Protein Molecular Weight Calculator

Protein molecular weight — often abbreviated as MW and expressed in Daltons (Da) or kilodaltons (kDa) — is the sum of the atomic masses of every atom in a polypeptide chain. It is one of the most fundamental physical properties used in biochemistry, structural biology, and proteomics.

Knowing the molecular weight of a protein is essential for designing SDS-PAGE gels, interpreting mass spectrometry data, calculating molar concentrations from spectrophotometric absorbance readings, and determining stoichiometric ratios in binding assays.

The mass a protein has is not a rounding of its sequence length. Two proteins of the same residue count can differ by tens of kilodaltons, because tryptophan alone contributes 204.23 Da per residue and leucine only 113.16 Da, while a glycine residue adds 57.02 Da. Sequence order changes nothing: only the composition, the chain count and the bridges between chains move the number.

The calculator sums the molar mass of each free amino acid in the sequence. Each peptide bond is formed by a condensation reaction that releases one water molecule (18.01528 Da on average atomic weights, 18.010565 Da monoisotopic). A chain of n residues has n - 1 peptide bonds, and c chains joined only by peptide bonds have n - c bonds in total.

If the protein contains disulfide bridges (S-S bonds between cysteine residues), each bridge removes two hydrogen atoms (2.01565 Da). The final molecular weight is: MW = sum(n_i x m_i) - (N - c) x 18.01528 - b x 2.01565. Two chains of 21 and 30 residues share 49 peptide bonds rather than 50, which is where most hand calculations slip.

The extinction coefficient at 280 nm is calculated using the Pace convention: ε₂₈₀ = 5,500 × nTrp + 1,490 × nTyr + 125 × nCys-free, in M⁻¹ cm⁻¹. This value is used by UV spectrophotometers to estimate protein concentration via the Beer-Lambert law.

Molecular Weight (Da / kDa): The calculated mass of the entire protein or complex. 1 kDa = 1,000 Da.

Extinction Coefficient at 280 nm (M⁻¹ cm⁻¹): How strongly the protein absorbs UV light at 280 nm. Divide the measured absorbance (A₂₈₀) by this coefficient to get the molar concentration.

Residue Composition Table: the count, mass contribution and share of the joined residue mass for each amino acid type, sorted by mass.

Amount Conversion: If an amount was entered, the result shows the equivalent mass (moles → µg/mg) or moles (mg → µmol).

• Post-translational modifications: Glycosylation, phosphorylation, acetylation, ubiquitination, and lipid anchoring all add mass that cannot be predicted from the sequence alone.
• Disulfide bonds: each S-S bridge subtracts 2.01565 Da. Antibodies have many of them, which is why an IgG heavy chain pair lands well below the sum of its free residues.
• Mass type: Average masses are suitable for weighing, gel estimation, and centrifugation; monoisotopic masses are needed for high-resolution mass spectrometry peak assignment.

• SDS-PAGE gel design: Choose an appropriate acrylamide percentage and molecular weight marker ladder.
• Mass spectrometry experiment planning: Predict intact-mass peaks and verify peptide fragment masses after tryptic digestion.
• Spectrophotometric protein quantitation: Combine the extinction coefficient with A₂₈₀ readings to calculate molar concentrations without a Bradford or BCA assay.
• Reagent preparation: Convert between molar amounts (nmol, µmol) and mass (µg, mg) for reconstituting lyophilised proteins.

• Assumes standard, unmodified amino acids. Post-translational modifications are not accounted for.
• The extinction coefficient formula assumes all non-bridged cysteines are reduced; oxidized cysteines contribute differently.
• Ambiguity codes (B, Z, J, X) use the arithmetic mean of the possible residues, introducing small uncertainty.