Does this use average or monoisotopic masses?

Average masses are used, which match the values reported by most protein analysis tools (e.g., ExPASy ProtParam) and are appropriate for SDS-PAGE comparisons. Monoisotopic masses are used in high-resolution mass spectrometry but are not calculated here.

Why is one water molecule added?

When amino acids are joined into a peptide chain, a water molecule is lost at each peptide bond. However, the free N-terminus (H) and free C-terminus (OH) collectively represent one water molecule that is not lost, so it is added back to the sum of residue masses.

What single-letter codes are accepted?

The 20 standard amino acids: A (Alanine), C (Cysteine), D (Aspartate), E (Glutamate), F (Phenylalanine), G (Glycine), H (Histidine), I (Isoleucine), K (Lysine), L (Leucine), M (Methionine), N (Asparagine), P (Proline), Q (Glutamine), R (Arginine), S (Serine), T (Threonine), V (Valine), W (Tryptophan), Y (Tyrosine).

Are disulfide bonds or post-translational modifications included?

No. The calculator computes the unmodified, linear sequence mass. Disulfide bonds reduce the mass by 2 Da per bond. Post-translational modifications (phosphorylation, glycosylation, etc.) must be added manually.

How accurate is this compared to ExPASy ProtParam?

Results match ExPASy ProtParam to within rounding (2 decimal places) because both use the same IUPAC average residue masses.

Protein Molecular Weight Calculator

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

Paste a protein sequence in single-letter amino acid codes and instantly get the molecular weight with a per-residue breakdown.

Amino Acid Sequence

Enter single-letter codes (e.g. MKVLWAALLVTFLAGSKATA). Spaces and line breaks are ignored.

Molecular Weight Daltons (Da)

Molecular Weight kiloDaltons (kDa)

Residue Count amino acids

Residue Composition

Residue	Code	Count	Residue Mass (Da)	Total Mass (Da)	% of MW

Enter a sequence above and click Calculate to see the molecular weight.

Summary

Paste a protein sequence in single-letter amino acid codes and instantly get the molecular weight with a per-residue breakdown.

How it works

Paste or type your amino acid sequence using IUPAC single-letter codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y).
Invalid characters (spaces, digits, ambiguous codes) are flagged but ignored in the calculation.
The tool looks up the average residue mass for each amino acid.
All residue masses are summed, then one water molecule (18.02 Da) is added to account for the free N- and C-termini.
The total molecular weight is displayed in Da and kDa alongside a composition breakdown table.

Use cases

Estimate the expected mass of a recombinant protein before SDS-PAGE or mass spectrometry.
Verify that a synthesized peptide matches its theoretical mass.
Calculate mass for gel filtration column calibration.
Quickly compare molecular weights of protein variants or mutants.
Support biochemistry coursework and laboratory planning.
Check the mass contribution of individual residues in a peptide sequence.

Frequently Asked Questions

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