Protein Molecular Weight
Calculate protein and peptide molecular weight from amino acid sequence. Free kDa calculator for Western blot, SDS-PAGE, mass spec, and biochemistry research.
About This Calculator
The Protein Molecular Weight Calculator computes the mass of any protein or peptide from its amino acid sequence. Researchers, students, and lab professionals use it to predict protein migration in SDS-PAGE gels, identify bands in Western blotting, and determine peptide masses for mass spectrometry and biochemical assays. The calculator supports all 20 standard amino acids with their full names, three-letter codes, and one-letter codes.
The calculation follows the standard biochemical formula: the molecular weight of a protein is the sum of the individual amino acid masses minus the mass of water (18.0153 Da) lost for each peptide bond formed during protein synthesis. For a sequence of n amino acids, there are (n - 1) peptide bonds, so the water loss is 18.0153 × (n - 1) Da. The result is displayed in both daltons (Da) — the unified atomic mass unit — and kilodaltons (kDa), where 1 kDa = 1000 Da.
The average molecular weight of an amino acid residue in a protein is approximately 110 Da (0.11 kDa), but individual amino acids vary significantly — from glycine at 75.07 Da to tryptophan at 204.23 Da. This calculator uses precise individual masses for each of the 20 standard amino acids rather than an average, ensuring accurate results for any sequence composition. Isoleucine and leucine are isomers with identical masses (131.17 Da) and are both correctly handled.
Regional Notes
Worldwide: The Dalton (Da) and kilodalton (kDa) are the universal standard units for protein molecular weight in biochemistry and molecular biology. The unified atomic mass unit (u) is equivalent to the dalton (1 u = 1 Da). In SI units, the molar mass in g/mol has the same numerical value as the molecular weight in daltons. Researchers in all regions (IN, US, UK, EU) use the same units and formula for protein molecular weight calculations in Western blotting, mass spectrometry, and protein characterization.
Frequently Asked Questions
How do I calculate the molecular weight of a protein?
Select the amino acids in your protein sequence from the dropdown menus. The calculator sums the individual amino acid masses and subtracts 18.0153 Da for each peptide bond formed between consecutive amino acids. The result is displayed in both daltons (Da) and kilodaltons (kDa).
What is the formula used for protein molecular weight calculation?
The protein molecular weight is calculated as: Protein MW = (Sum of all amino acid masses) - (18.0153 × (n - 1)), where n is the number of amino acids in the sequence. The water molecule (18.0153 Da) is subtracted for each peptide bond formed during protein synthesis.
What is the difference between Da, kDa, and g/mol?
Dalton (Da) and unified atomic mass unit (u) are the standard units for molecular weight at the atomic scale. 1 kDa = 1000 Da. G/mol measures molar mass, the weight of one mole (6.022 × 10²³ particles) of a substance. Although numerically nearly identical, Da measures a single molecule while g/mol measures one mole.
Why do you subtract water when calculating protein molecular weight?
When amino acids join to form a protein, a peptide bond is created between them, and a water molecule (H₂O) is released and expelled. This water is no longer part of the protein molecule, so its mass (18.0153 Da) must be subtracted for each peptide bond. For a chain of n amino acids, there are (n - 1) peptide bonds.
How is protein molecular weight used in Western blotting?
In Western blotting, proteins are separated by size using SDS-PAGE electrophoresis. Smaller proteins migrate faster through the gel. Knowing the molecular weight of your target protein helps predict its position on the gel, identify the correct band, and verify that you are analyzing the right protein using molecular weight markers.
What is the average molecular weight of an amino acid?
The average molecular weight of a single amino acid residue in a protein is approximately 110 Da (0.11 kDa). However, individual amino acids range from 75.07 Da (glycine) to 204.23 Da (tryptophan). The calculator uses precise individual masses for each of the 20 standard amino acids.
Can I calculate the molecular weight of any protein sequence?
Yes, you can build any protein sequence by selecting up to 30 amino acids from the dropdown menus. Each of the 20 standard amino acids is available with its full name, three-letter code, and one-letter code. For longer sequences, calculate the weight of segments separately and sum them.
Which amino acids have the same molecular weight?
Isoleucine (Ile) and Leucine (Leu) are isomers and have the same molecular weight of 131.17 Da. This is because they share the same chemical formula (C₆H₁₃NO₂) but differ in their structural arrangement. The calculator correctly handles both amino acids with identical mass values.