Protein molecular weight calculator

What is molecular weight?

Molecular weight (MW) is a fundamental property of proteins, representing the sum of atomic masses of all atoms in the molecule. This calculator determines the molecular weight of protein sequences based on their amino acid composition, providing results in Daltons (Da).

Knowing a protein's molecular weight is essential for many laboratory techniques. SDS-PAGE uses MW for band identification, while mass spectrometry relies on accurate mass predictions for peak assignment. Calculating stoichiometric ratios for protein complexes also requires precise MW values.

For a comprehensive analysis that includes molecular weight along with other physicochemical properties, see our Protein Parameters calculator.

How to calculate molecular weight?

The molecular weight is calculated by summing the average isotopic masses of all amino acid residues in the sequence. During protein synthesis, peptide bonds form between amino acids, releasing one water molecule per bond. The calculator accounts for this water loss.

For a protein with $n$ amino acids, the molecular weight is:

$$MW = \sum_{i=1}^{n} m_i - (n - 1) \times m_{H_2O}$$

Where $m_i$ is the residue mass of each amino acid and $m_{H_2O}$ is the mass of water (18.015 Da). The term $(n-1)$ represents the number of peptide bonds formed.

Amino acid masses

The calculator uses standard average isotopic masses for each amino acid residue. These values represent the weighted average of all naturally occurring isotopes:

Understanding the results

The output table displays three columns for each sequence:

• Protein ID: The identifier extracted from the FASTA header
• Number of Amino Acids: The total sequence length
• Molecular Weight: The calculated mass in Daltons (Da)

Results are reported to two decimal places. For proteins in the typical size range of 10-100 kDa, this provides sufficient precision for most laboratory applications.

Limitations

The calculated molecular weight represents the theoretical mass based on the primary sequence alone. Post-translational modifications (PTMs) such as glycosylation, phosphorylation, and acetylation will alter the actual mass. Similarly, the calculation assumes all cysteines are in reduced form and does not account for disulfide bonds.

For proteins where PTMs are expected, the observed mass from mass spectrometry may differ significantly from the calculated value. Use this tool for initial estimates and SDS-PAGE planning, but validate with experimental measurements for modified proteins.