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Biology Tools · Updated October 21, 2026 · Reviewed by FormatFlow Editorial

Protein Molecular Weight Calculator

You can calculate the average molecular weight of a protein from its one-letter sequence, with residue count, amino acid composition and the result in both daltons and kilodaltons.

Runs in your browserFree · No sign-up · No watermark
PROTEIN → MOLECULAR WEIGHTRuns in your browser
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Everything runs locally in this tab. No file is uploaded while the tool loads.

This tool runs in your tab. Nothing is uploaded and no copy is stored.

How files are handled

At a glance

Works with
PROTEIN → MOLECULAR WEIGHT
Processing
In your browser
Price
Free, no account
Updated
October 21, 2026
All Biology Tools

About Protein Molecular Weight Calculator

The molecular weight of a protein follows directly from its sequence once you know the average mass of each residue: add the residues and one water molecule for the free ends. Average masses are convenient for general calculations, while mass spectrometry usually reports monoisotopic masses instead.

This calculator reads a one-letter amino acid sequence, ignores stop markers, flags unknown letters, and returns average molecular weight in daltons and kilodaltons, residue count and a composition table with mass contributions. The composition table shows which residues dominate the mass, and the working line displays the residue total plus the water term so the result can be checked by hand.

What this tool does

The details that matter when you use Protein Molecular Weight Calculator for real work.

  • Average molecular weight

    The 20 standard average residue masses are summed and one water molecule is added, reported in both Da and kDa.

  • One-letter or FASTA input

    Paste a raw sequence, a whitespace-separated sequence or a FASTA record; headers and formatting are removed automatically.

  • Stop characters reported

    * markers are ignored as residues but counted and reported separately, so a translated sequence can be pasted directly.

  • Amino acid composition

    A table lists each residue's count, share of the chain and mass contribution, with totals that match the molecular weight.

  • Unknown letters flagged

    Letters outside the 20 standard codes are excluded and named, so a DNA sequence or malformed input is caught quickly.

  • Working shown

    The residue mass total, water mass and final molecular weight are displayed so the calculation can be checked or copied.

How to use Protein Molecular Weight Calculator

No account, no installation — the whole job happens in this browser tab.
  1. 01

    Paste the protein sequence

    Use the one-letter amino acid code, either raw, separated by spaces or in a FASTA record.

  2. 02

    Check for warnings

    Stop markers, unknown letters and ignored characters are reported above the result so the input can be corrected.

  3. 03

    Read the molecular weight

    The summary shows the average molecular weight in daltons and kilodaltons and the number of residues.

  4. 04

    Review the composition table

    Each residue's count, percentage and mass contribution is listed, with a total row that adds up to the molecular weight.

  5. 05

    Use the result appropriately

    Treat the value as the average mass of an unmodified chain and note that modifications or disulfide bonds would change it.

How this tool works

Works with
PROTEIN → MOLECULAR WEIGHT
Processing
Client-side, in your browser. Nothing is uploaded.
Requirements
Chrome, Edge, Firefox or Safari · JavaScript enabled

Limitations worth knowing

  • Reports average molecular weight only; monoisotopic mass, post-translational modifications, disulfide bonds, signal peptide cleavage and terminal modifications are not modelled.
  • Only the 20 standard amino acids are counted; selenocysteine, pyrrolysine and ambiguity codes are flagged and excluded from the mass.
  • Assumes a single unmodified peptide chain; protein complexes, multimers and non-standard residues are outside its scope.

Privacy and file handling

The protein sequence you paste stays in this browser tab. Parsing, the mass calculation and the composition table run with JavaScript on your device, so nothing is uploaded, stored or logged, and closing the page discards the input.

Read the full privacy policy

Protein Molecular Weight Calculator FAQ

Short, direct answers to the questions people ask before using this tool.
How is protein molecular weight calculated from a sequence?
Each amino acid is assigned its average residue mass, the masses are added for every residue in the chain, and one water molecule is added for the free N- and C-termini. The result is the average molecular weight of the unmodified peptide in daltons.
Why is one water molecule added to the residue masses?
The residue mass table gives the mass of each amino acid as it appears inside a chain, after the loss of water during peptide bond formation. Adding one water molecule back accounts for the intact termini of the full chain, so the result matches the chemical formula of the peptide.
What is the difference between average and monoisotopic mass?
Average mass uses the natural abundance of each element's isotopes, which is what this calculator reports. Monoisotopic mass uses only the most abundant isotope of each element and is the value mass spectrometry usually reports, so the two differ by a small amount that grows with size.
Why does my calculated mass differ from a mass spectrometry result?
The most common reasons are average versus monoisotopic mass, post-translational modifications, disulfide bonds, signal peptide cleavage or other processing. This calculator models an unmodified single chain, so a measured mass that differs suggests one of those factors is present.
Which letters are counted as amino acids?
Only the 20 standard one-letter codes are counted. Selenocysteine (U), pyrrolysine (O) and ambiguity codes such as B, Z, X or J are not modelled; they are excluded from the mass and listed in a warning so you can see what was skipped.
Does the calculator account for disulfide bonds?
No. Every cysteine is treated as a reduced residue. Each disulfide bond formed between two cysteines removes two hydrogen atoms, so a real protein with disulfide bonds has a slightly lower mass than the calculated reduced-chain value.
What do the percentages in the composition table mean?
They are the share of residues in the chain, calculated as the count of that amino acid divided by the total residue count. They describe composition, not mass, so each percentage is a residue fraction rather than a contribution to the molecular weight.
Is my protein sequence uploaded anywhere?
No. Parsing, mass summation and the composition table all run with JavaScript in this browser tab, so the sequence is never uploaded, stored or logged, and closing the page discards it.

Background reading

Format guides that explain the trade-offs behind Protein Molecular Weight Calculator.