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Protein Molecular Weight Calculator
Paste a protein or peptide sequence (one-letter codes or FASTA). You get the average and monoisotopic molecular weight, amino-acid composition, and the molar extinction coefficient and A280 of a 1 mg/mL solution for UV concentration measurements.
How to use the protein molecular weight calculator
- Paste the sequence in one-letter code. FASTA format is fine because the header line, spaces, numbers and line breaks are removed.
- The calculator adds the average (or monoisotopic) residue mass of every amino acid, plus one water for the free N- and C-termini.
- Read the molecular weight in Da and kDa. Use average mass for SDS-PAGE and buffers, and monoisotopic mass for high-resolution mass spectrometry of peptides.
- Use the extinction coefficient with Beer–Lambert (c = A280 / ε·l) to find concentration from a UV reading.
Worked examples
Insulin A chain (21 aa)
GIVEQCCTSICSLYQLENYCN
2383.71 Da average · 2382.00 Da monoisotopic
ε280 = 2 Tyr × 1490 + 2 cystines × 125 = 3230 M−1cm−1
Human ubiquitin (76 aa)
8564.84 Da (8.56 kDa)
One Tyr, no Trp: ε280 = 1490 M−1cm−1
Concentration from A280
A protein with ε = 43,824 M−1cm−1 reads A280 = 0.55 in a 1 cm cuvette.
c = 0.55 ÷ 43,824 = 12.6 µM
How protein molecular weight is calculated
When amino acids join, each peptide bond releases one water, so a protein is a chain of residues (amino acid minus H2O) plus one water for the terminal H and OH:
MW = Σ (residue mass) + 18.015 Da (average) MWmono = Σ (monoisotopic residue mass) + 18.011 Da
Average residue masses use natural isotope abundances and are what SDS-PAGE, gel filtration and weighing relate to. Monoisotopic masses use only the most abundant isotope (12C, 1H, 14N, 16O, 32S) and match the first peak in a high-resolution mass spectrum of a peptide. A quick estimate is 110 Da per residue.
Extinction coefficient at 280 nm
Absorbance at 280 nm comes from Trp, Tyr and disulfide-bonded cysteines. Using the Pace et al. (1995) values:
ε280 = 5500 × n(Trp) + 1490 × n(Tyr) + 125 × n(cystine)
For small molecules use the molecular weight calculator; to view a protein structure from the PDB, open the MolDraw protein viewer.
Studying a protein–ligand complex? View PDB structures in 3D and prepare ligands for docking with MolDraw's free tools.
Open protein viewerFrequently asked questions
How do you calculate the molecular weight of a protein?
Add the residue mass of every amino acid in the sequence and add 18.015 Da for one water. The average residue mass is about 110 Da, so 300 residues is roughly 33 kDa.
What is the difference between average and monoisotopic mass?
Average mass uses natural isotope abundances and suits bulk measurements. Monoisotopic mass uses only the lightest stable isotopes and matches high-resolution mass spectrometry of peptides.
How do I convert Da to kDa?
Divide by 1000. 8564.84 Da = 8.56 kDa. One dalton equals 1 g/mol.
How is the extinction coefficient calculated?
ε280 = 5500 × Trp + 1490 × Tyr + 125 × cystines (M−1 cm−1). Two values are given, depending on whether the cysteines form disulfides.
Why does my protein run at a different size on SDS-PAGE?
Post-translational modifications, unusual charge or incomplete unfolding change gel mobility. The calculated value is for the unmodified chain.
Does the calculator handle FASTA format?
Yes. Header lines that start with '>' are ignored, as are spaces, line breaks, numbers and stop symbols (*).
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