Protein Molecular Weight Calculator

Add up the average residue masses of every amino acid in the sequence, then add one water molecule (18.015 Da) for the free N- and C-termini. Each peptide bond expels a water molecule when it forms, so residue masses are the amino acid masses minus water. This calculator does the sum automatically when you paste a sequence.

MW = sum of residue masses + 18.015 Da. Equivalently, MW = sum of full amino acid masses - (n - 1) x 18.015 Da, where n is the number of residues. Both forms give the same result; this tool uses the residue-mass form.

Forming a peptide bond is a condensation reaction: each bond releases one water molecule (H2O, 18.015 Da). A chain of n amino acids has n - 1 peptide bonds, so n - 1 waters are lost. The free ends keep one water's worth of mass (H at the N-terminus, OH at the C-terminus), which is why the residue-sum formula adds a single 18.015 Da back.

This calculator uses average residue masses, the same convention as ExPASy ProtParam's default. Average mass matches what you see on SDS-PAGE and is right for most bench calculations. Monoisotopic mass (using the lightest isotope of each element) is about 0.06% lower and is preferred for mass spectrometry; this tool does not compute it, and says so openly.

Using the Pace (1995) method: epsilon280 = 5500 x (number of tryptophan) + 1490 x (number of tyrosine) + 125 x (number of cysteine), in M-1 cm-1. Only these three residues absorb significantly at 280 nm. The cysteine term assumes reduced cysteines; disulfide-bonded cystines absorb slightly differently.

It is the theoretical absorbance at 280 nm of a 1 mg/mL protein solution in a 1 cm cuvette, equal to epsilon280 divided by the molecular weight. It lets you convert a measured A280 into mg/mL: concentration (mg/mL) = measured A280 / (A280 of 1 mg/mL). Measuring concentration from real absorbance data is the job of our Protein Concentration Calculator.

About 110 Da (0.11 kDa) per residue. It is a handy rule of thumb: a 300-residue protein is roughly 33 kDa. Real proteins vary because residues range from glycine (57.05 Da) to tryptophan (186.21 Da), so use this calculator for the exact number.

A dalton is the standard unit of molecular mass: 1 Da = 1 g/mol numerically. A kilodalton is 1000 daltons, so a 50 kDa protein has a molecular weight of 50,000 Da, or 50,000 g/mol. The unit converter mode on this page converts between Da, kDa, and g/mol.

A standard 6xHis tag adds about 0.84 kDa (840.86 Da): six histidine residues (6 x 137.14 Da) plus the terminal water (18.015 Da). Common alternatives: GST ~26 kDa, MBP ~42.5 kDa, GFP ~27 kDa. The tag adjuster mode adds any of these, or a custom tag mass, to your protein's weight.

Calculated MW is the bare polypeptide. SDS-PAGE measures apparent mass, which shifts with glycosylation, phosphorylation, incomplete denaturation, very hydrophobic sequences, or a high charge density. Post-translational modifications are not included in this calculator's result, so treat gel bands as approximate.

For molecular weight, extinction coefficient, and composition, yes: it uses the same average masses and the same Pace extinction coefficients as ProtParam, runs 100% in your browser with nothing uploaded, and adds a tag adjuster and unit converters ProtParam lacks. It does not compute isoelectric point, instability index, or other ProtParam extras.

Yes. Header lines starting with '>' are ignored, and whitespace and line breaks are stripped automatically. Only the 20 standard one-letter amino acid codes are accepted; anything else triggers an honest error naming the exact position.

No, and that is a stated limitation. Phosphorylation (+79.97 Da), glycosylation, disulfide bond formation (-2.02 Da per bond), N-terminal acetylation (+42.01 Da), and other modifications are not included. Add known modification masses to the result yourself, or use the custom tag field for a fixed-mass addition.

The calculator refuses to guess. It shows an error listing every invalid character with its 1-based position (for example, X at position 5), so you can fix the sequence. Ambiguity codes like B, Z, X, and U are not silently averaged; they are reported as invalid.

No. Nucleic acids use different residue masses and a different calculator. For DNA/RNA copy number and mass conversions, use our DNA Copy Number Calculator instead; this tool is protein-only.

No. It is an educational tool for biochemistry calculations. Results are theoretical values for research and study, not medical advice, and should not guide any clinical or therapeutic decision.