Input your protein's amino acid sequence to determine its total molecular weight.
Protein Molecular Weight Calculator
Use standard one-letter amino acid codes (e.g., A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V).
Yes (standard for intact peptide)
No (for terminal amino acids or fragments)
Most commonly, you'll want to include the water molecule removed during peptide bond formation.
Your Protein's Molecular Weight
The molecular weight is calculated by summing the average molecular weights of each amino acid residue in the sequence and optionally adding or subtracting the molecular weight of water based on whether it's an intact peptide.
Amino Acid Residue Molecular Weights
Average Monoisotopic Molecular Weights of Amino Acid Residues (Da)
Amino Acid (1-Letter)
Amino Acid (Full Name)
Residue Mass (Da)
Residue Mass with H2O (Da)
Molecular Weight Distribution by Amino Acid Type
Residue Mass
Residue Mass (with H2O)
What is Protein Molecular Weight Calculation?
Protein molecular weight calculation is the process of determining the total mass of a protein molecule, expressed in Daltons (Da) or kilodaltons (kDa). This calculation is primarily based on the protein's amino acid sequence. Each of the 20 standard amino acids has a specific average molecular weight. By summing these weights for every amino acid in a given sequence, and accounting for the formation of peptide bonds (which involves the loss of a water molecule), we can estimate the protein's total mass. This is a fundamental step in many biological and biochemical analyses.
Who should use it:
Biologists and biochemists studying protein structure and function.
Researchers designing synthetic peptides or proteins.
Students learning about protein chemistry.
Anyone needing to estimate the mass of a protein from its known sequence for experimental planning (e.g., mass spectrometry, gel electrophoresis).
Common misconceptions:
Confusing amino acid mass with residue mass: The mass of a free amino acid is different from its mass when incorporated into a peptide chain. During peptide bond formation, a water molecule (H₂O) is lost, so the residue mass is the amino acid mass minus the mass of water. Our calculator accounts for this difference.
Ignoring the terminal water molecule: For an intact peptide chain, the calculation typically includes the mass of one water molecule, representing the N-terminus and C-terminus. Our calculator allows you to toggle this feature.
Using exact isotopic masses instead of average masses: For general estimations, average isotopic masses are sufficient. For high-precision mass spectrometry, specific isotopic compositions are considered, but this calculator uses standard average weights.
Protein Molecular Weight Calculation Formula and Mathematical Explanation
The molecular weight of a protein is determined by summing the average masses of its constituent amino acid residues and accounting for the loss of water during peptide bond formation. For a peptide chain of n amino acids, n-1 peptide bonds are formed.
∑(Residue Massi) is the sum of the average molecular weights of each amino acid residue (i) in the sequence. The residue mass is the average molecular weight of the amino acid minus the average molecular weight of a water molecule (approx. 18.015 Da).
MWH₂O is the molecular weight of a water molecule (approx. 18.015 Da). This is added for intact peptides, representing the terminal hydrogen at the N-terminus and the hydroxyl group at the C-terminus that are not involved in peptide bonds.
Step-by-step derivation:
Identify each amino acid in the sequence.
For each amino acid, find its corresponding average residue mass (mass of free amino acid – mass of H₂O).
Sum all the residue masses.
If the calculation is for an intact peptide (which is the default), add the average molecular weight of a water molecule (18.015 Da) to the sum of residue masses.
Variable Explanations:
The core variables involved are the average molecular weights of the 20 standard amino acids and the molecular weight of water.
Variables Table:
Key Variables in Protein Molecular Weight Calculation
Variable
Meaning
Unit
Typical Range / Value
Amino Acid Sequence
The ordered list of amino acids in the protein chain, represented by one-letter codes.
Sequence String
e.g., MWST…YVV
Number of Amino Acids (n)
The total count of amino acids in the sequence.
Count
1 to thousands
Average Residue Mass (Ri)
The average molecular weight of a specific amino acid after the removal of a water molecule during peptide bond formation.
Daltons (Da)
~71 (Ala) to ~204 (Trp)
Molecular Weight of Water (MWH₂O)
The average molecular weight of a water molecule.
Daltons (Da)
~18.015
Total Molecular Weight (MW)
The final calculated mass of the protein or peptide.
