight, you can predict where it will appear relative to a molecular weight ladder. This helps confirm a successful expression or purification step and detect degradation products or unexpected isoforms.