Protein Molecular Weight Calculator

Calculate the molecular weight of any protein from its amino acid sequence — in Daltons (Da) and kilodaltons (kDa) — with full residue-level composition analysis.

Try:
Molecular Weight
0.000 g/mol
Calculation Breakdown
Element Atomic Mass Atoms Total %
Total Molecular Weight
Elements in this compound
In formula
Other elements

Quick Examples

Click any compound to calculate its molecular weight instantly.

Water
H₂O
18.015 g/mol
Carbon Dioxide
CO₂
44.009 g/mol
Sodium Chloride
NaCl
58.443 g/mol
Glucose
C₆H₁₂O₆
180.156 g/mol
Ethanol
C₂H₅OH
46.069 g/mol
Sulfuric Acid
H₂SO₄
98.077 g/mol

How to Use the Protein Molecular Weight Calculator

To calculate the molecular weight of a protein, enter its amino acid sequence or chemical formula into the input field and click "Calculate." The calculator returns the total molecular weight in Daltons along with individual residue contributions and amino acid composition statistics.

Follow these 4 steps to calculate protein molecular weight:

  1. Enter the amino acid sequence using standard one-letter codes (e.g., M for methionine, A for alanine, K for lysine). Remove any spaces, numbers, or FASTA headers before pasting. Alternatively, enter the chemical formula directly.
  2. Confirm the sequence represents the mature protein. If the protein undergoes signal peptide cleavage or propeptide processing, enter only the sequence of the final processed form for accurate results.
  3. Press "Calculate" or hit Enter. The calculator assigns each residue its standard molecular weight, sums them, and adds 18.02 Da for the terminal water molecule retained at the N-terminus and C-terminus.
  4. Read the result in Da or kDa. Use the breakdown to verify amino acid composition, identify the percentage contribution of each residue type, and cross-reference with mass spectrometry data.

This calculator serves proteomics researchers, biochemists designing recombinant proteins, and students learning about polypeptide chain mass calculations. The output helps verify expression constructs, plan gel electrophoresis experiments, and prepare protein standards.

How the Protein Molecular Weight Calculator Works

The protein molecular weight calculator determines the mass of a polypeptide chain by summing amino acid residue weights. During protein synthesis, each peptide bond formed between two amino acids releases one water molecule (18.02 Da). Residue weights already account for this loss, so the calculator sums residue weights and adds back one water molecule for the intact chain's terminal groups.

The calculation method and key values:

MW
Protein MW Formula
MW = Σ(amino acid residue weights) + 18.02 Da. The added 18.02 Da accounts for the water molecule retained at the N-terminal and C-terminal ends of the chain.
aa
Residue Weight Range
Glycine (Gly, G): 57.02 Da — lightest. Tryptophan (Trp, W): 186.08 Da — heaviest. Average residue: ~110 Da. All 20 standard amino acids have precisely known residue masses.
≈
Quick Estimation
Estimated MW ≈ number of residues × 110 Da. A 350-residue protein ≈ 38.5 kDa. Useful for quick checks before running detailed calculations.
PTM
Post-Translational Modifications
Sequence-based MW does not include PTMs. Common additions: phosphorylation (+80 Da per site), N-glycosylation (+1,000–3,000 Da per site), acetylation (+42 Da).

For human hemoglobin alpha chain (141 amino acids), the calculator sums residue weights starting from the N-terminal valine through the C-terminal arginine and adds 18.02 Da. The calculated molecular weight is approximately 15,126 Da (15.1 kDa), matching the value confirmed by mass spectrometry for the unmodified chain.

Protein molecular weight calculations are used in Western blot band identification, size-exclusion chromatography column selection, dynamic light scattering analysis, and recombinant protein expression verification. The calculated value serves as the baseline for detecting post-translational modifications by comparing against experimentally measured masses.

Common Compound Molecular Weights

Reference table of frequently searched chemical compounds.

Chemical Formula Compound Name Molecular Weight
H₂O Water 18.015 g/mol
CO₂ Carbon Dioxide 44.009 g/mol
NaCl Sodium Chloride 58.443 g/mol
NH₃ Ammonia 17.031 g/mol
CH₄ Methane 16.043 g/mol
H₂SO₄ Sulfuric Acid 98.077 g/mol
CaCO₃ Calcium Carbonate 100.086 g/mol
C₆H₁₂O₆ Glucose 180.156 g/mol
C₂H₅OH Ethanol 46.069 g/mol
HCl Hydrochloric Acid 36.461 g/mol
NaOH Sodium Hydroxide 39.997 g/mol
Ca(OH)₂ Calcium Hydroxide 74.092 g/mol
HNO₃ Nitric Acid 63.012 g/mol
KMnO₄ Potassium Permanganate 158.032 g/mol
CuSO₄ Copper(II) Sulfate 159.607 g/mol

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Protein Molecular Weight Calculator FAQs and Common Questions

Answers to common questions about calculating protein molecular weight, amino acid residue masses, and practical applications in proteomics.

How is the molecular weight of a protein calculated from its amino acid sequence?
The molecular weight of a protein is calculated by summing the residue molecular weights of each amino acid in the sequence and adding 18.02 Da for the terminal water molecule. Each amino acid residue weight represents the amino acid mass minus one water molecule (lost during peptide bond formation). For a protein with N amino acids: MW = Σ(residue weights) + 18.02 Da.
What is the average molecular weight of an amino acid?
The average molecular weight of an amino acid residue in a protein is approximately 110 Da (Daltons). This average accounts for the 20 standard amino acids weighted by their typical occurrence in natural proteins. The lightest residue is glycine (57.02 Da) and the heaviest is tryptophan (186.08 Da).
Can I estimate a protein's molecular weight from the number of amino acids?
Yes. Multiply the number of amino acid residues by 110 Da for a rough estimate. A 500-residue protein has an estimated molecular weight of approximately 55,000 Da (55 kDa). This approximation is within 5–10% of the actual value for most proteins but becomes less accurate for proteins enriched in unusually heavy or light amino acids.
Does the molecular weight from this calculator match SDS-PAGE results?
No, there can be differences. SDS-PAGE estimates molecular weight based on electrophoretic mobility, which is influenced by protein shape, charge, glycosylation, and SDS binding efficiency. The sequence-based calculated molecular weight reflects the unmodified polypeptide chain only. Post-translational modifications (glycosylation, phosphorylation, lipidation) add mass not captured by the amino acid sequence alone.
What is the difference between reduced and non-reduced protein molecular weight?
Reduced protein molecular weight is the mass of individual polypeptide chains after breaking disulfide bonds with reducing agents like DTT or β-mercaptoethanol. Non-reduced molecular weight includes intact disulfide-linked subunits. For multi-subunit proteins like antibodies (IgG, ~150 kDa), reduced conditions yield separate heavy chains (~50 kDa) and light chains (~25 kDa).
How accurate is a sequence-based protein molecular weight calculation?
A sequence-based protein molecular weight calculation is accurate to within 0.01% for the unmodified polypeptide chain, since it uses known amino acid residue masses. The calculation does not account for post-translational modifications (PTMs) such as glycosylation, phosphorylation, acetylation, or signal peptide cleavage. For proteins with significant PTMs, the measured molecular weight (by mass spectrometry or gel electrophoresis) will differ from the calculated value.