Daltons (Da)
Varies widely based on sequence length and composition.
Practical Examples (Real-World Use Cases)
Example 1: Insulin (Human) Fragment
Let's calculate the approximate molecular weight for a short peptide fragment, mimicking a portion of insulin's A-chain: GAPVL
Inputs:
Sequence: GAPVL
Account for Water: Yes (intact peptide assumption)
Calculation Steps:
Number of amino acids = 5
Number of peptide bonds = 5 – 1 = 4
Sum of Residue Masses:
Glycine (G): 71.079 Da
Alanine (A): 89.094 Da
Proline (P): 115.131 Da
Valine (V): 101.104 Da
Leucine (L): 113.159 Da
Sum = 71.079 + 89.094 + 115.131 + 101.104 + 113.159 = 489.567 Da
Add Water Mass (for intact peptide): 489.567 Da + 18.015 Da = 507.582 Da
Results:
Total Amino Acids: 5
Average Residue Mass Sum: 489.567 Da
Water Mass Added: 18.015 Da
Total Molecular Weight: ~507.58 Da
Interpretation: This short peptide fragment has a molecular weight of approximately 507.58 Daltons. This value is crucial for experimental techniques like mass spectrometry, where precise mass measurements are used to identify and quantify peptides.
Example 2: Small Protein – Villin Headpiece (Synthetic)
Consider the sequence of the 36-amino acid villin headpiece, a common protein folding model: (Sequence omitted for brevity, but assume it's entered)
Inputs:
Sequence: (36 amino acids entered)
Account for Water: Yes
Calculation Steps (performed by calculator):
The calculator identifies all 36 amino acids.
It retrieves the average residue mass for each of the 36 amino acids.
It sums these 36 residue masses.
It adds the mass of one water molecule (18.015 Da) because we selected "Yes" for accounting for water.
Hypothetical Results (based on typical sequences of this length):
Total Amino Acids: 36
Average Residue Mass Sum: ~3900-4100 Da
Water Mass Added: 18.015 Da
Total Molecular Weight: ~3918-4118 Da (Example: 4050.5 Da)
Interpretation: A protein of this size falls into the category of a small protein or a large peptide. Its molecular weight is approximately 4.05 kDa. This information helps in selecting appropriate gel electrophoresis conditions (like SDS-PAGE) or interpreting results from purification steps.
How to Use This Protein Molecular Weight Calculator
Using this calculator is straightforward. Follow these steps to get your protein's molecular weight:
Step-by-step instructions:
Enter the Amino Acid Sequence: In the "Amino Acid Sequence" field, type or paste the sequence of your protein or peptide. Use the standard one-letter codes for amino acids (e.g., A for Alanine, R for Arginine, N for Asparagine, etc.). Ensure there are no spaces or special characters within the sequence itself unless they are part of a non-standard notation you are handling separately.
Account for Water Molecule: Decide whether to include the mass of a water molecule.
Select "Yes (standard for intact peptide)" if you are calculating the weight of a complete peptide or protein chain. This is the most common scenario and accounts for the termini.
Select "No (for terminal amino acids or fragments)" if you are calculating the weight of individual amino acids or specific fragments where water loss is not relevant to your definition.
Calculate: Click the "Calculate" button.
How to read results:
After clicking "Calculate", the calculator will display:
Total Molecular Weight: This is the primary result, shown prominently in Daltons (Da).
Total Amino Acids: The total count of amino acids in your entered sequence.
Average Residue Mass Sum: The sum of the molecular weights of all amino acid residues in the sequence, before accounting for the terminal water molecule.
Water Mass Added: Indicates whether the water molecule's mass was added (18.015 Da) or not.
Molecular Weight Table: A table detailing the average residue masses for each standard amino acid, which you can reference.
Molecular Weight Chart: A visual representation comparing the residue mass versus the residue mass including the water molecule, and showing the distribution across amino acid types.
Decision-making guidance:
The molecular weight is a critical parameter for experimental design. For instance:
Mass Spectrometry: A precise molecular weight is essential for interpreting mass spectrometry data. Ensure you are using the correct calculation (e.g., monoisotopic vs. average mass, inclusion of water).
