A professional tool to determine protein mass, amino acid composition, and sequence properties.
Accepts standard 1-letter amino acid codes. Whitespace and numbers are ignored.
Please enter a valid protein sequence.
Average Isotopic Mass (Standard)
Monoisotopic Mass (Mass Spec)
Select "Average" for general use or "Monoisotopic" for high-res mass spectrometry.
Total Molecular Weight
0.00 Da
Mass in Kilodaltons: 0.00 kDa
Amino Acid Count
0
Extinction Coeff. (M⁻¹cm⁻¹)
0
Absorbance (0.1% @ 280nm)
0.000
Property
Value
% Contribution
Hydrophobic Residues
0
0%
Polar (Uncharged)
0
0%
Acidic (Negative Charge)
0
0%
Basic (Positive Charge)
0
0%
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What is the Calculation of Protein Molecular Weight?
To calculate molecular weight of protein sequences is a fundamental task in biochemistry, proteomics, and molecular biology. The molecular weight (MW) represents the sum of the atomic masses of all atoms constituting the protein molecule. It is most commonly expressed in Daltons (Da) or Kilodaltons (kDa).
This calculation is critical for researchers needing to verify the identity of a purified protein via SDS-PAGE or Mass Spectrometry, prepare molar solutions for assays, or determine the correct dosage for therapeutic proteins. Unlike simple chemical compounds, proteins are macromolecules where the weight depends heavily on the specific sequence of amino acids and the isotopic composition of the atoms (Carbon, Hydrogen, Nitrogen, Oxygen, Sulfur).
A common misconception is that one can simply multiply the number of amino acids by an average weight (approx. 110 Da). While this gives a rough estimate, a precise calculate molecular weight of protein process requires summing the specific residue weights and accounting for the water molecule gained or lost during peptide bond formation and hydrolysis.
Protein Weight Formula and Mathematical Explanation
The core mathematical principle to calculate molecular weight of protein involves summing the weights of individual amino acid residues and adding the mass of the water molecule associated with the N-terminus and C-terminus.
When amino acids link to form a peptide bond, a water molecule ($H_2O$) is released (dehydration synthesis). Therefore, the weight of a protein of length $n$ is calculated using the residue masses (mass of amino acid minus water), plus one water molecule for the free termini.
A researcher needs to prepare a 1mM solution of a specific BSA fragment for an assay. The fragment sequence has 583 amino acids. By inputting the sequence into the tool to calculate molecular weight of protein:
Input: Full 583 AA sequence of BSA precursor.
Calculation: Sum of 583 residue weights + 18.015 Da.
Output: ~66,463 Da (66.5 kDa).
Application: The researcher now knows that to get a 1mM solution, they need 66.46 mg/mL.
Example 2: Mass Spectrometry Validation
A scientist analyzes a small peptide drug (Insulin B-chain) using Mass Spectrometry. They need to verify if the synthesized peptide is correct.
Sequence: FVNQHLCGSHLVEALYLVCGERGFFYTPKT (30 AA).
Settings: Select "Monoisotopic Mass" because Mass Spec measures specific isotopes.
Output: 3429.6 Da (Monoisotopic).
Result Analysis: If the instrument reads 3430.0, the synthesis is confirmed. If it reads 3500+, there may be an unwanted modification (e.g., phosphorylation).
How to Use This Protein Weight Calculator
This tool is designed for simplicity and precision. Follow these steps to accurately calculate molecular weight of protein sequences:
Enter Sequence: Paste your amino acid sequence into the text area. The tool accepts standard 1-letter codes (e.g., M, A, G, K). It automatically ignores numbers and whitespace, making it easy to paste directly from databases like UniProt or NCBI.
Select Weight Basis:
Choose Average Isotopic Mass for standard lab calculations (SDS-PAGE, Molarity).
Choose Monoisotopic Mass for high-resolution Mass Spectrometry applications.
Review Results: The "Total Molecular Weight" will update instantly.
Analyze Composition: Check the "Sequence Analysis Breakdown" table and chart to understand the hydrophobic vs. hydrophilic nature of your protein, which aids in buffer selection.
Copy Data: Use the "Copy Results" button to save the data for your lab notebook.
Key Factors That Affect Molecular Weight Results
When you calculate molecular weight of protein, several biological and chemical factors can influence the final mass compared to the theoretical value derived from the sequence alone.
Post-Translational Modifications (PTMs): Common modifications like phosphorylation (+80 Da), acetylation (+42 Da), or glycosylation (variable) add significant mass. Theoretical calculators often assume a "naked" peptide chain.
Disulfide Bridges: The formation of a disulfide bond between two Cysteine residues results in the loss of two hydrogen atoms (~2 Da). For proteins with many disulfides (like antibodies), this shift is measurable.
Isotopic Distribution: Elements naturally exist as mixtures of isotopes (e.g., C12 and C13). "Average" weight accounts for this natural abundance, while "Monoisotopic" uses the mass of the most abundant isotope.
N-Terminal Processing: In vivo, the initial Methionine is often cleaved off. If your sample is mature protein, ensure you remove the leading 'M' from your input sequence.
Buffer pH and Protons: While MW is constant, the measured mass in techniques like Mass Spec can vary based on protonation (H+ adducts), though the neutral mass remains the biological reference.
Sequence Accuracy: Errors in database sequencing or cloning mutations (e.g., D to E mutation) will shift the mass by specific amounts (e.g., +14 Da for D->E).
Frequently Asked Questions (FAQ)
What is the difference between Da and kDa?
Dalton (Da) is the standard unit of atomic mass. 1 Kilodalton (kDa) equals 1,000 Daltons. Small peptides are usually described in Da, while large proteins are described in kDa (e.g., 50 kDa).
Why does the calculator differ from my SDS-PAGE result?
SDS-PAGE estimates apparent molecular weight based on migration speed, which is affected by protein shape, hydrophobicity, and PTMs. This calculator provides the exact theoretical mass of the amino acid chain.
Does this tool account for water weight?
Yes. The formula sums the residue masses and adds exactly 18.015 Da to account for the free N-terminal hydrogen and C-terminal hydroxyl group.
Can I use 3-letter codes?
Currently, this tool is optimized for 1-letter codes (e.g., A, R, N) as they are the standard for bioinformatics data. Please convert 3-letter codes before pasting.
How is the Extinction Coefficient calculated?
It is estimated based on the number of Tryptophan (W), Tyrosine (Y), and Cystine (C-C) residues, using the equation: $\epsilon_{280} = (nW \times 5500) + (nY \times 1490) + (nC \times 125)$.
Should I include the stop codon (*) in the sequence?
No. Stop codons signal the end of translation and do not add mass to the protein. Please remove asterisks or stop indicators.
Does this calculate pI (Isoelectric Point)?
This tool focuses on mass and composition. While it shows acidic/basic residue counts which influence pI, a dedicated pI calculator is recommended for precise pH calculations.
What is the average weight of an amino acid?
The weighted average mass of an amino acid in a protein is approximately 110 Da. This is useful for rough estimates but not for precise work.
Related Tools and Internal Resources
Enhance your laboratory calculations with our suite of biochemical tools. Explore these related resources:
Molarity Calculator – Convert between mass, volume, and concentration for solution preparation.