Peptide mass calculator
Paste an amino acid sequence and get its molecular formula, average molecular weight and monoisotopic mass. N-terminal acetyl, C-terminal amide and disulfide bonds are handled, and the sequence of every single-compound peptide in our catalogue is one click away.
For in-vitro laboratory work only. Nothing on this site is guidance for human or veterinary use.
Sequence to mass
A peptide is a chain of amino acid residues. Each residue is its amino acid less one water, lost when the peptide bond forms, and the chain as a whole gains one water back for its free ends. Summing the residues gives the elemental formula; the formula gives the mass.
Worked example. GEPPPGKPADDAGLV (BPC-157) is fifteen residues, C62H98N16O22, average mass 1,419.5 g/mol and monoisotopic mass 1,418.70 Da. The monoisotopic figure is the one an LC-MS report compares its observed mass against.
The result is for the bare peptide as written. Compounds supplied as a salt, a copper complex or with a PEG or lipid chain weigh more; the figure on the batch certificate is the one to use for those. Our reconstitution and molarity calculator takes the mass from here to solution concentrations.
- Residues
- 15
- Formula
- C62H98N16O22
- Average mass
- 1,419.54 g/mol
- Monoisotopic mass
- 1,418.7042 Da
- 5.0 mg is
- 3.522 µmol · 3,522.3 nmol
Masses are for the free peptide as written. Salts, counter-ions, metal complexes (GHK-Cu, say) and modifications other than N-acetylation, C-amidation and disulfides are not included; where the certificate states the form supplied, use its figure.
Residue masses
The residue masses the calculator uses, average and monoisotopic. Isoleucine and leucine share a formula and so a mass; glutamine and lysine differ by only 0.036 Da, which is why identity is confirmed by LC-MS with retention time rather than by mass alone.
| Residue | Formula | Average | Monoisotopic |
|---|---|---|---|
| Ala (A) | C3H5NO | 71.08 | 71.037 |
| Arg (R) | C6H12N4O | 156.19 | 156.101 |
| Asn (N) | C4H6N2O2 | 114.10 | 114.043 |
| Asp (D) | C4H5NO3 | 115.09 | 115.027 |
| Cys (C) | C3H5NOS | 103.14 | 103.009 |
| Glu (E) | C5H7NO3 | 129.12 | 129.043 |
| Gln (Q) | C5H8N2O2 | 128.13 | 128.059 |
| Gly (G) | C2H3NO | 57.05 | 57.021 |
| His (H) | C6H7N3O | 137.14 | 137.059 |
| Ile (I) | C6H11NO | 113.16 | 113.084 |
| Leu (L) | C6H11NO | 113.16 | 113.084 |
| Lys (K) | C6H12N2O | 128.17 | 128.095 |
| Met (M) | C5H9NOS | 131.19 | 131.040 |
| Phe (F) | C9H9NO | 147.18 | 147.068 |
| Pro (P) | C5H7NO | 97.12 | 97.053 |
| Ser (S) | C3H5NO2 | 87.08 | 87.032 |
| Thr (T) | C4H7NO2 | 101.11 | 101.048 |
| Trp (W) | C11H10N2O | 186.21 | 186.079 |
| Tyr (Y) | C9H9NO2 | 163.18 | 163.063 |
| Val (V) | C5H9NO | 99.13 | 99.068 |
Published molecular weights for each compound we stock, with sequence, CAS number and formula, are on the compound monographs; the measured mass of each batch is on its certificate in the register.
Questions about the calculator
How is a peptide's molecular weight calculated from its sequence?
Each amino acid residue in the chain is the free amino acid minus one water, because a water molecule is lost when each peptide bond forms. Add up the residue masses, then add one water for the free N- and C-terminal ends. BPC-157 (GEPPPGKPADDAGLV) comes to C62H98N16O22, 1,419.5 g/mol.
What is the difference between average and monoisotopic mass?
Average mass uses the natural isotope mix of each element, so it is the figure to use for weighing and molar calculations. Monoisotopic mass uses the most abundant isotope of each element only (carbon-12, hydrogen-1 and so on) and is the figure a mass spectrometer's main peak corresponds to, which is why it appears on LC-MS certificates.
Why does my result differ from the certificate or the product page?
Usually one of three reasons: the compound is supplied as a salt or counter-ion (acetate, trifluoroacetate), as a metal complex such as GHK-Cu, or with a modification the calculator does not model, such as a PEG spacer or a fatty-acid chain. The calculator gives the mass of the bare peptide as written; the certificate gives the form actually supplied.
What do Ac- and -NH2 mean at the ends of a sequence?
Ac- is an acetyl group on the N-terminus, which adds C2H2O (42.04 g/mol). -NH2 means the C-terminus is an amide rather than a free acid, which replaces OH with NH2 and lowers the mass by about 0.98 g/mol. Both are common in synthetic research peptides and the calculator reads them automatically.
How does a disulfide bond change the mass?
Forming a disulfide between two cysteine residues removes two hydrogen atoms, so each bond lowers the mass by 2.016 g/mol. Enter the number of bonds for cyclic or folded peptides; for linear peptides leave it at zero.
Is this calculator for human or veterinary use?
No. It is a laboratory tool for sequence arithmetic and solution preparation. Nothing on this site is guidance for use in people or animals, and everything we supply is for research use only.