Utility July 13, 2026 · 8 Min Read

Protein Molecular Weight Calculator – Guide & Formulas

Calculate protein molecular weight from amino acid sequence. Supports average and monoisotopic masses, disulfide bonds, and molar mass conversions.

Calculate protein molecular weight from amino acid sequence. Supports average and monoisotopic residue masses, disulfide bond corrections, and kDa/Da unit conversions.

Key Takeaway

Use the free Protein Molecular Weight Calculator to calculate protein molecular weight from amino acid sequence. supports average and monoisotopic masses, disulfide bonds, and molar mass conversions. Get instant results with step-by-step explanations.

How to Use the Protein Molecular Weight Calculator

  1. Enter your protein or peptide amino acid sequence using standard one-letter codes (e.g., MVLSPADKTN).
  2. Select mass type: Average (for SDS-PAGE) or Monoisotopic (for mass spectrometry).
  3. Optionally specify the number of disulfide bonds for correction.
  4. Review molecular weight in Da and kDa, amino acid composition, and sequence length.

The Formula

Molecular Weight (Da) = Sum of all amino acid residue masses + 18.015 Da (water for N-terminus H and C-terminus OH).

Variable Definitions

  • MW: Molecular Weight of the protein in Daltons (Da) or g/mol
  • m_i: Residue mass of each amino acid (not the free amino acid mass)
  • 18.015: Mass of water molecule added for N-terminal H and C-terminal OH groups
  • Da: Dalton — the standard unit of molecular mass (1 Da = 1 g/mol)
  • kDa: Kilodalton — 1,000 Daltons
  • Disulfide Bond: Covalent bond between two cysteine residues, removing 2H (2.016 Da) per bond

Calculating Molecular Weight for Peptide "ACDEF"

Determine the average molecular weight of the 5-amino acid peptide ACDEF.

  1. Step 1: Look up average residue masses: A=71.08, C=103.14, D=115.09, E=129.12, F=147.18.
  2. Step 2: Sum residue masses: 71.08 + 103.14 + 115.09 + 129.12 + 147.18 = 565.61 Da.
  3. Step 3: Add water for termini: 565.61 + 18.015 = 583.625 Da.
  4. Step 4: Convert to kDa: 583.625 / 1000 = 0.584 kDa.
  5. Step 5: The molecular weight of peptide ACDEF is approximately 583.63 Da (0.584 kDa).

Frequently Asked Questions

What is the difference between average and monoisotopic mass?

Average mass is the weighted average of all naturally occurring isotopes, used for SDS-PAGE and general biochemistry. Monoisotopic mass is the mass of the molecule containing only the most abundant isotope of each element, used for high-resolution mass spectrometry.

Why do I add 18.015 Da to the sequence?

When amino acids form peptide bonds, a water molecule (H₂O, 18.015 Da) is removed for each bond. However, the N-terminus retains an extra H and the C-terminus retains an extra OH, so one water molecule is effectively added back to calculate the intact protein mass.

How do disulfide bonds affect molecular weight?

Each disulfide bond between two cysteine residues removes 2 hydrogen atoms (2.016 Da) as the S-S bond forms. For each disulfide bond, subtract 2.016 Da from the calculated molecular weight.

What are ambiguous amino acid codes?

B represents Asx (average of D/N), Z represents Glx (average of E/Q), and J represents I/L (identical mass). X represents any amino acid. These are used when the exact identity is unknown.

How accurate is this calculator for large proteins?

For proteins under 100 kDa, the calculator is accurate to within 0.01% when using monoisotopic masses. For very large proteins (>100 kDa), average masses are preferred because monoisotopic isotope envelopes overlap.