How to Use Protein Molecular Weight Calculator
The Protein Molecular Weight Calculator determines the theoretical molecular weight of a protein from its amino acid sequence using standard residue masses. This is useful for gel electrophoresis planning, mass spectrometry interpretation, and experimental design.
- Select Mass Type – Choose between average molecular mass and monoisotopic mass.
- Enter Amino Acid Sequence – Type or paste the protein sequence using single-letter amino acid codes (e.g., ACDEFGHIKLMNPQRSTVWY). Non-standard characters and spaces are automatically ignored.
- Review the Result – The Protein Molecular Weight Calculator shows the molecular weight in Da and kDa, sequence length, and a breakdown of amino acid composition with count and percentage.
The Protein Molecular Weight Calculator processes sequences of any length entirely in your browser.
Formula & Theory - Protein Molecular Weight Calculator
The Protein Molecular Weight Calculator uses this core formula or rule: the standard residue mass summation:
MW = Σ (Residue Mass × Count) + H2OWhere each amino acid residue mass represents the amino acid minus water (because peptide bond formation releases water). The water molecule is added back once at the end to account for the free amino- and carboxyl-termini of the complete polypeptide.
| Symbol | Meaning |
|---|---|
| Residue Mass | Mass of amino acid minus H₂O (Da) |
| H₂O | 18.01524 Da (average) or 18.01056 Da (monoisotopic) |
| Σ | Sum over all residues in the sequence |
Example residue masses (average):
| Amino Acid | Code | Residue Mass (Da) |
|---|---|---|
| Glycine | G | 57.05 |
| Alanine | A | 71.08 |
| Tryptophan | W | 186.21 |
Assumptions and Limits
This calculator uses standard unmodified residue masses. It does not account for disulfide bridges, glycosylation, phosphorylation, signal peptides cleavage, or any other post-translational modification. The result is the theoretical mass of the linear, unmodified peptide chain.
Use Cases for Protein Molecular Weight Calculator
The Protein Molecular Weight Calculator is widely used in molecular biology, biochemistry, and biomedical research:
- SDS-PAGE Planning – Estimate the expected migration position of a recombinant protein before running a gel.
- Mass Spectrometry Interpretation – Calculate theoretical precursor masses for database searching and peptide identification.
- Protein Expression Verification – Compare the theoretical mass to the observed mass from Western blot or MS to confirm correct expression and processing.
- Education and Learning – Students learning about protein structure can use this tool to connect amino acid composition to molecular weight concepts.