Calculate protein molecular weight from amino acid sequence. Determine MW in Daltons and kilodaltons for your protein.
Last updated: March 2026
Protein molecular weight is the sum of the atomic masses of all atoms in a protein molecule, expressed in Daltons (Da) or kilodaltons (kDa). One Dalton equals 1/12 the mass of a carbon-12 atom (approximately 1.66 × 10⁻²⁴ grams). Molecular weight is fundamental for protein identification, purification, and characterization.
The calculation accounts for peptide bond formation: when amino acids link together, each bond releases one water molecule (H₂O, 18.015 Da). For a protein with n amino acids, there are (n-1) peptide bonds, so the total molecular weight equals the sum of amino acid masses minus 18.015 × (n-1). This subtraction is critical for accurate MW determination.
Molecular weight is essential for: SDS-PAGE interpretation (proteins migrate based on MW), calculating molar concentrations, determining protein stoichiometry in complexes, mass spectrometry validation, and selecting appropriate purification columns. Typical proteins range from 5 kDa (insulin, 51 amino acids) to over 500 kDa (titin, ~27,000 amino acids).
This calculator reports the average molecular weight of a protein, which is appropriate for most biochemical and molecular biology applications. Mass spectrometry often reports monoisotopic mass, which is calculated using the exact mass of the most abundant isotope of each element. As a result, monoisotopic masses are slightly different from average molecular weights reported by this calculator.
Calculate MW for a small peptide: AVGC
Theoretical molecular weight is calculated directly from the amino acid sequence, but the mass of the mature protein can differ because of biological processing or experimental modifications.
Modifications such as phosphorylation, glycosylation, acetylation, methylation and lipidation increase the molecular weight beyond the theoretical value calculated from the primary amino acid sequence.
Many proteins undergo cleavage of signal peptides, transit peptides or propeptides after translation. The mature protein therefore has a lower molecular weight than the precursor sequence.
Affinity tags such as His-tags, GST, MBP or fluorescent proteins add additional amino acids and increase the molecular weight of the final expressed protein.
Formation of each disulfide bond removes two hydrogen atoms, decreasing the molecular weight by approximately 2.016 Da while stabilizing the protein's three-dimensional structure.
The following resources provide additional information on protein sequences, molecular weight calculations and protein annotation.
Comprehensive protein sequence and functional annotation database, including calculated molecular weights for curated protein entries.
Calculates theoretical molecular weight, extinction coefficient, amino acid composition and other physicochemical properties directly from a protein sequence.
Search experimentally determined and predicted protein sequences from a wide range of organisms.
Official definitions of chemical terminology, including molecular mass, relative molecular mass and related concepts.
Peptide bond formation is a dehydration synthesis reaction. When two amino acids join, the carboxyl group of one (−COOH) reacts with the amino group of another (−NH₂), releasing H₂O. Each bond loses 18.015 Da, so n amino acids release (n-1) water molecules.
Average mass uses the weighted average of all isotopes (e.g., C is 12.011 Da). Monoisotopic mass uses only the most abundant isotope (C-12 = 12.000 Da). This calculator uses average masses. Mass spectrometry often reports monoisotopic masses for small proteins.
No. This calculates the theoretical MW from the primary sequence only. Real proteins often have modifications (phosphorylation +80 Da, acetylation +42 Da, glycosylation +hundreds to thousands Da) that increase MW. Add these manually if known.
SDS-PAGE estimates MW based on migration distance using protein standards. Anomalous migration occurs with: highly charged proteins, glycoproteins (run higher), membrane proteins, unusual shapes. Use mass spectrometry for accurate MW determination.
Disulfide bonds (Cys-Cys) form by removing 2H (−2.016 Da per bond). This calculator doesn't account for them automatically. If you know the number of disulfide bonds, subtract 2.016 × (number of bonds) from the result.
For theoretical MW from sequence: very accurate (±0.01%). However, real protein MW differs due to: processing (signal peptide cleavage), modifications, bound ligands/metals, and isotopic variation. Mass spectrometry typically shows ±1-2 Da difference from calculated values.
This calculator uses one-letter amino acid codes only (A, R, N, D, etc.). Convert three-letter codes to one-letter: Ala→A, Arg→R, Asn→N, Asp→D, Cys→C, Glu→E, Gln→Q, Gly→G, His→H, Ile→I, Leu→L, Lys→K, Met→M, Phe→F, Pro→P, Ser→S, Thr→T, Trp→W, Tyr→Y, Val→V.
Daltons (Da) and kilodaltons (kDa) measure molecular mass. 1 kDa = 1,000 Da. Small peptides use Da (insulin = 5,734 Da), larger proteins use kDa (BSA = 66 kDa). It's the same unit, just different scale like grams vs kilograms.
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