Peptide Mass Calculator
Enter an amino acid sequence to calculate its theoretical molecular mass, formula and residue count. Compare neutral monoisotopic mass with average molecular mass in one free tool.
Calculate from a sequence
The calculation runs in your browser. Your sequence is not included in our analytics events.
Method and sources
This peptide molecular weight calculator supports the 20 standard amino acids in a linear chain with free termini. It is distinct from a dosage or reconstitution calculator: sequence mass describes a molecule, while vial mass describes an amount of material.
How to Use
Paste the one-letter sequence without a FASTA header. Spaces, line breaks and lowercase letters are accepted.
Confirm that the molecule is linear, unmodified and has free N- and C-termini. Cysteines are treated as reduced.
Select Calculate molecular mass to see both masses, molecular formula and length.
Use the same molecular form when comparing with a laboratory report. Modifications, salts, adducts and charge states require additional interpretation.
How peptide molecular mass is calculated
Each amino acid contributes a residue formula. Add those formulas, then add H₂O for the free N- and C-termini. Equivalently, add the free amino-acid formulas and subtract one H₂O for each peptide bond: a linear chain of n residues has n − 1 bonds.
Peptide formula = sum of residue formulas + H₂O
Mass = sum of (atom count × atomic mass)
For AG, alanine contributes C₃H₅NO and glycine contributes C₂H₃NO. Adding H₂O gives C₅H₁₀N₂O₃. Monoisotopic mass uses the most abundant isotope of each of these elements; average mass uses abundance-weighted atomic weights. The table lists the fixed UW/Unimod values used here.
| Element | Monoisotopic (Da) | Average (Da) |
|---|---|---|
| C | 12 | 12.0107 |
| H | 1.007825035 | 1.00794 |
| N | 14.003074 | 14.0067 |
| O | 15.99491463 | 15.9994 |
| S | 31.9720707 | 32.065 |
Method: linear-free-termini-v1. Documentation updated September 17, 2026. These fixed values make calculations reproducible; other tools may use different atomic-weight conventions or rounding. Displayed decimal places do not represent experimental measurement precision.
Sources: University of Washington mass table and Unimod mass conventions.
Worked sequence examples
Enter any sequence below to reproduce the displayed result. Each assumes the same unmodified linear chain with free termini. In CC, both cysteines are reduced; no disulfide bond is inferred.
| Sequence | Formula | Monoisotopic (Da) | Average (Da) |
|---|---|---|---|
| GOne glycine: free termini | C2H5NO2 | 75.03203 | 75.0666 |
| AGOne peptide bond | C5H10N2O3 | 146.06914 | 146.1445 |
| CCTwo reduced cysteines | C6H12N2O3S2 | 224.02893 | 224.3011 |
| MSulfur-containing methionine | C5H11NO2S | 149.05105 | 149.2113 |
| ILIsoleucine and leucine | C12H24N2O3 | 244.17869 | 244.3306 |
| PEPTIDEA seven-residue example | C34H53N7O15 | 799.35996 | 799.8225 |
| ACDEFGHIKLMNPQRSTVWYAll 20 standard residues | C107H159N29O30S2 | 2394.12491 | 2395.7137 |
Isoleucine (I) and leucine (L) have the same elemental formula and mass. Sequence order also leaves the total formula unchanged. A matching mass alone therefore cannot confirm a peptide’s identity, purity or structure.
Download the reference or cite this tool
Use the example data in a worksheet, or link to this page from a teaching guide or resource list. Downloads contain the public examples, not your entered sequence. No account is required.
Suggested citation
PurePeptideHub. Peptide Mass Calculator. Method linear-free-termini-v1. Documentation updated September 17, 2026. https://purepeptidehub.com/tools/peptide-mass-calculator
A documented calculation method is not a laboratory result or independent scientific review.
Frequently Asked Questions
What is the difference between monoisotopic and average mass?
Monoisotopic mass uses the most abundant isotope of each element. Average mass uses abundance-weighted atomic weights. These conventions give different values for the same molecular formula.
Does this calculate m/z for mass spectrometry?
No. It calculates the neutral molecule. An observed mass-to-charge ratio also depends on charge state, adducts and the instrument measurement.
Can it calculate amidated or cyclic peptide mass?
No. The current tool supports free termini on an unmodified linear chain. Do not remove modification annotations and treat the resulting number as the mass of the modified molecule.
Is molecular weight a measure of peptide purity?
No. A theoretical formula or matching mass alone cannot quantify purity, confirm every structural feature or show how much peptide is in a vial.
Does the tool support selenocysteine or ambiguous codes?
No. U, O, B, J, X and Z are rejected. It supports exactly ACDEFGHIKLMNPQRSTVWY.
Can I download the examples or cite the calculator?
Yes. Download the public example CSV and method JSON from this page, or cite the canonical calculator URL and method version linear-free-termini-v1. Downloads contain reference examples, not your entered sequence. The Copy calculation button copies your own result and its assumptions locally.