Calculator inputs
Use the form below to calculate neutral mass, ion m/z, and optional quantity conversions.
Formula used
The calculator sums the selected amino acid residue masses for the cleaned peptide sequence, then adds one water molecule to represent the complete neutral peptide termini.
Neutral peptide mass = Σ(residue masses) + H2O + N-terminal adjustment + C-terminal adjustment − disulfide loss.
For ion mode outputs, the page converts the neutral mass into m/z by adding or removing proton mass and dividing by the charge state when needed.
Optional sample and target fields extend the result into practical quantity calculations by converting weighed mass into moles, or moles into required mass.
How to use this calculator
- Paste or type a peptide sequence using one-letter amino acid codes.
- Choose average or monoisotopic mass, depending on your workflow.
- Select the ion mode if you want neutral mass or an estimated ion m/z.
- Add optional terminal mass adjustments or the number of disulfide bonds.
- Enter optional sample mass to estimate moles from an existing quantity.
- Enter optional target amount to estimate the peptide mass you must weigh.
- Press Calculate peptide mass to show results above the form.
- Use the CSV and PDF buttons to export the current calculation for records or reporting.
Example data table
| Sequence | Length | Average mass (Da) | Monoisotopic mass (Da) | [M+H]+ m/z |
|---|---|---|---|---|
ACDEFGHIK |
9 | 1019.1401 | 1018.45419 | 1019.46147 |
PEPTIDE |
7 | 799.8328 | 799.35994 | 800.36722 |
MKWVTFISLL |
10 | 1237.5659 | 1236.69403 | 1237.70131 |
Frequently asked questions
What sequence format does this calculator accept?
Use one-letter amino acid codes. Spaces, line breaks, numbers, and punctuation are removed automatically. Invalid letters are flagged before calculation so the mass output stays reliable.
What is the difference between average and monoisotopic mass?
Average mass uses weighted elemental isotope averages. Monoisotopic mass uses the exact mass of the most abundant isotopes. Mass spectrometry workflows often rely on monoisotopic values.
Why is water added to the sequence mass?
A complete peptide has terminal hydrogen and hydroxyl groups. Adding one water molecule converts the summed residue masses into the neutral peptide molecular weight.
When should I use the ion mode setting?
Use ion mode when you need m/z values for MS interpretation. Neutral mode reports molecular weight, while protonated or deprotonated modes estimate observed ion masses.
How do terminal modification inputs work?
Enter known mass offsets for N- or C-terminal modifications. Positive values add mass, negative values subtract mass. Leave both at zero for an unmodified peptide.
What does the disulfide bond field change?
Each disulfide bond removes two hydrogens from the neutral peptide total. This slightly lowers the calculated molecular weight and affects the reported ion values.
Can I estimate moles from a weighed sample?
Yes. Enter an optional sample mass to estimate moles from the computed molecular weight. You can also enter a target amount to estimate how much peptide mass is needed.
Does this calculator handle nonstandard residues automatically?
No. The tool is designed for the 20 standard amino acids. Use the custom terminal mass fields or edit the source code for specialized residues and modifications.