Protein Molecular Weight Calculator

Written by Great Medico

Updated September 25, 2026 •2 min read

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Protein size is often reported in daltons or kilodaltons, but a sequence can be converted into a useful theoretical molecular-weight estimate before a protein is purified or run on a gel. The Protein Molecular Weight Calculator adds the average residue masses in an amino-acid sequence and returns the calculated mass in kDa and Da.

What this calculator does

Paste a protein sequence using the standard one-letter amino-acid codes. The calculator removes non-letter separators, converts letters to uppercase, checks that every code is supported, and sums the average residue masses. It adds one water molecule for the peptide termini, then reports total molecular weight, residue count, average mass per residue, and the most common residues in the entered sequence.

How to use it

Use the mature sequence that matches the protein form you want to estimate. Remove tags, signal peptides, propeptides, or fusion partners only if they are not part of the target molecule. Ambiguous or nonstandard residue letters are rejected rather than silently assigned a mass. Sequence length is not a substitute for sequence composition; two proteins with the same number of residues can have different molecular weights.

How the calculation works

The calculation starts with the sum of the average residue masses for all amino acids in the sequence. Those residue masses represent amino acids as incorporated into a peptide chain, so one H₂O mass is added for the complete linear polypeptide. The displayed kilodalton value is total daltons divided by 1,000.

Example

For the default sequence MKWVTFISLLFLFSSAYSRGVFRR, which contains 24 residues, the calculator estimates a molecular weight of about 2.912 kDa, or 2,912.5 Da. The average residue contribution is about 120.60 Da before the terminal water is included. The most frequent residues in this sequence include phenylalanine and serine.

How to interpret the result

The result is the theoretical average mass of the entered unmodified polypeptide. It is useful for planning electrophoresis, chromatography, expression checks, or rough reagent calculations. Apparent molecular weight on SDS-PAGE may differ because migration depends on more than mass, and measured mass by mass spectrometry can differ depending on isotopic convention and molecular processing.

Limitations and notes

This calculator does not automatically account for post-translational modifications, disulfide formation, glycosylation, phosphorylation, acetylation, lipidation, bound cofactors, cleavage, isotopic labeling, or nonstandard amino acids. It uses a sequence-text workflow rather than a selector interface for individual residues. For analytical work, specify whether you need average mass, monoisotopic mass, or the mass of a modified mature protein.

Calculator update: This calculator was re-audited against the current reference workflow in v3.39.0. Parity classification: PASS.