Protein Molecular Weight Calculator
Calculate the estimated molecular weight of a protein from its amino acid sequence. Get protein length, amino acid composition, molecular weight in Daltons and kilodaltons, and a step-by-step calculation.
Protein Molecular Weight Calculator
Enter a protein or peptide sequence using the standard one-letter amino acid codes. The calculator counts each amino acid and estimates the molecular weight of the unmodified polypeptide.
Enter Protein Sequence
Enter a protein or peptide sequence using the standard one-letter amino acid codes.
Protein Molecular Weight Result
| Amino Acid | Count |
|---|
Step-by-Step Calculation
What Is Protein Molecular Weight?
Protein molecular weight is the estimated mass of a protein molecule. It is commonly expressed in Daltons (Da) or kilodaltons (kDa).
A protein is made up of amino acids linked together to form a polypeptide chain. The molecular weight can therefore be estimated from the amino acid sequence.
How Is Protein Molecular Weight Calculated?
The molecular weight is estimated by adding the molecular masses of the amino acid residues present in the protein sequence.
Protein MW ≈ Sum of Amino Acid Residue Masses
Molecular Weight (kDa) = Molecular Weight (Da) ÷ 1000
During peptide formation, water is released when amino acids form peptide bonds. Therefore, protein sequence calculations use residue masses rather than simply adding the free amino acid molecular masses.
How to Use the Protein Molecular Weight Calculator
- Enter a protein or peptide sequence.
- Use the standard one-letter amino acid codes.
- Spaces and line breaks can be included.
- Click Calculate Molecular Weight.
- Review the estimated molecular weight in Da and kDa.
- Review the amino acid composition and step-by-step calculation.
Standard Amino Acid Codes
A — Alanine
R — Arginine
N — Asparagine
D — Aspartic acid
C — Cysteine
E — Glutamic acid
Q — Glutamine
G — Glycine
H — Histidine
I — Isoleucine
L — Leucine
K — Lysine
M — Methionine
F — Phenylalanine
P — Proline
S — Serine
T — Threonine
W — Tryptophan
Y — Tyrosine
V — Valine
Protein Molecular Weight Example
Protein Sequence:
ACDEFGHIKLMNPQRSTVWY
Sequence length = 20 amino acids.
The sequence contains each of the 20 standard amino acids once.
The calculator adds the appropriate residue mass for each amino acid to estimate the molecular weight.
Daltons vs Kilodaltons
A Dalton (Da) is a unit commonly used to express molecular mass. A kilodalton (kDa) equals 1,000 Daltons.
1 kDa = 1,000 Da
kDa = Da ÷ 1,000
Important Factors That Can Affect Protein Mass
The calculated molecular weight is an estimate based on the entered amino acid sequence. The experimentally observed mass of a protein can differ because of additional factors.
- Post-translational modifications
- Signal peptide processing
- Proteolytic cleavage
- Glycosylation
- Phosphorylation
- Other chemical modifications
- Bound cofactors or other molecules
Standard Amino Acid Residue Mass Reference
The calculator uses average amino acid residue masses in Daltons for its sequence-based estimate. The reference below shows the values used by the calculation engine.
| Amino Acid | Code | Residue Mass (Da) |
|---|---|---|
| Alanine | A | 71.0788 |
| Arginine | R | 156.1875 |
| Asparagine | N | 114.1038 |
| Aspartic acid | D | 115.0886 |
| Cysteine | C | 103.1388 |
| Glutamic acid | E | 129.1155 |
| Glutamine | Q | 128.1307 |
| Glycine | G | 57.0519 |
| Histidine | H | 137.1411 |
| Isoleucine | I | 113.1594 |
| Leucine | L | 113.1594 |
| Lysine | K | 128.1741 |
| Methionine | M | 131.1926 |
| Phenylalanine | F | 147.1766 |
| Proline | P | 97.1167 |
| Serine | S | 87.0782 |
| Threonine | T | 101.1051 |
| Tryptophan | W | 186.2132 |
| Tyrosine | Y | 163.1760 |
| Valine | V | 99.1326 |
How to Interpret the Molecular Weight Result
The result is reported in both Daltons (Da) and kilodaltons (kDa). A longer sequence will generally have a larger molecular mass, but proteins with the same length can have different masses because their amino acid compositions differ.
The amino acid composition table helps you see which residues contribute to the sequence. This is useful when checking a sequence manually or explaining why two proteins of similar length can have different estimated molecular weights.
Sequence Quality and Common Input Issues
- Use the standard one-letter codes for the 20 common proteinogenic amino acids.
- Spaces and line breaks are removed automatically, which is useful for pasted FASTA-like sequences without the header.
- Do not include a FASTA header, numbers, punctuation or nucleotide bases such as U unless they are part of a supported amino acid code.
- Check the sequence carefully when a measured experimental mass is being compared with the calculated value.
Calculated Mass vs Experimental Mass
A sequence-based result is a theoretical estimate for the molecular mass of the entered chain under the calculator’s assumptions. An experimentally observed mass can differ when a protein has been processed, chemically modified, glycosylated, phosphorylated, or associated with another molecule.
For research applications, the calculated value is best treated as a reference for comparison rather than as a substitute for an experimentally measured molecular mass.
Frequently Asked Questions
What is a protein molecular weight calculator?
It estimates the molecular weight of a protein from its amino acid sequence.
What units are used for protein molecular weight?
Protein molecular weight is commonly expressed in Daltons (Da) or kilodaltons (kDa).
Can I enter a peptide sequence?
Yes. The calculator can estimate the molecular weight of both short peptide sequences and longer protein sequences.
Which amino acid codes are accepted?
The calculator accepts the standard one-letter amino acid codes for the 20 commonly occurring proteinogenic amino acids.
Does the calculator include post-translational modifications?
No. The basic calculation estimates the molecular weight from the unmodified amino acid sequence.
How accurate is a sequence-based molecular weight?
It provides an estimate based on the entered sequence. Experimental molecular mass can differ because of modifications, processing, or other molecular factors.
How do I convert Daltons to kilodaltons?
Divide the molecular weight in Daltons by 1,000 to obtain the value in kilodaltons.
Does protein length determine molecular weight?
Length is an important factor, but amino acid composition also affects molecular weight, so two sequences with the same length can have different masses.
Can I paste a multiline protein sequence?
Yes. The calculator removes whitespace and line breaks before validating and calculating the sequence.
Why might the calculated mass differ from a laboratory measurement?
Processing, post-translational modifications, chemical modifications, bound molecules and other experimental factors can change the observed molecular mass.
What is the difference between Da and kDa?
One kilodalton equals 1,000 Daltons. Divide a value in Da by 1,000 to convert it to kDa.
Protein Molecular Weight Calculator Disclaimer
This calculator is provided for general educational and informational purposes only. The molecular weight is an estimate based on the amino acid sequence entered and the assumptions used by the calculator. Actual experimentally measured protein mass may differ because of post-translational modifications, processing, chemical modifications, bound molecules and other factors. For research or clinical applications, verify calculations using appropriate scientific methods and validated laboratory resources.