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.
Formula
Neutral linear peptide = sum of amino acid residue formulas + H₂O for the free termini. Each atomic count is multiplied by its monoisotopic or average atomic mass.Example
Alanine–glycine (AG) has formula C5H10N2O3, neutral monoisotopic mass 146.06914 Da and average mass 146.1445 Da. The corresponding free amino acids lose one water molecule when their peptide bond forms.
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.