Peptide calculator

Sequence

One-letter or hyphenated three-letter code, up to 200 residues. How to write caps, D-residues, disulfides and bridges.

N-terminus Free amine (H-)Acetyl (Ac-) C-terminus Free acid (-OH)Amide (-NH2) Disulfide bonds Calculate

Try: KPV · Oxytocin, with its disulfide · A lactam-bridged ring · Pyroglutamate and an amide

Writing a sequence

What the calculator reads

Write	For
KPV	One-letter code, standard amino acids. Spaces, position numbers and a FASTA header line are ignored.
KpV	Lower case in one-letter code: a D-amino acid.
Lys-Pro-Val	Three-letter code, hyphenated, in any case.
H- Ac- Hexenoyl-	The N-terminus written in the sequence: free amine, acetyl or trans-3-hexenoyl. It takes precedence over the menu.
-OH -NH2	The C-terminus written in the sequence: free acid or amide. It takes precedence over the menu.
D-Phe	A D-amino acid in three-letter code; D-(Leu-Ala-Gly) makes every residue D.
Cys(1)-…-Cys(1)	A disulfide bond: number each pair. In one-letter code, give the number of bonds in the menu instead.
cyclo[Asp-…-Lys]	A side-chain lactam bridge between Asp and Lys (one water lost).
Pyr Aib Nle Orn 2Nal Dmt Mrp	Non-standard residues: pyroglutamate (first position only), α-aminoisobutyric acid, norleucine, ornithine, 3-(2-naphthyl)alanine, 2,6-dimethyltyrosine (also written Tyr(2,6-diMe)), 2-methyltryptophan.

How it calculates

Masses add up the residues and termini, less two hydrogens per disulfide and one water per lactam bridge: average mass from the IUPAC 2021 standard atomic weights, monoisotopic mass from the AME2020 atomic mass evaluation. Charge and isoelectric point use the EMBOSS pKa set, which takes every group as independent, so they are estimates; a real peptide's values shift with its neighbors, its salt form and the solvent. Absorbance at 280 nm is the Pace method (tryptophan, tyrosine and cystine), and hydropathy is the Kyte–Doolittle average over standard residues. The sequence variants are general peptide chemistry applied to the sequence.

It calculates the properties of the molecule only: it gives no amounts, volumes or concentrations, and a calculated value is not a measurement. Measured values for a lot are on its certificate of analysis; how to read one is in How to read a certificate of analysis.

Sources & Further Reading

1. Prohaska T, Irrgeher J, Benefield J, Böhlke JK, Chesson LA, Coplen TB, et al. Standard atomic weights of the elements 2021 (IUPAC Technical Report). Pure and Applied Chemistry 2022;94(5):573–600. doi:10.1515/pac-2019-0603
2. Wang M, Huang WJ, Kondev FG, Audi G, Naimi S. The AME 2020 atomic mass evaluation (II). Tables, graphs and references. Chinese Physics C 2021;45(3):030003. doi:10.1088/1674-1137/abddaf
3. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics 2000;16(6):276–277. doi:10.1016/S0168-9525(00)02024-2
4. Pace CN, Vajdos F, Fee L, Grimsley G, Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Science 1995;4(11):2411–2423. doi:10.1002/pro.5560041120
5. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 1982;157(1):105–132. doi:10.1016/0022-2836(82)90515-0
6. Meija J, Coplen TB, Berglund M, Brand WA, De Bièvre P, Gröning M, et al. Isotopic compositions of the elements 2013 (IUPAC Technical Report). Pure and Applied Chemistry 2016;88(3):293–306. doi:10.1515/pac-2015-0503
7. Roepstorff P, Fohlman J. Letter to the editors: proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomedical Mass Spectrometry 1984;11(11):601. doi:10.1002/bms.1200111109
8. Biemann K. Contributions of mass spectrometry to peptide and protein structure. Biomedical and Environmental Mass Spectrometry 1988;16(1–12):99–111. doi:10.1002/bms.1200160119
9. Geiger T, Clarke S. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. Journal of Biological Chemistry 1987;262(2):785–794. doi:10.1016/S0021-9258(19)75855-4
10. Manning MC, Chou DK, Murphy BM, Payne RW, Katayama DS. Stability of protein pharmaceuticals: an update. Pharmaceutical Research 2010;27(4):544–575. doi:10.1007/s11095-009-0045-6
11. D'Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, et al. Related impurities in peptide medicines. Journal of Pharmaceutical and Biomedical Analysis 2014;101:2–30. doi:10.1016/j.jpba.2014.06.012

Cosmic Peptides. (2026, October 25). Peptide calculator. Cosmic Peptides Research Library. Retrieved October 26, 2026, from https://cosmicpeptides.com/research/tools/peptide-calculator

@misc{cosmicpeptides_research_tools_peptide_calculator,
  author       = {{Cosmic Peptides}},
  title        = {Peptide calculator},
  howpublished = {Cosmic Peptides Research Library},
  year         = {2026},
  month        = oct,
  url          = {https://cosmicpeptides.com/research/tools/peptide-calculator},
  urldate      = {2026-10-26},
  note         = {Last reviewed 2026-10-25}
}

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