Protein Molecular Weight Calculator

Created by Łucja Zaborowska, MD, PhD candidate
Reviewed by Bogna Szyk and Jack Bowater
Last updated: Apr 06, 2022

With our protein molecular weight calculator, you can efficiently compute your protein's weight in kDa and u by selecting the amino acids that comprise it.

In the article below, we'll talk about genetic code, the reason why we use amino acid to kDa calculators, the conversion of amino acids to kilodaltons (kDa), and the use of kDa in molecular weight.

Why do we need the protein weight calculator?

If you are a student who is just learning about proteins and wants to run some quick calculations, then this peptide molecular weight calculator is just the tool for you. There is a more specific use, however - Western Blot, a special technique used to differentiate proteins in a sample.

In the Western Blot technique, a mixture of different proteins is placed onto a special gel and then separated using an electric field. All the substances in the mixture move by an amount determined by their protein molecular weight (MW). The lower the protein MW, the greater the distance it'll travel through the gel.

Electrophoresis starting point
Adding the mixture to the starting point - heavy elements will stay near the starting point, while light contents will travel far away.

Protein MW calculators allow us to predict the exact location our proteins will move to - so we know where to look.

Amino acids are one of the most common buffers in the human body - to learn more, check out our buffer calculator.

How to use the protein molecular weight calculator?

The protein mass calculator is the simplest tool you could imagine - just choose the desired combination of amino acids using the ready-to-go list. All the elements are enumerated with their full name and both their 3- and 1-letter codes.

Our protein kDa calculator will show you your results in both unified atomic mass unit (u) and kilodaltons (kDa).

💡 1 u = 1 Da
1 Da = 0.001 kDa

You may also like to try the atomic weight calculator!

How to calculate protein molecular weight from the sequence?

It's just as simple as it seems - add together all the molecular weights of the amino acids present in your sequence. You also need to subtract the molecular weight of water for every bond created.

Why do we need to subtract the water's weight? 💧

With every peptide bond formed between two amino acids, a particle of water is created and expelled. It does not longer constitute a part of the protein.

We used the following formula in our amino acid calculator for molecular weight:

Protein MW = Aminoacid MW.1 +... Aminoacid MW.n -(18.0153 * (n-1))


  • n - a total number of used amino acids.

If you use 2 amino acids in total, you need to subtract 18.02 u.

If you use 45 aminoacids in total, you need to subtract 44 * 18.02 u = 792.88 u.

💡0.11 kDa is the average molecular weight of an amino acid

A word about units - kDa, u, g/mol

Our protein size calculator shows your results in kilodaltons (kDa) and unified atomic mass units (u) - but why not g/mol?

  • Da and u are the basic units of molecular weight (molecular mass) - they are at the scale of single atoms or particles, and so are easy to use. Kilodaltons are 1000 bigger than daltons.

  • g/mol tells us the weight of one mole of a substance - that is, a total of 6.02214076 * 10²³ particles (the so-called Avogadro's number). That's the unit of the molar mass.

Although both of these variables usually take almost identical values, we must remember their different definitions.

Do you already know what's the difference between molarity and molality? If not, take a look at the molality calculator!

Łucja Zaborowska, MD, PhD candidate
You can add up to 20 amino acids.
1st Amino acid
Alanine (Ala, A)
2nd Amino acid
Molecular weight: 0.089 kDa = 89.09 u
Your protein: Ala
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