Protein Molecular Weight Calculator
Paste your amino acid sequence in single-letter code (FASTA format accepted) and get the protein molecular weight instantly in Daltons and kilodaltons. You also get the residue count, molar extinction coefficient at 280 nm, and the amino acid composition. Switch between average mass (standard biochemistry) and monoisotopic mass (mass spectrometry). Results update as you type.
Formula
Worked example
For a 3-residue peptide Ala-Trp-Gly: residue masses are 71.079 + 186.213 + 57.052 = 314.344 Da. Adding terminal water: 314.344 + 18.015 = 332.359 Da (0.332 kDa). The extinction coefficient is (0 x 5500) + (0 x 1490) + (0 x 125) = 0 since there is no Trp, Tyr or Cys. Wait, Trp IS present: (1 x 5500) = 5500 M^-1 cm^-1.
How protein molecular weight is calculated
A protein is a chain of amino acids linked by peptide bonds. Each peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of the next, releasing a water molecule. This means the mass of the full chain is not simply the sum of the free amino acid masses. Instead, it equals the sum of the residue masses (free amino acid mass minus one water molecule each) plus one water molecule added back for the H at the N-terminus and the OH at the C-terminus. The formula is: MW = sum of all residue masses + 18.015 Da. Residue masses for all 20 standard amino acids range from 57.05 Da (glycine) to 186.21 Da (tryptophan), giving an average of about 111 Da per residue.
Average mass versus monoisotopic mass
Two conventions exist for reporting mass. Average mass uses the natural abundance of all isotopes for each element, for example carbon has both carbon-12 and carbon-13 in its natural mix. This is the value measured by gel electrophoresis, Bradford assay, and most routine laboratory methods. Monoisotopic mass uses only the most abundant isotope of each element (carbon-12, hydrogen-1, nitrogen-14, oxygen-16, sulfur-32). For most proteins below about 2 kDa, the monoisotopic peak is the most intense peak in the mass spectrum, making this the preferred unit for high-resolution mass spectrometry. As protein mass increases above roughly 5 kDa, the monoisotopic peak becomes very small compared to the isotope envelope and average mass becomes more practical. Use average mass for SDS-PAGE and most biochemical work, and monoisotopic mass for mass spectrometry.
Molar extinction coefficient and protein concentration
The molar extinction coefficient (epsilon) at 280 nm tells you how strongly a protein absorbs UV light. It is estimated using the Edelhoch method: each tryptophan residue contributes 5500 M^-1 cm^-1, each tyrosine contributes 1490 M^-1 cm^-1, and each cysteine involved in a disulfide bond contributes 125 M^-1 cm^-1. This calculator uses the reduced cysteine value (125) as a conservative default. Once you know epsilon, Beer-Lambert law gives you protein concentration: concentration (M) = absorbance at 280 nm divided by epsilon, divided by path length in cm. For a 1 cm cuvette this simplifies to c = A280 / epsilon. This method is rapid, non-destructive, and accurate when Trp and Tyr content is known. If the protein has no Trp, Tyr or Cys, the extinction coefficient is zero and A280-based quantification is unreliable.
Practical applications and limitations
Protein molecular weight matters for gel electrophoresis (choosing the right percentage polyacrylamide), size exclusion chromatography (column selection), dialysis membrane cutoffs, ultrafiltration spin column selection, and estimating expression yields. This calculator assumes a linear, unmodified polypeptide. Post-translational modifications add extra mass: glycosylation can add several to tens of kDa, phosphorylation adds about 80 Da per site, and PEGylation can add very large amounts. Disulfide bonds remove 2 Da per bond. Signal peptides that are cleaved after translation should be excluded from the sequence. For the most accurate molecular weight of a modified protein, mass spectrometry is the gold standard.
