Peptide properties calculator: molecular weight, formula, extinction coefficient and hydropathy

Molecular formula: the sum of the 20 standard residue formulas (each amino acid minus one water) plus one water for the free termini. An Ac- prefix adds C2H2O, a -NH2 suffix replaces the C-terminal OH with NH2 (adds N and H, removes O), and each disulfide bond removes two hydrogens.

Masses: the average molecular weight multiplies the formula by IUPAC standard atomic weights (C 12.0107, H 1.00794, N 14.0067, O 15.9994, S 32.065); use it for weighing and molarity. The monoisotopic mass uses the lightest isotope of each element; use it for high-resolution mass spectra and the expected m/z calculator.

Extinction coefficient at 280 nm: ε280 = 5500 × nTrp + 1490 × nTyr + 125 × nCystine (Pace et al., 1995), shown for all-reduced cysteines and for cysteines paired as cystines. For comparison with older protocols, the denatured-protein value in 6 M guanidine-HCl (Gill and von Hippel, 1989: 5690 × nTrp + 1280 × nTyr + 120 × nCys), which the Northwestern calculator reported, is shown too. Concentration then follows from Beer–Lambert, c = A280 / (ε × path length).

Molecular volume: estimated as 1.21 ų per dalton of average mass, from a typical partial specific volume of 0.73 cm³/g (the same estimate the Northwestern calculator used, often needed for small-angle scattering contrast work). Hydropathy: the Kyte–Doolittle index averaged over the whole sequence (GRAVY) and over a sliding window you choose (9 residues by default). Positive values are hydrophobic. pI and net charge use the same EMBOSS pKa set and code as our pI calculator.

BPC-157 (GEPPPGKPADDAGLV): C62H98N16O22, average mass 1419.54 g/mol, monoisotopic 1418.7042 Da; PubChem lists 1419.5 g/mol. Thymosin alpha-1 (Ac-SDAAVDTSSEITTKDLKEKKEVVEEAEN): C129H215N33O55, 3108.28 g/mol; PubChem CID 16130571 lists 3108.3 g/mol. Glycine alone: C2H5NO2, 75.07 g/mol.

Neither BPC-157 nor thymosin alpha-1 contains Trp or Tyr, so both have ε280 = 0. They cannot be quantified at 280 nm; use weight with net peptide content, amino-acid analysis, or absorbance at 205–214 nm.

Only the 20 standard amino acids and the Ac-, -NH2 and disulfide options are modelled. Lipidation, PEGylation, phosphorylation, D-amino acids, non-natural residues and counter-ions (TFA or acetate salts) change the mass and must be added by hand; the salt form also changes how much of a weighed powder is peptide (see net peptide content).

ε280 values computed from sequence are typically within about 5% for proteins that contain Trp (Pace et al., 1995); peptides with only one or two Tyr residues are less accurate, and turbidity or other absorbing species add error. Hydropathy indices are estimates, not measured solubility.

The embed code below is a self-contained HTML block that shows formula, masses and ε280 in the reader's browser. It makes no network requests and sets no cookies. To cite the calculator in a protocol or methods section, use: Vitality Chems, "Peptide properties calculator", https://vitalitychems.com/resources/peptide-properties-calculator, accessed on the date you used it.