Protein Molecular Weight Calculator
Advanced sequence analysis: calculate molecular weight (Da, kDa), isoelectric point (pI), extinction coefficient, and amino acid composition.
Comprehensive Protein Sequence Analysis
A protein molecular weight calculator determines the mass of a protein from its amino acid sequence. Calculate protein molecular weight by summing the molecular weights of all amino acid residues and accounting for water loss during peptide bond formation. Protein molecular weight is typically reported in Daltons (Da) or kilodaltons (kDa).
Paste your 1-letter amino acid sequence below. The calculator ignores spaces, line breaks, and numbers, making it easy to copy-paste directly from FASTA files or databases like UniProt.
Physical Properties Dashboard
Total Molecular Weight
Length
-- AA
Est. pI
--
Isoelectric point
Ext. Coeff.
--
M⁻¹ cm⁻¹ at 280nm
Abs 0.1%
--
(1 g/l) at 280nm
Spaces, numbers, and symbols are automatically ignored. Letters that are not standard 1-letter amino acid codes (like B, J, O, U, X, Z) were excluded from the calculation.
Sequence Composition Profile
How is protein molecular weight calculated?
When amino acids connect to form a protein via peptide bonds, a molecule of water (H₂O) is lost for every bond formed. Therefore, the weight of a protein is not simply the sum of the free amino acid weights.
To correctly calculate the molecular weight, this tool uses the residue mass for each amino acid (which is the free mass minus water). Once all residue masses are summed up, we add the mass of a single water molecule to account for the N-terminus (H) and C-terminus (OH) at the ends of the chain.
Total MW = (Sum of Residue Masses) + 18.015 Da
The result is typically given in Daltons (Da) or kiloDaltons (kDa). For reference, 1 kDa = 1,000 Da. An average amino acid residue contributes roughly 110 Daltons to the protein's overall mass.
Further reading: The ExPASy ProtParam tool by the Swiss Institute of Bioinformatics computes various physical and chemical parameters, including theoretical molecular weight, for given protein sequences.
Amino Acid Average Residue Masses
This calculator uses the following average isotopic masses for amino acid residues. Average mass accounts for the natural abundance of isotopes (like Carbon-13), which is standard practice for analyzing proteins in biology and biochemistry.
| Amino Acid | 1-Letter | 3-Letter | Residue Mass (Da) |
|---|
Further reading: UniProt's amino acid properties guide offers a comprehensive reference for standard residue masses, chemical structures, and codes used across biological databases.
Average vs. Monoisotopic Mass
You might notice that mass spectrometry tools sometimes give slightly different molecular weights. This is due to isotopes.
- Average Mass (Used here): Calculated using the natural abundance of all isotopes of each element (e.g., ~99% Carbon-12 and ~1% Carbon-13). This is the standard measurement for large proteins.
- Monoisotopic Mass: Calculated using only the mass of the most abundant, primary isotope (e.g., purely Carbon-12). This is mostly used in high-resolution mass spectrometry for small peptides.
Common laboratory applications
Knowing the exact molecular weight, pI, and extinction coefficient of your protein sequence is a critical first step for several routine laboratory and bioinformatics workflows.
SDS-PAGE & Western Blotting
MW determines which percentage polyacrylamide gel to cast and which prestained molecular weight ladder to use to accurately visualize your target band.
Protein Purification
The Isoelectric Point (pI) informs which buffer pH to use during Ion Exchange Chromatography (IEX) to ensure your protein binds to or flows through the column.
Assay Stoichiometry
MW and extinction coefficient are essential for accurately converting absorbance readings to molarity for enzyme kinetics or SPR binding assays.
Converting Protein Concentration: mg/mL to Molarity
The most common reason researchers calculate a protein's molecular weight and extinction coefficient is to determine its true molar concentration (like mM or µM) using a spectrophotometer (e.g., NanoDrop).
