Frequently Asked Questions
Everything you need to know about the Protein Molecular Weight Calculator.
How is protein molecular weight calculated?
Sum the average residue mass of each amino acid in the sequence, then add 18.02 Da for one water molecule, which accounts for the free amino and carboxyl termini of the finished chain.
Why is a water molecule added?
Each peptide bond formed between two amino acids releases a water molecule. Using 'residue mass' already subtracts that water per bond, so one water is added back at the end to account for the two free ends of the chain.
What format should I enter my sequence in?
Standard single-letter amino acid codes (like MVLSPADK…), the format used by UniProt, GenBank, and most sequence databases. Spaces and numbers (like FASTA line numbers) are ignored automatically.
Does this use average or monoisotopic mass?
Average residue masses, which reflect the natural isotopic abundance of each element. This is standard for estimating bulk molecular weight, as opposed to monoisotopic mass used in high-precision mass spectrometry.
Does the calculator account for post-translational modifications?
No — it calculates the weight of the unmodified polypeptide chain only. Modifications like phosphorylation, glycosylation, or disulfide bonds will change the actual mass.
What does kDa mean?
kDa (kilodalton) equals 1,000 daltons. Protein sizes are commonly reported in kDa since dalton values for full proteins are often in the tens of thousands.
Can I use three-letter amino acid codes?
No, this calculator expects single-letter codes only. Convert three-letter codes (like Ala, Gly) to their single-letter equivalents (A, G) before entering the sequence.
What if my sequence contains an invalid character?
The calculator flags the exact invalid character. Only the 20 standard amino acid letters are recognized; ambiguity codes like X or B aren't supported.
Is this accurate enough for lab work?
It gives a solid estimate for typical use, but for precise, publication-grade values, use dedicated bioinformatics tools like ExPASy's ProtParam, which use the same underlying method with additional validation.
Is this calculator free to use?
Yes, completely free with no sign-up, and it runs entirely in your browser.