Paste a peptide sequence in one-letter code to get its molecular formula, average and monoisotopic mass and approximate net charge at pH 7. Choose the terminal groups and count any disulfide or lactam bridges. The residue formulas are the ones on the amino acid codes and residue masses page, and the calculator reproduces the published formulas of compounds on this site.
Molecular weight
One-letter code, N-terminus first. Lowercase letters (D forms) weigh the same as capitals. Write modified residues in brackets: [Aib], [Nle], [Nal] or [Dmt].
How the calculator works
It adds the residue formula of each amino acid in the sequence, adds one water for the free ends of a linear chain, then applies the terminal groups and bridges: an N-terminal acetyl group adds C₂H₂O, a C-terminal amide replaces OH with NH₂, each disulfide bridge removes two hydrogens and each lactam bridge removes one water.
Average mass uses the standard atomic weights C 12.011, H 1.008, N 14.007, O 15.999 and S 32.06, which is the figure for weighing and solution math. Monoisotopic mass uses the most abundant isotope of each element, which is the lightest peak in a mass spectrum.
Net charge is a count at pH 7: plus one for each lysine and arginine and for a free N-terminus, minus one for each aspartate and glutamate and for a free C-terminal carboxyl. Histidine is counted as neutral, and the count ignores shifts in side-chain pKa inside a folded peptide, so treat it as an estimate. The peptide solubility guide explains how labs use the charge to choose a solvent.
Worked examples
- BPC-157. GEPPPGKPADDAGLV with free ends gives C₆₂H₉₈N₁₆O₂₂ and about 1419.56 g/mol, net charge about -2.
- Ipamorelin. [Aib]H[Nal]FK with a C-terminal amide gives C₃₈H₄₉N₉O₅ and about 711.87 g/mol, net charge +2.
- Melanotan 2. [Nle]DHFRWK with an acetylated N-terminus, a C-terminal amide and one lactam bridge gives C₅₀H₆₉N₁₅O₉ and about 1024.20 g/mol.
- Oxytocin. CYIQNCPLG with a C-terminal amide and one disulfide bridge gives C₄₃H₆₆N₁₂O₁₂S₂ and about 1007.19 g/mol.
Each formula matches the one given in that compound's guide; the weights differ from published values only in the second decimal place, from rounding of atomic weights. The peptide reference table lists the published figures for every compound with a guide.
What the calculator does not cover
It reports the free peptide. A salt form adds its counterions, such as acetate or trifluoroacetate, and a lyophilized powder also holds some water, so the net peptide content on a lot's certificate is the figure to use for weighing (see TFA vs acetate peptide salts and What is a COA?). It does not model metal complexes such as GHK-Cu, PEG chains, lipid tails, or residues other than the four bracketed ones.
Frequently asked questions
How do you calculate the molecular weight of a peptide?
Add the residue masses of its amino acids, add one water (18.02 Da) for the two free ends, then apply terminal groups and bridges: an amide subtracts 0.98 Da, an acetyl group adds 42.04 Da and a disulfide bridge subtracts 2.02 Da.
What is the difference between average and monoisotopic mass?
Average mass uses standard atomic weights and suits weighing and molar calculations. Monoisotopic mass uses the most abundant isotope of each element and matches the lightest peak in a mass spectrum.
How do you estimate the net charge of a peptide?
At pH 7, count plus one for each lysine, arginine and free N-terminus and minus one for each aspartate, glutamate and free C-terminal carboxyl. Histidine is close to neutral at that pH.
Do D-amino acids change the molecular weight?
No. A D-amino acid has the same formula and mass as its L form, so the calculator reads lowercase letters the same way as capitals.
Why does a certificate show a different weight?
Certificates and product listings often describe a salt form or report measured content, which includes counterions and water. Rounding of atomic weights also moves the second decimal place.
Related guides
- Amino acid codes and residue masses
- Peptide molecular weights
- Peptide solubility
- TFA vs acetate peptide salts
- Peptide reconstitution calculator
- Research hub
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