Protein Molecular Weight Calculator
Calculate the molecular mass of any protein or peptide from its amino acid sequence. Uses standard monoisotopic masses with automatic water subtraction.
Enter one-letter or three-letter amino acid codes (case insensitive)
Each peptide bond removes one water molecule (18.015 Da)
How is protein molecular weight calculated?
Molecular weight is calculated by summing the monoisotopic masses of each amino acid in the sequence. For proteins, each peptide bond removes one water molecule (18.015 Da), so for N amino acids creating N-1 peptide bonds, subtract 18.015 × (N-1). The calculator automatically handles this adjustment. Monoisotopic masses are used for highest accuracy, where each mass represents the most abundant isotope of each element.
Should I use monoisotopic or average molecular weight?
Use monoisotopic masses for exact mass spectrometry interpretation (gives integer-like masses). Use average masses for solution chemistry and buffer calculations where natural isotope distribution matters. The standard amino acid masses in this calculator are monoisotopic. For mass spectrometry analysis, verify whether your instrument uses monoisotopic or average masses.
What if my sequence contains unknown or unusual amino acids?
Standard single-letter codes (20 amino acids) are supported. Unknown characters are ignored, and non-standard amino acids (selenocysteine U, pyrrolysine O) are not included. For modified amino acids or non-standard residues, calculate their mass separately and add manually. Some programs support custom residue masses - this calculator uses IUPAC standard amino acid masses.
How accurate is this calculator compared to mass spectrometry?
This calculator provides theoretical monoisotopic mass with ~0.001% accuracy for standard amino acids. Real samples may show deviations due to: isotopic distribution (gives average mass), post-translational modifications (phosphorylation adds ~79.97 Da per phosphate), truncations or extensions, and sample impurities. For critical applications, verify experimentally by mass spectrometry.