Gel Electrophoresis: Knowledge of molecular weight helps in choosing the correct percentage for SDS-PAGE gels to achieve optimal separation.
Protein Purification: Molecular weight can inform choices about chromatography techniques (e.g., size exclusion chromatography).
Key Factors That Affect Protein Molecular Weight Results
While the amino acid sequence is the primary determinant of a protein's molecular weight, several factors and assumptions influence the calculated value and its practical interpretation:
Amino Acid Sequence Accuracy: The most crucial factor. Any errors or omissions in the sequence directly alter the sum of residue masses. Ensure the sequence is correct and complete.
Average vs. Monoisotopic Mass: This calculator uses average isotopic masses (weighted average of isotopes). For high-precision applications like mass spectrometry, monoisotopic masses (mass of the most abundant isotope combination) might be required. The difference is usually small but can be significant for accurate mass assignments.
Post-Translational Modifications (PTMs): Many proteins undergo modifications after translation, such as glycosylation (adding sugar chains), phosphorylation, acetylation, or methylation. These modifications add significant mass to the protein and are *not* accounted for by simply calculating from the amino acid sequence alone. A glycosylated protein will be much heavier than its calculated sequence-based weight.
N-terminal Modifications: The N-terminal methionine is often cleaved off in mature proteins. Other N-terminal modifications, like acetylation, add mass. This calculator assumes a standard N-terminus unless specifically modified in the sequence input.
C-terminal Modifications: Some proteins are C-terminally amidated, which involves the loss of ammonia and addition of an amide group, slightly altering the terminal mass compared to a simple hydroxyl group.
Inclusion/Exclusion of Water: As discussed, whether the mass of a water molecule is included (for intact peptides) or excluded (for terminal residues/fragments) significantly impacts the final value. Always be clear about this assumption.
Non-Standard Amino Acids: While this calculator uses the 20 standard amino acids, some proteins contain non-standard or modified amino acids (e.g., selenocysteine, hydroxyproline). Their unique masses must be incorporated for accurate calculations if present.
Frequently Asked Questions (FAQ)
Q1: What is the difference between amino acid mass and residue mass?
A: The mass of a free amino acid includes all its atoms. When it forms a peptide bond, a water molecule (H₂O) is removed. The residue mass is the mass of the amino acid minus the mass of that water molecule.
Q2: Should I include the water molecule for calculating the weight of a single amino acid?
A: No. A single amino acid is not a peptide. You should use the full amino acid mass. The water molecule mass is relevant when considering peptide bond formation or the termini of peptide chains.
Q3: My protein is glycosylated. Will this calculator give me the correct weight?
A: No. This calculator determines the weight based solely on the amino acid sequence. Glycosylation (adding sugar chains) significantly increases the protein's mass. You would need to know the composition and size of the attached glycans to add their mass separately.
Q4: What does "Da" stand for?
A: "Da" stands for Dalton, the standard unit of molecular mass. One Dalton is approximately the mass of one hydrogen atom. Kilodaltons (kDa) are often used for proteins, where 1 kDa = 1000 Da.
Q5: How accurate are these average molecular weights?
A: The average molecular weights are highly accurate for most general purposes and estimations. They are derived from the natural abundance of isotopes of each element (C, H, N, O, S). For very high-resolution mass spectrometry, monoisotopic masses might be preferred.
Q6: Can this calculator handle sequences with gaps or unknown amino acids?
A: This calculator is designed for standard, contiguous sequences using one-letter codes. It does not currently support gaps or ambiguous characters (like 'X' for unknown). You would need to either resolve the unknowns or calculate segments separately.
Q7: Why is knowing the molecular weight of a protein important?
A: It's fundamental for experimental planning (e.g., setting up gels, estimating elution times in chromatography), interpreting results (e.g., mass spectrometry), and understanding protein behavior in biological systems.
Q8: Does the calculator account for the N-terminal methionine being cleaved?
A: Not automatically. If the N-terminal methionine is typically cleaved in the mature protein you are studying, you should either input the sequence *without* the methionine, or manually subtract its residue mass (approx. 131.19 Da) from the calculated total weight.