Protein Molecular Weight Calculator (Da / kDa)
Paste a protein sequence to estimate molecular weight in Daltons. If you do not have a sequence, use amino-acid length mode for a quick approximation.
A protein dalton calculator helps you convert a protein sequence (or protein length) into an estimated molecular weight. This is useful when you are designing gels, planning chromatography, interpreting mass spectrometry, or documenting protein constructs.
What is a Dalton?
A Dalton (Da) is a unit of molecular mass. In biochemistry, it is commonly used for proteins, peptides, DNA fragments, and metabolites. You will also see kDa, which means kilodalton (1 kDa = 1,000 Da).
- Small peptides: often a few hundred to a few thousand Da
- Typical enzymes: often 20–100 kDa
- Large complexes: hundreds of kDa to megadalton scale
How this protein dalton calculator works
1) Sequence mode (best when sequence is known)
The calculator sums the average residue mass of each amino acid in your one-letter sequence. If selected, it adds terminal water mass (18.015 Da) to represent intact polypeptide termini.
Protein MW ≈ Σ(residue masses) + 18.015
2) Length mode (quick estimate)
If sequence is unknown, enter amino-acid count. The tool multiplies length by an average residue mass (default 110 Da), then optionally adds terminal water mass. This is good for fast planning and back-of-the-envelope checks.
3) Ambiguous and uncommon amino acids
The calculator supports common ambiguity codes:
- B as average of D/N
- Z as average of E/Q
- J as average of I/L
- X as 110 Da estimate
- U (selenocysteine) and O (pyrrolysine) are also supported
Quick Da and kDa reference
| Daltons (Da) | kDa | Approximate Protein Size Context |
|---|---|---|
| 5,000 Da | 5 kDa | Very small peptide/protein fragment |
| 14,000 Da | 14 kDa | Small globular protein range |
| 50,000 Da | 50 kDa | Common enzyme size |
| 150,000 Da | 150 kDa | Antibody-scale molecular weight |
Why protein molecular weight matters
- SDS-PAGE: choose gel percentage and estimate migration range.
- Size-exclusion chromatography: select appropriate fractionation range.
- Mass spectrometry: verify measured masses against expected sequence masses.
- Construct design: estimate the impact of tags, linkers, and truncations.
- Documentation: report expected MW in methods, figures, and protocols.
Common pitfalls in protein mass estimation
Post-translational modifications
Phosphorylation, glycosylation, lipidation, and other modifications can change apparent or measured mass. Sequence-only estimates typically do not include these unless you add them manually.
Signal peptides and propeptides
If mature protein is cleaved from a precursor, use the mature sequence for practical mass estimates.
Tags and fusion partners
His-tags, GST, MBP, fluorescent proteins, and linkers can significantly increase molecular weight. Always calculate the full expressed construct for experiment planning.
Example calculation
Suppose you have a recombinant protein of 300 amino acids and no full sequence handy. In length mode using 110 Da average residue mass:
- Base estimate:
300 × 110 = 33,000 Da - With terminal water:
33,018 Da - In kDa:
33.018 kDa
This estimate is usually good for quick protocol setup, while sequence mode gives a better molecular-weight prediction.
FAQ
Is this monoisotopic or average mass?
This calculator uses average residue masses for practical biochemical estimation.
Can I use this for peptides?
Yes. It works for peptides and proteins as long as you provide a valid one-letter amino-acid sequence.
Does it include disulfide effects?
No explicit disulfide-state correction is applied here. For most routine estimates, sequence mass with terminal water is sufficient.
Bottom line
This protein dalton calculator gives you a fast, practical way to estimate molecular weight in Da and kDa. Use sequence mode whenever possible, and use length mode when you only need a rapid approximation.