What input formats are accepted?

One-letter codes (e.g., MASTVK) entered as a continuous string, or three-letter codes (e.g., Met-Ala-Ser-Thr-Val-Lys) separated by hyphens, spaces, or commas. The tool detects the format automatically.

Does this use average or monoisotopic masses?

Average masses are used, matching the values reported by ExPASy ProtParam and suitable for SDS-PAGE comparisons. Monoisotopic masses are relevant only in high-resolution mass spectrometry and are not calculated here.

Why is one water molecule added to the sum?

Peptide bond formation removes water between residues. The free N-terminus (H) and free C-terminus (OH) together equal one uncleaved water molecule (18.02 Da), which is added back to give the correct mass of the intact protein.

Are post-translational modifications included?

No. The calculator gives the unmodified, linear sequence mass. Modifications such as phosphorylation, glycosylation, or disulfide bonds must be accounted for manually.

How do results compare to ExPASy ProtParam?

Results match ExPASy ProtParam to within rounding differences because both tools use the same IUPAC average residue masses.

What happens with ambiguous or unknown characters?

Unknown one-letter characters or unrecognized three-letter codes are flagged in an error list and skipped from the mass calculation. The result still shows the mass of all valid residues found.

Molecular Weight of Protein Calculator

Name: Molecular Weight of Protein Calculator
Availability: InStock
Author: Nham Vu

Paste a protein sequence in one-letter or three-letter amino acid codes and get the molecular weight in Da and kDa with a residue composition table.

Amino Acid Sequence

Paste sequence (one-letter or three-letter codes)

Try a sample

Enter a sequence on the left and click Calculate

Molecular Weight (Da)

Molecular Weight (kDa)

Residues:

Format detected:

Water added: 18.02 Da

Residue Composition

Amino Acid	1-Letter	Count	Residue Mass	Total Mass (Da)	% of MW
Total					100%

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Summary

Paste a protein sequence in one-letter or three-letter amino acid codes and get the molecular weight in Da and kDa with a residue composition table.

How it works

Paste or type your amino acid sequence using either one-letter codes (MASTVK...) or three-letter codes separated by spaces or hyphens (Met-Ala-Ser...).
The tool automatically detects whether the input is one-letter or three-letter format.
Each residue is matched to its IUPAC average molecular mass.
All residue masses are summed and one water molecule (18.02 Da) is added for the free N- and C-termini.
The total is displayed in Da and kDa, alongside a table showing count and mass contribution per residue type.

Use cases

Estimate protein mass before SDS-PAGE or mass spectrometry experiments.
Work from lab notebooks that use three-letter amino acid codes.
Verify synthetic peptide mass against theoretical values.
Calculate mass contributions of individual residue types in a sequence.
Support biochemistry coursework with both notation styles.
Cross-check results when analyzing protein variants or mutants.

Frequently Asked Questions

Last updated: 2026-07-01 · Reviewed by Nham Vu