Protein molecular weight calculator
Paste a protein sequence in one-letter code; FASTA headers, spaces, numbers and a final stop “*” are ignored. The calculator adds the residue masses, gives the average and monoisotopic molecular weight, and estimates the extinction coefficient at 280 nm from tryptophan, tyrosine and cystine — with all cysteines paired and with none paired.
Runs in your browser: nothing you enter is sent anywhere.
How to use it
- Paste the sequence in one-letter code (upper or lower case).
- Read the average molecular weight in daltons and kilodaltons, and the monoisotopic mass.
- Use the extinction coefficient that matches your protein: “cystines” if its cysteines form disulfide bonds, “reduced” if not or if a reducing agent is present.
- MW = Σ residue masses + 18.01524 (average); monoisotopic with 18.01056
- ε₂₈₀ = 5500 × n(Trp) + 1490 × n(Tyr) + 125 × n(cystine), M⁻¹·cm⁻¹
- A280 (1 mg/mL) = ε₂₈₀ ÷ MW
Residue masses: ExPASy average and monoisotopic tables (e.g. Gly 57.0519, Trp 186.2132).
Worked example
The dipeptide GG: 2 × 57.0519 + 18.01524 = 132.12 Da.
The default sequence, the 30-residue B chain of human insulin (FVNQHLCGSHLVEALYLVCGERGFFYTPKT), weighs 3,429.96 Da (monoisotopic 3,427.6845 Da). It has no tryptophan, two tyrosines and two cysteines: ε = 2 × 1490 = 2,980 M⁻¹·cm⁻¹ reduced, or 3,105 if the two cysteines formed one cystine, so 1 mg/mL gives an A280 of about 0.87–0.91.
Tips
- SDS-PAGE is approximate. Bands can run noticeably above or below the calculated mass, especially for glycosylated or very acidic proteins.
- Check the start. Many mature proteins lack the first methionine (−131.19 Da).
- Tags count. A His-tag, linker or fusion partner adds its own residues; paste the full expressed sequence.
Frequently asked questions
How is a protein’s molecular weight calculated?
Each amino acid in a chain has lost one water when the peptide bond formed, so the mass is the sum of the residue masses plus one water for the two free ends. The calculator uses the ExPASy table of residue masses: average masses for the molecular weight (water 18.01524) and monoisotopic masses (water 18.01056).
Average or monoisotopic mass — which do I need?
The average mass reflects the natural mix of isotopes and suits SDS-PAGE, gel filtration and concentration work. The monoisotopic mass uses only the most common isotope of each element and matches the first peak in high-resolution mass spectra of small peptides.
How is the extinction coefficient estimated?
With the method of Pace et al. (1995), also used by ProtParam: ε₂₈₀ = 5500 × Trp + 1490 × Tyr + 125 × cystines, in M⁻¹·cm⁻¹. A cystine is a pair of cysteines in a disulfide bond, so the value is given both with every cysteine paired and with all reduced.
What is A280 of 1 mg/mL used for?
It is ε divided by the molecular weight: the absorbance a 1 mg/mL solution gives in a 1 cm cuvette. Divide a measured A280 by it to get the concentration in mg/mL. A protein with no Trp or Tyr does not absorb at 280 nm, and this method cannot be used.
Are modifications included?
No. Glycosylation, phosphorylation, a removed initiator methionine or signal peptide all change the real mass; add or remove them yourself. Only the 20 standard amino acids are accepted.