Protein Molecular Weight Calculator
Paste a protein sequence (FASTA or raw letters) and calculate molecular weight. Choose average or monoisotopic mass, optionally remove the initiator Met, and get a mini amino acid composition visual + steps.
Background
Protein molecular weight (MW) is computed by summing amino acid residue masses and adding the mass of one water molecule to represent the N- and C-termini.
How to use this calculator
- Paste a protein sequence (FASTA or raw letters).
- Choose Average or Monoisotopic mass.
- Optional: remove the initiator Met if your sequence starts with M.
- Click Calculate to see MW in Da and kDa plus a composition visual.
- Use the Mass ↔ Moles mini-row under the result to convert (e.g., µg ↔ nmol).
How this calculator works
- Clean the input (remove FASTA headers, whitespace, digits, and non-letters).
- Convert to uppercase amino acid letters.
- Sum residue masses for all letters in the sequence.
- Add one water molecule mass to represent termini.
- Ambiguous letters (B/Z/J) use averaged masses; unknown letters are excluded and reported.
Formula & Equation Used
Molecular weight (Da): MW = Σ(residue masses) + H₂O
Water mass: average ≈ 18.0153 Da, monoisotopic ≈ 18.01056 Da
Mass ↔ moles: n = m / MW and m = n × MW
Note: 1 Da is numerically equivalent to 1 g/mol, so MW(Da) can be used directly as MW(g/mol).
Example Problems & Step-by-Step Solutions
Example 1 — Convert a peptide MW to kDa
You calculate MW = 12,345 Da. Convert to kDa: 12,345 Da ÷ 1000 = 12.345 kDa.
Example 2 — Mass ↔ moles using MW
A protein has MW = 50,000 g/mol. How many nmol are in 25 µg?
- Convert mass: 25 µg = 25×10⁻⁶ g
- n = m/MW = (25×10⁻⁶) / 50,000 = 5×10⁻¹⁰ mol
- Convert to nmol: 5×10⁻¹⁰ mol = 0.5 nmol
Example 3 — Initiator Met removal
If a sequence begins with M and you check “Remove initiator Met”, the calculator removes the first residue before computing MW.
Frequently Asked Questions
Q: Does MW in Da equal g/mol?
Numerically, yes. That’s why the mass↔moles mini-row works directly from MW(Da).
Q: Why do you add H₂O?
Residue masses represent amino acids after forming peptide bonds. Adding H₂O accounts for the termini.
Q: What happens to unknown letters?
Unknown letters are excluded from the MW sum and reported as “ignored”.
Q: Should I pick Average or Monoisotopic?
Average is typical for many lab contexts; monoisotopic is common in MS workflows.
