Protein Molecular Weight Calculator
Knowing the molecular weight of a protein is fundamental for planning SDS-PAGE experiments, calculating molar concentrations, and interpreting mass spectrometry results. This calculator takes a protein or peptide sequence in one-letter IUPAC amino acid code and sums the average residue masses from NIST/Unimod tables, then adds 18.02 Da for the terminal water molecule. The result is expressed in both Daltons (Da) and kilodaltons (kDa). Enter your sequence below and invalid characters are automatically ignored.
Protein molecular weight formula
MW = sum(residue masses) + 18.02 Da
The 18.02 Da accounts for one water molecule: 2 H (2.016 Da) on the N-terminus and one O (15.999 Da) on the C-terminus. Residue masses used are average isotopic masses from the NIST amino acid mass table (NIST Standard Reference Database).
Average residue masses (Da)
- A (Alanine): 71.08 | C (Cysteine): 103.14 | D (Asp): 115.09 | E (Glu): 129.12 | F (Phe): 147.18
- G (Glycine): 57.05 | H (His): 137.14 | I (Ile): 113.16 | K (Lys): 128.17 | L (Leu): 113.16
- M (Met): 131.20 | N (Asn): 114.10 | P (Pro): 97.12 | Q (Gln): 128.13 | R (Arg): 156.19
- S (Ser): 87.08 | T (Thr): 101.10 | V (Val): 99.13 | W (Trp): 186.21 | Y (Tyr): 163.18
Protein molecular weight: frequently asked questions
How is protein molecular weight calculated?
Protein molecular weight is the sum of the residue weights of all amino acids in the sequence, plus the weight of one water molecule (18.02 Da) for the free N and C termini. Residue weights are the amino acid monoisotopic or average masses minus water.
What is a Dalton (Da)?
A Dalton is a unit of atomic mass equal to 1/12 the mass of a carbon-12 atom, approximately 1.66 x 10^-24 grams. Protein masses are commonly expressed in kilodaltons (kDa), where 1 kDa = 1,000 Da.
What one-letter amino acid codes does the calculator accept?
The calculator accepts the standard 20 IUPAC one-letter amino acid codes: A (Alanine), C (Cysteine), D (Aspartic acid), E (Glutamic acid), F (Phenylalanine), G (Glycine), H (Histidine), I (Isoleucine), K (Lysine), L (Leucine), M (Methionine), N (Asparagine), P (Proline), Q (Glutamine), R (Arginine), S (Serine), T (Threonine), V (Valine), W (Tryptophan), Y (Tyrosine).
Why does the calculated MW differ from the SDS-PAGE band?
SDS-PAGE separates proteins by apparent molecular weight, which can differ from the true MW due to post-translational modifications (glycosylation, phosphorylation), unusual amino acid composition affecting SDS binding, or disulfide bonds in non-reducing gels.
What is the average vs monoisotopic mass?
Average mass uses the natural isotopic abundances of each element. Monoisotopic mass uses only the most abundant isotope of each element. For proteins larger than ~2 kDa, average mass is used; monoisotopic mass is used for small peptides analysed by high-resolution mass spectrometry.
Official sources
- NIST Chemistry WebBook, amino acid masses: NIST WebBook.
- UniProt/Swiss-Prot protein sequence database: UniProt.
Reviewed by the CalculatorHub team, edited by James Graham, 14 June 2026. See our methodology.