Peptide molecular weight calculator
Enter a single-letter amino-acid sequence to calculate the average molecular weight, molecular formula and net charge of any research peptide. Free, no sign-up, and accurate to the standard average residue masses used in analytical chemistry.
How the peptide molecular weight is calculated
A peptide is a chain of amino acids joined by peptide bonds. Each bond forms by condensation — two residues join and one molecule of water is expelled. So the molecular weight of a peptide is not the sum of its free amino acids; it is the sum of the residue masses (each amino acid minus the water lost in bond formation), plus a single molecule of water (18.015 g/mol) returned at the free N- and C-termini.
The calculation this tool performs is therefore:
MW = Σ (residue masses) + 18.015
This calculator uses average isotopic masses rather than monoisotopic masses. Average mass weights each element by the natural abundance of its isotopes, and it is the convention used when quoting a molecular weight on a certificate of analysis or when weighing out lyophilised powder. Monoisotopic mass — which uses only the lightest isotope of each element — is what you compare against a mass spectrometry peak. For a peptide of around 1,000 Da the two differ by roughly 0.5 Da, which matters for MS identification but not for solution preparation.
A worked example: BPC-157
The 15-residue sequence GEPPPGKPADDAGLV is a useful check, because its molecular weight is widely published and you can confirm this tool against it. Summing the residue masses gives 1,401.52 Da; adding one water (18.015) gives a final average molecular weight of 1,419.54 g/mol, with the molecular formula C62H98N16O22. Both match the values quoted on a typical certificate of analysis.
The same sequence carries one basic residue (K) and three acidic residues (D, D, E). With the free termini contributing +1 and −1, that gives a net charge of about −2 at pH 7 — which is why it is classed as net-negative and dissolves best in a slightly basic buffer. You can see that logic in the peptide solubility calculator.
Press any of the preset buttons above the results to load a known sequence and check the tool against a value you already trust.
Why molecular weight matters for reconstitution
You need an accurate molecular weight to convert a lyophilised mass into a molar concentration — the two are linked by n = m / MW, so an error in the molecular weight propagates directly into every concentration you calculate downstream. Once you have it, our reconstitution calculator works out the reconstitution volume, the molarity calculator converts mass to mM or µM, and the solubility calculator recommends the right solvent for the sequence.
Two practical cautions when comparing this figure against a real vial:
- This tool calculates the free (unmodified) peptide. Common modifications shift the mass — C-terminal amidation removes about 0.98 Da, N-terminal acetylation adds about 42.04 Da, and each intramolecular disulfide bond removes about 2.02 Da.
- Synthetic peptides are usually supplied as a salt — most often a TFA or acetate salt — and often contain residual water. The gross powder mass in the vial is therefore higher than the net peptide mass. Where peptide content is stated on the certificate of analysis, use it.
Amino-acid residue mass reference
These are the exact average residue masses and Kyte–Doolittle hydropathy values this calculator uses. Residue mass is the amino acid mass minus one water — the mass each residue contributes once it is inside the chain. Note that leucine and isoleucine are structural isomers with an identical mass (113.1576 Da), so they cannot be told apart by molecular weight alone.
Average residue masses and Kyte–Doolittle hydropathy values used by this calculator| Code | 3-letter | Amino acid | Residue mass (Da) | Hydropathy (KD) |
|---|
| A | Ala | Alanine | 71.0779 | 1.8 |
| R | Arg | Arginine | 156.1857 | -4.5 |
| N | Asn | Asparagine | 114.1026 | -3.5 |
| D | Asp | Aspartic acid | 115.0874 | -3.5 |
| C | Cys | Cysteine | 103.1429 | 2.5 |
| E | Glu | Glutamic acid | 129.1140 | -3.5 |
| Q | Gln | Glutamine | 128.1292 | -3.5 |
| G | Gly | Glycine | 57.0513 | -0.4 |
| H | His | Histidine | 137.1393 | -3.2 |
| I | Ile | Isoleucine | 113.1576 | 4.5 |
| L | Leu | Leucine | 113.1576 | 3.8 |
| K | Lys | Lysine | 128.1723 | -3.9 |
| M | Met | Methionine | 131.1926 | 1.9 |
| F | Phe | Phenylalanine | 147.1766 | 2.8 |
| P | Pro | Proline | 97.1152 | -1.6 |
| S | Ser | Serine | 87.0773 | -0.8 |
| T | Thr | Threonine | 101.1039 | -0.7 |
| W | Trp | Tryptophan | 186.2099 | -0.9 |
| Y | Tyr | Tyrosine | 163.1733 | -1.3 |
| V | Val | Valine | 99.1311 | 4.2 |
Frequently asked questions
How do you calculate the molecular weight of a peptide?
Add together the average residue mass of every amino acid in the sequence, then add 18.015 g/mol for the single molecule of water at the free N- and C-termini. Residue masses are used rather than free amino acid masses because each peptide bond expels one water when it forms. For the sequence GEPPPGKPADDAGLV this gives 1,419.54 g/mol.
What is the difference between average mass and monoisotopic mass?
Average mass weights each element by the natural abundance of all its isotopes, and is the value quoted on certificates of analysis and used when weighing out powder. Monoisotopic mass uses only the lightest isotope of each element and is what you match against a mass spectrometry peak. For a peptide near 1,000 Da they differ by roughly 0.5 Da. This calculator reports average mass.
Why does my calculated molecular weight differ from the vial label?
Usually because of salt form or modification. Synthetic peptides are typically supplied as TFA or acetate salts and may carry residual water, so the gross powder mass exceeds the net peptide mass. Modifications also shift the figure: C-terminal amidation removes about 0.98 Da, N-terminal acetylation adds about 42.04 Da, and each disulfide bond removes about 2.02 Da. This tool calculates the free, unmodified peptide.
Can this calculator work out the molecular formula and net charge too?
Yes. Alongside average molecular weight it returns the molecular formula, the net charge at approximately pH 7, the Kyte–Doolittle GRAVY hydropathy score, and a count of basic versus acidic residues. Net charge is estimated by counting lysine and arginine as +1, aspartic and glutamic acid as −1, histidine as approximately +0.1 at pH 7, and adding the free termini.
Does the calculator work for proteins as well as short peptides?
The arithmetic is identical for any chain length, so a long sequence will return a correct sum of residue masses. The practical limit is that large proteins are far more likely to carry post-translational modifications, disulfide bonding and bound cofactors, none of which a sequence-only calculation can account for. It is most reliable for synthetic peptides up to roughly 50 residues.
Is the peptide molecular weight calculator free to use?
Yes — it is free, requires no sign-up, and runs entirely in your browser, so no sequence you enter is sent to a server. It is provided for in-vitro laboratory research use only.
For in-vitro laboratory research use only. Molecular weights are calculated from the sequence you enter; always confirm against the batch-specific certificate of analysis for any material you are working with.
For in-vitro laboratory research use only. Not for human or veterinary use, consumption, or therapeutic application. No medical claims are made.