Absorbance = Ext. Coeff. × Path Length × Molarity
Molarity (M) = [Absorbance at 280nm] ÷ [Ext. Coeff.]
Quick mass-to-moles conversion: If you already know your concentration in mg/mL from a Bradford assay, you can use the MW.
Molarity (mM) = Concentration (mg/mL) ÷ MW (kDa)
Further reading: The NEBioCalculator by New England Biolabs provides additional interactive tools for mass-to-moles conversions of both proteins and nucleic acids.
Typical protein size benchmarks
Not sure if your result makes sense? Here is a reference guide featuring common standard proteins used in biochemistry labs to help contextualize your calculated molecular weight.
| Protein | Approx. MW | Description |
|---|---|---|
| Insulin | ~5.8 kDa | A very small peptide hormone. Often considered the boundary between "peptide" and "protein". |
| GFP (Green Fluorescent Protein) | ~27 kDa | A widely used fluorescent tag. Represents a small-to-average sized single-domain protein. |
| BSA (Bovine Serum Albumin) | ~66 kDa | The classic laboratory standard for Bradford assays and blocking buffers. |
| IgG Antibody | ~150 kDa | A large multi-chain complex (two heavy chains at ~50 kDa, two light chains at ~25 kDa). |
Frequently Asked Questions
What is a Dalton (Da)?
A Dalton (Da) is a standard unit of mass that quantifies mass on an atomic or molecular scale. It is effectively synonymous with the unified atomic mass unit (u). One Dalton is roughly equivalent to the mass of a single proton or neutron.
How do I interpret kDa?
kDa stands for kiloDalton, which is 1,000 Daltons. Because proteins are macromolecules, their masses are very large numbers in standard Daltons. Biochemists typically use kDa for easier reading. For example, a 50,000 Da protein is simply referred to as a 50 kDa protein.
Does this calculator handle post-translational modifications?
No. This calculator assumes a standard, unmodified linear peptide chain with standard H- and -OH termini. It does not account for glycosylation, phosphorylation, disulfide bond formation (which removes 2 Da per bond), or missing terminal waters in cyclic peptides.
Can I paste sequence numbers and spaces?
Yes! The calculator automatically strips out spaces, numbers, line breaks, and formatting characters. You can copy a sequence block straight out of a FASTA file or a database website, paste it in, and the tool will only process the valid alphabetical letters.
What is the average weight of a single amino acid?
While the exact weight varies depending on the specific amino acid (from about 57 Da for Glycine to 186 Da for Tryptophan), the average molecular weight of an amino acid residue in a typical protein is widely estimated to be about 110 Daltons.
How accurate is this theoretical molecular weight?
This theoretical calculation is extremely accurate for the unmodified, linear amino acid sequence based on standard atomic weights. However, in physical lab experiments (like SDS-PAGE), the apparent molecular weight might differ by up to 10% due to factors like protein folding, charge distribution, or how the protein interacts with the gel.
Why does my mass spectrometry result not match this calculation exactly?
Mass spectrometers often measure the monoisotopic mass (using the exact mass of the most abundant isotopes) for small peptides, whereas this calculator provides the average isotopic mass. Additionally, your physical sample might have lost terminal sequences (clipping), formed disulfide bonds (reducing mass by 2 Da per bond), or acquired modifications like phosphorylation.
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Disclaimer: This calculator provides theoretical average molecular weights based on standard isotopic abundances. It is intended for educational, informational, and general laboratory estimation purposes only. Real-world experimental masses measured via mass spectrometry or SDS-PAGE may vary significantly from these theoretical values due to biological factors such as post-translational modifications (e.g., glycosylation, phosphorylation), sequence truncations, and disulfide bond formation, as well as analytical factors like buffer adducts, ionization states, or unexpected isotopic distribution variations. Always verify critical measurements against empirical data and peer-reviewed literature. Do not use these results as the sole basis for medical, diagnostic, or strict quantitative analytical conclusions.
Last updated: May 31, 2026