Protein Molecular Weight Calculator
Paste a protein or peptide sequence in one-letter or three-letter code to get its molecular weight in daltons and kilodaltons, monoisotopic mass, theoretical pI, net charge, extinction coefficient at 280 nm, molecular formula and amino acid composition.
Last updated:
Amino acid composition
Net charge vs pH
Concentration from A280
How to use the Protein Molecular Weight Calculator
- Paste the sequence in one-letter code (plain or FASTA) or switch to 3-letter input for sequences like Tyr-Gly-Gly-Phe.
- Choose average or monoisotopic mass. Use average mass for SDS-PAGE and solution work, monoisotopic for high-resolution mass spectrometry.
- Read the results: molecular weight, pI, net charge at your chosen pH, extinction coefficient and formula update instantly.
- Enter an A280 reading to convert absorbance into mg/mL and µM using the calculated extinction coefficient.
- Copy the results or download the amino acid composition as CSV.
Formulas used
- Molecular weight:
MW = Σ (count × residue mass) + 18.01524 Da(average) or+ 18.010565 Da(monoisotopic). Residue masses are listed below. - Net charge at pH: each basic group (N-terminus, K, R, H) contributes
+1 / (1 + 10pH − pKa)and each acidic group (C-terminus, D, E, C, Y) contributes−1 / (1 + 10pKa − pH). - Isoelectric point (pI): the pH where the net charge is 0, found by bisection between pH 0 and 14.
- Extinction coefficient (Pace method):
ε280 = 5,500 × nTrp + 1,490 × nTyr + 125 × nCystineM⁻¹cm⁻¹.Abs 0.1% = ε / MWis the absorbance of a 1 g/L solution in a 1 cm cell. - Concentration from A280 (Beer–Lambert):
c (M) = A280 / (ε × path length), and mg/mL = M × MW. - GRAVY: the average Kyte–Doolittle hydropathy value over all residues. Aliphatic index:
A + 2.9 × V + 3.9 × (I + L), using mole percentages.
Amino acid residue masses
| Amino acid | Codes | Residue average mass (Da) | Residue monoisotopic mass (Da) | Residue formula |
|---|---|---|---|---|
| Glycine | Gly, G | 57.0519 | 57.02146 | C2H3NO |
| Alanine | Ala, A | 71.0788 | 71.03711 | C3H5NO |
| Serine | Ser, S | 87.0782 | 87.03203 | C3H5NO2 |
| Proline | Pro, P | 97.1167 | 97.05276 | C5H7NO |
| Valine | Val, V | 99.1326 | 99.06841 | C5H9NO |
| Threonine | Thr, T | 101.1051 | 101.04768 | C4H7NO2 |
| Cysteine | Cys, C | 103.1388 | 103.00919 | C3H5NOS |
| Leucine / Isoleucine | Leu L / Ile I | 113.1594 | 113.08406 | C6H11NO |
| Asparagine | Asn, N | 114.1038 | 114.04293 | C4H6N2O2 |
| Aspartic acid | Asp, D | 115.0886 | 115.02694 | C4H5NO3 |
| Glutamine | Gln, Q | 128.1307 | 128.05858 | C5H8N2O2 |
| Lysine | Lys, K | 128.1741 | 128.09496 | C6H12N2O |
| Glutamic acid | Glu, E | 129.1155 | 129.04259 | C5H7NO3 |
| Methionine | Met, M | 131.1926 | 131.04049 | C5H9NOS |
| Histidine | His, H | 137.1411 | 137.05891 | C6H7N3O |
| Phenylalanine | Phe, F | 147.1766 | 147.06841 | C9H9NO |
| Arginine | Arg, R | 156.1875 | 156.10111 | C6H12N4O |
| Tyrosine | Tyr, Y | 163.1760 | 163.06333 | C9H9NO2 |
| Tryptophan | Trp, W | 186.2132 | 186.07931 | C11H10N2O |
Tips for reliable numbers
- Use the mature chain. Remove signal peptides, propeptides and tags that are cleaved off, or include a His-tag if it stays on the protein you purify.
- SDS-PAGE bands rarely match exactly. Glycosylation, high proline or charged content can make a protein run 10–20% away from its calculated MW.
- Check disulfides. Each disulfide lowers the mass by 2.016 Da; for intact-mass MS of a protein with 4 disulfides, subtract about 8.06 Da.
- Working from DNA? Translate the coding sequence with the DNA to Protein Translator first, then paste the protein here.
Frequently asked questions
How is protein molecular weight calculated?
The molecular weight is the sum of the residue masses of every amino acid in the chain plus one water molecule (18.015 Da average) for the free N-terminal H and C-terminal OH. Residue masses are the free amino acid masses minus water, because one water is lost for every peptide bond formed.
What is the difference between average and monoisotopic mass?
Average mass uses the natural mix of isotopes for each element and matches what you measure in bulk, for example by gel filtration or SDS-PAGE. Monoisotopic mass uses only the most abundant isotope (12C, 1H, 14N, 16O, 32S) and matches the first peak of a high-resolution mass spectrum.
How do I convert daltons to kilodaltons?
Divide by 1,000. A protein of 14,313 Da is 14.3 kDa. As a quick estimate, the average amino acid residue weighs about 110 Da, so a 300-residue protein is roughly 33 kDa.
How is the extinction coefficient at 280 nm estimated?
With the Pace et al. (1995) method: ε280 = (number of Trp × 5,500) + (number of Tyr × 1,490) + (number of cystines × 125) M⁻¹cm⁻¹. A cystine is a disulfide-bonded pair of cysteines, so the value is shown both with all Cys paired and with all Cys reduced. Proteins without Trp and Tyr cannot be measured reliably at 280 nm.
Why does the pI differ from other tools?
The theoretical pI is the pH where the summed charges of the termini and the ionizable side chains (D, E, C, Y, H, K, R) equal zero. Different tools use different pKa values, so the result can shift by a few tenths. Choose EMBOSS, Lehninger, DTASelect or Solomon to compare. Real pI also depends on folding and modifications.
Does it include post-translational modifications?
No. The mass is for the unmodified chain as written. Disulfide bonds remove 2.016 Da each, phosphorylation adds about 79.97 Da per site, and glycosylation can add thousands of daltons, so adjust by hand if your protein carries modifications.
Is my sequence sent anywhere?
No. Every calculation runs locally in your browser, so proprietary sequences stay on your device.
Are all the tools on FreeToolCabin tested for quality and accuracy?
Yes! Every tool on our site undergoes automated Q/A testing in real browser environments to ensure high precision, correct output, and zero errors. If you happen to spot a bug or have a suggestion, please contact us at [email protected] and our team will review it right away.