The 20 standard amino acids and their residue masses
| Code | Name | Three-letter | Avg residue mass (Da) | Monoisotopic residue mass (Da) |
|---|---|---|---|---|
| A | Alanine | Ala | 71.079 | 71.037 |
| R | Arginine | Arg | 156.188 | 156.101 |
| N | Asparagine | Asn | 114.104 | 114.043 |
| D | Aspartate | Asp | 115.089 | 115.027 |
| C | Cysteine | Cys | 103.139 | 103.009 |
| E | Glutamate | Glu | 129.116 | 129.043 |
| Q | Glutamine | Gln | 128.131 | 128.059 |
| G | Glycine | Gly | 57.052 | 57.021 |
| H | Histidine | His | 137.141 | 137.059 |
| I | Isoleucine | Ile | 113.159 | 113.084 |
| L | Leucine | Leu | 113.159 | 113.084 |
| K | Lysine | Lys | 128.174 | 128.095 |
| M | Methionine | Met | 131.193 | 131.04 |
| F | Phenylalanine | Phe | 147.177 | 147.068 |
| P | Proline | Pro | 97.117 | 97.053 |
| S | Serine | Ser | 87.078 | 87.032 |
| T | Threonine | Thr | 101.105 | 101.048 |
| W | Tryptophan | Trp | 186.213 | 186.079 |
| Y | Tyrosine | Tyr | 163.176 | 163.063 |
| V | Valine | Val | 99.133 | 99.068 |
Residue mass = free amino acid mass minus water (18.015 Da). Values are average masses (natural isotope abundance).
Frequently asked questions
Why does the calculator subtract water from amino acid masses?
When two amino acids form a peptide bond, one water molecule (H2O, 18.015 Da) is released in the condensation reaction. In a chain of n amino acids there are n-1 such bonds, so n-1 water molecules are lost. However, the two chain termini each retain an H (at the N-terminus) and an OH (at the C-terminus), which together equal one water molecule. The net result is: protein mass = sum of individual free amino acid masses minus (n-1) water molecules = sum of residue masses plus one water molecule. Residue mass is simply the free amino acid mass minus one water.
What is the difference between Daltons, g/mol and kDa?
These three units all describe the same quantity. One Dalton (Da) is defined as one unified atomic mass unit, equal to one twelfth the mass of a carbon-12 atom, which is 1.66054 x 10^-24 grams. For a pure substance, the molar mass in grams per mole numerically equals the molecular mass in Daltons: a protein of 15,000 Da has a molar mass of 15,000 g/mol. One kilodalton (kDa) equals 1000 Da, so that same protein is 15 kDa. Biochemists almost always report protein masses in kDa because proteins range from a few kDa (small peptides) to several hundred kDa (large complexes).
Can I paste a FASTA sequence into this calculator?
Yes. Lines starting with ">" (the FASTA header) are automatically ignored. Spaces, digits, asterisks, and line breaks are stripped. Only standard single-letter amino acid codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y) are counted. Any other characters are silently skipped and the number of skipped characters is shown in the Note output so you can check for any unexpected symbols.
Which proteins have a zero extinction coefficient at 280 nm?
A protein has an extinction coefficient of zero at 280 nm only if it contains no tryptophan, no tyrosine, and no cysteine residues. These are rare because most proteins contain at least a few tyrosines. Examples of naturally Trp-free, Tyr-free proteins include some small structural peptides. If your calculated extinction coefficient is zero, consider alternative quantification methods such as the Bradford assay (Coomassie dye binding), the BCA assay (bicinchoninic acid, which detects peptide bonds), or nanodrop absorbance at 205 nm (peptide bond absorption).
Does this include signal peptides and propeptides?
No. This calculator computes the mass of the exact sequence you enter. If you paste the full preprotein sequence including signal peptide or propeptide, the result will include their mass. For the mature processed protein, you should paste only the sequence after cleavage. Signal peptide prediction tools such as SignalP can predict the cleavage site. Many database entries (UniProtKB) provide the canonical and mature sequences separately.
How accurate is this calculation compared to mass spectrometry?
For an unmodified, linear polypeptide composed of the 20 standard amino acids, this calculation is theoretically exact using the published atomic masses. Discrepancies with measured mass spectrometry results usually arise from post-translational modifications (glycosylation, phosphorylation, acetylation, etc.), disulfide bonds (each removes 2.016 Da), signal peptide cleavage, or incomplete sequence information. SDS-PAGE migration is less accurate than mass spectrometry and can deviate by 5-15% from theoretical mass, especially for very basic, very acidic, or membrane proteins.