Peptide calculator

Cosmic Peptides

This is Leu-enkephalin in the peptide reference.

Have observed masses? Check them against this sequence.

Structure

Three-letter code: H-Tyr-Gly-Gly-Phe-Leu-OH

One-letter code: YGGFL

5 residues
N-terminus: free amine
C-terminus: free acid

Calculated properties

Calculated from the structure
Property	Value
Molecular formula	C₂₈H₃₇N₅O₇
Average molecular weight	555.63 g/mol
Monoisotopic mass	555.2693 Da
Net charge at pH 7	0.0
Isoelectric point	6.09
Molar absorption coefficient, 280 nm	1,490 M⁻¹ cm⁻¹
Hydropathy (GRAVY)	0.90

Net charge across the pH range
pH 2	pH 4	pH 6	pH 7	pH 8	pH 10	pH 12
1.0	0.3	0.0	0.0	-0.2	-1.4	-2.0

Composition: Gly 2, Leu 1, Phe 1, Tyr 1.

Expected mass spectrometry ions

The protonated ions expected in positive-mode electrospray, from the monoisotopic mass, and the common sodium and potassium adducts. MALDI spectra show mainly [M+H]⁺.

Expected ions (monoisotopic)
Ion	m/z
[M+H]⁺	556.2766
[M+2H]²⁺	278.6419
[M+Na]⁺	578.2585
[M+K]⁺	594.2325

Isotope pattern

Natural carbon-13, nitrogen-15, oxygen-18, sulfur-34 and deuterium spread each ion over a cluster of peaks about 1 Da apart (1/z on the m/z scale). The monoisotopic peak is the most abundant.

Calculated isotope pattern of the neutral molecule, from IUPAC isotopic abundances.

Isotope peaks (relative abundance, most abundant = 100)
Peak	Abundance	Neutral mass	[M+H]⁺	[M+2H]²⁺
M (monoisotopic)	100.0	555.2693	556.2766	278.6419
M+1	32.8	556.2723	557.2796	279.1434
M+2	6.7	557.2750	558.2823	279.6448
M+3	1.0	558.2776	559.2848	280.1461

Fragment ions (MS/MS)

Collision-induced fragmentation breaks peptide bonds along the backbone. Fragments that keep the N-terminus are b ions; those that keep the C-terminus are y ions. Reading the ladder confirms the sequence residue by residue. Singly charged monoisotopic values. The b ion containing every residue is rarely seen and the y ion containing every residue is the precursor itself, so neither is listed.

b and y ions
b#	b⁺	Residue	y⁺	y#
1	164.0706	Tyr	—	5
2	221.0921	Gly	393.2132	4
3	278.1135	Gly	336.1918	3
4	425.1819	Phe	279.1703	2
5	—	Leu	132.1019	1

Immonium ions (low-mass markers of the residues present): Gly 30.0338, Leu 86.0964, Phe 120.0808, Tyr 136.0757.

What to watch for analytically

Variants this sequence can give, from its chemistry. They are what an HPLC or mass spectrometry result for this peptide is read against; none is a statement about a particular lot. Where synthesis variants come from is explained in How synthetic peptides are made.

Sequence-specific variants
Variant	Mass change	Why
Synthesis-related variants	minus a residue (deletion)	As for any synthetic peptide, deletion sequences and incompletely deprotected forms can occur.

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

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
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
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
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
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
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
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
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
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
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
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

Cite this page

Text

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

BibTeX

@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}
}

RIS

TY  - ELEC
AU  - Cosmic Peptides
TI  - Peptide calculator
T2  - Cosmic Peptides Research Library
PB  - Cosmic Peptides
PY  - 2026
DA  - 2026/10/25
UR  - https://cosmicpeptides.com/research/tools/peptide-calculator
Y2  - 2026/10/26
LA  - en
ER  -

Cite the date the page was last reviewed, October 25, 2026, as its version. Reference managers such as Zotero can save this page directly.

Changes to this page

October 25, 2026 Updated Peptide mass match, isotope patterns and fragment ions
Check the masses from a spectrum or a certificate against a sequence; every reference entry and calculation now shows its isotope pattern and its b- and y-ion ladder.
October 25, 2026 Published Peptide calculator
Formula, average and monoisotopic mass, charge across pH, isoelectric point, absorbance and the mass spectrometry ions to expect, for any sequence, recalculated as you type.

Changes of substance are listed here; wording changes are not. Every correction is also on the corrections log.

For in vitro laboratory research only. Not for human or veterinary use. This library describes chemistry, analytical methods and published laboratory research; it gives no guidance on use in people or animals.

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