Protein Molecular Weight Calculator
Paste a protein or peptide sequence in one-letter amino acid code to estimate molecular weight.
What this protein molecular weight calculator does
This tool estimates the molecular weight of a protein from its amino acid sequence. It sums residue masses, adds the mass of water to represent a complete polypeptide chain, and optionally adjusts for disulfide bonds. The result is shown in both Daltons (Da) and kilodaltons (kDa), which are common units used in biochemistry, proteomics, and molecular biology.
Why molecular weight matters in the lab
Knowing a protein’s expected mass helps with experiment planning and data interpretation. Before running SDS-PAGE, western blotting, or mass spectrometry, a quick theoretical mass check can save time and prevent confusion.
- SDS-PAGE: Compare apparent gel migration with expected size.
- Mass spectrometry: Validate observed precursor ions against theoretical mass.
- Protein purification: Confirm identity after expression or tag cleavage.
- Construct design: Predict the size impact of added tags or mutations.
How the calculation works
1) Sequence cleanup
The calculator removes spaces and line breaks, then checks each character against the 20 standard amino acids. Non-standard letters such as B, J, O, U, X, and Z are flagged as invalid for this calculation.
2) Residue mass summation
Each amino acid contributes a residue-specific mass. You can choose average mass (useful for many routine calculations) or monoisotopic mass (commonly used for high-resolution mass spectrometry).
3) Terminal water and disulfide correction
A complete peptide chain includes terminal groups equivalent to adding one water molecule. If disulfide bonds are present, the tool subtracts ~2.016 Da per bond, reflecting hydrogen loss during bond formation.
Practical interpretation tips
- Calculated vs observed mass may differ: post-translational modifications (glycosylation, phosphorylation, oxidation, acetylation), processing events, and adducts can change measured mass.
- SDS-PAGE is approximate: proteins with unusual charge, structure, or membrane domains can migrate anomalously.
- Include known chemistry: if you know disulfide status, include it for a better estimate.
Example workflow
Suppose you design a recombinant enzyme with a known amino acid sequence. Before expression, you calculate its expected molecular weight to determine whether a future gel band near that size is plausible. After purification, you compare observed MS data against the expected neutral mass and charge-state m/z values to confirm identity.
Frequently asked questions
Does this include PTMs automatically?
No. This calculator uses the unmodified sequence plus optional disulfide adjustment. Add known modifications separately if you need exact theoretical mass for modified proteoforms.
Should I choose average or monoisotopic mass?
Use average mass for general biochemical reference, and monoisotopic mass when matching high-resolution MS data and isotopic peaks.
Can I use FASTA text?
You should paste only the sequence letters. Headers (lines starting with >) and punctuation are not accepted.