Peptide Molecular Weight Calculator
Theoretical neutral mass
Enter a sequence or select Try AGC to see the calculation.
Elemental formula
- N-terminus
- Peptide chain
- C-terminus
Compare terminal forms
Select a terminal form. The comparison uses your chosen modification counts for each row.
| Terminal form | Average | Monoisotopic |
|---|---|---|
Show mass calculation
| Step | Average | Monoisotopic |
|---|---|---|
| Unmodified free ends | ||
| Additional modifications | ||
| Terminal shift | ||
| Selected form |
Theoretical positive-ion m/z
Proton-only values for the selected peptide form.
| Ion | m/z |
|---|---|
| [M+H]+ | |
| [M+2H]2+ | |
| [M+3H]3+ |
Normalized sequence and residue counts
This calculator models a single peptide of standard residues with a linear backbone and the documented changes you select. Options cover a free amine or N-acetyl N-terminus, a free acid or C-amide C-terminus, intrachain disulfides, methionine sulfoxide and S, T or Y phosphorylation. Head-to-tail cyclic peptides, custom residues, other modifications, salt or counterion forms and isotope-labeled material fall outside this model.
How to calculate peptide molecular weight
Enter one linear peptide sequence in one-letter or three-letter code to calculate its theoretical neutral average mass and monoisotopic mass in daltons. The result also gives the elemental formula, residue count and peptide bond count. Choose the state of each end and compare all four terminal combinations. You can also add optional counts for documented disulfides, methionine oxidation and S/T/Y phosphorylation.
Worked example
The example loads AGC (alanine, glycine, cysteine), a tripeptide with 3 residues and 2 peptide bonds, and sets both ends to their free states. With a free amine and a free acid, the formula is C8H15N3O4S, the average mass is 249.29 Da and the monoisotopic mass is 249.0783 Da. Switch one end to N-acetyl or C-amide to see the formula, the signed terminal shift and both masses update for the same sequence.
Formula and mass conventions
The calculator adds the residue formulas from the UW Proteomics Resource and converts the total formula to mass with elemental masses from Unimod. For free termini it adds one H2O to the summed residue formulas. This gives the same result as adding the intact amino acid formulas and subtracting one H2O for each peptide bond. Average mass weights each element by its natural isotopic abundance and is shown to 2 decimals. Monoisotopic mass uses the most abundant isotope of each element and is shown to 4 decimals.
Terminal choices then adjust the free-termini formula. N-acetyl adds C2H2O, a monoisotopic shift of +42.010565 Da. C-amide replaces the C-terminal OH with NH2, a net change of plus H and N and minus O, or −0.984016 Da monoisotopic. The result breakdown lists the free-termini mass, the terminal shift and the final mass on each basis, and the chain diagram labels the selected state at each end.
Peptide mass questions
Why does the peptide formula include an extra water?
Each residue formula already reflects the atoms lost when a peptide bond forms. Adding one H2O restores the hydrogen on the free amine and the hydroxyl on the free acid at the two ends. This matches adding intact amino acids and subtracting one water for every peptide bond.
What is the difference between average and monoisotopic mass?
Average mass uses the natural-abundance-weighted average of each element’s isotopic masses. Monoisotopic mass uses the most abundant isotope of each element. The calculator shows both side by side, so you can match the basis used in any report you compare.
Does amidation or acetylation change peptide mass?
Yes. N-terminal acetylation adds C2H2O, a monoisotopic shift of +42.010565 Da. C-terminal amidation replaces the free acid OH with NH2, a net change of −0.984016 Da monoisotopic. Select each terminal state to see the signed shift on both mass bases.
Why does a measured mass differ from the calculated value?
This calculator gives two kinds of theoretical value. The first is neutral mass. The second is m/z for proton-only ions at +1, +2 and +3. A report may use a different mass basis, list m/z for another charge state or an adduct, or describe a molecular form that includes chemistry outside this model. Before you compare numbers, match the mass basis, ion convention, charge and stated form.
Can two peptides have the same molecular weight?
Yes. Reordering the same residues keeps the formula and mass identical, and leucine and isoleucine share one elemental formula. A matching mass in a COA therefore supports consistency with the stated formula. Sequence identity and purity depend on the lot’s analytical methods and reported measurements.
How do disulfide, oxidation and phosphate counts change the mass?
Each documented intrachain disulfide removes H2 and pairs two cysteines. Each methionine sulfoxide adds O, which is +15.994915 Da monoisotopic. Each phosphorylated S, T or Y site adds HPO3, which is +79.966331 Da monoisotopic. Intact mass depends on how many of each change are present, so enter the counts documented for your peptide. These counts stay fixed while you compare terminal combinations.
What do the +1, +2 and +3 m/z values show?
These are theoretical m/z values for the peptide carrying one, two or three added protons. Each is calculated as (neutral monoisotopic mass + z × 1.00727646688 Da) ÷ z, where z is the charge. They sit apart from the neutral mass because they describe charged ions. Compare each value with a reported m/z at the same charge state. The table lists possible values and makes no prediction about which charge states appear in a spectrum.
Other sequence properties
Net charge is evaluated at a chosen pH from the pKa values assigned to ionizable groups. The isoelectric point (pI) is the pH at which that modeled net charge is zero. Hydropathy averages a residue scale across the sequence. An extinction coefficient estimates absorbance at a stated wavelength from the residues and disulfides that absorb there. This page reports mass and theoretical m/z only. For the estimates it supports, see the ExPASy ProtParam documentation. Bachem and AAT Bioquest also offer related calculators.
