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Protein and Peptide Molecular Weight Calculator

Calculate a protein or peptide's molecular weight from its sequence, as an average or monoisotopic mass, with options for an N-terminal acetyl and a C-terminal amide.

Formula

M=∑mresidue+H2OM = \sum m_{\text{residue}} + \mathrm{H_2O}
mresidue=mamino acid−H2Om_{\text{residue}} = m_{\text{amino acid}} - \mathrm{H_2O}
N-acetyl: +42.04 (average);C-amide: −0.98\text{N-acetyl: } +42.04\ (\text{average});\quad \text{C-amide: } -0.98
residue\text{residue}
an amino acid as it sits in a chain, having lost one water in forming the peptide bond
H2O\mathrm{H_2O}
added once for the free amine and carboxyl ends

How it works

A protein is a chain of amino-acid residues joined by peptide bonds, each formed by losing a molecule of water. The mass of the chain is the sum of the residue masses plus one water for the ends. The average mass uses the natural mix of isotopes and is what you want for weighing and calculating molar concentrations. The monoisotopic mass uses the lightest isotope of each element, and is what a mass spectrometer resolves for a small peptide.

Synthetic peptides are often capped: an acetyl group on the amino end and an amide on the carboxyl end remove the terminal charges, and both change the mass. Residue masses are calculated from the IUPAC atomic weights. They agree with the published tables to better than 0.01 Da per residue.

Worked example

Glucagon, a 29-residue peptide hormone: HSQGTFTSDYSKYLDSRRAQDFVQWLMNT.

  1. Sum the 29 residue masses.
  2. Add one water (18.015) for the free ends.

3,482.795 g/mol, about 3.483 kDa. The monoisotopic mass is 3,480.616 Da.

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • The 20 standard amino acids, as a linear chain with free or capped ends.
  • No disulfide bonds, phosphorylation, glycosylation, or other modifications, and no cofactors or metal ions.
  • Average masses use the IUPAC standard atomic weights; other tools use slightly different atomic weights and can differ in the fourth significant figure.

Common mistakes

  • Using the average mass when comparing with a mass-spectrometer peak, which reports a monoisotopic or an isotope-resolved value.
  • Forgetting that each disulfide bond removes two hydrogens (about 2 Da) from the mass.
  • Entering the sequence of a precursor when the mature protein is meant, with its signal peptide removed.

Related tools

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Related equipment

Service documentation, failure modes and parts for the instruments this calculation is used with.