Protein Molecular Weight Calculator

Protein molecular weight is the sum of the average masses of the amino acid residues in a polypeptide chain plus the mass of one water molecule at the termini. This calculator accepts the standard one-letter codes for the twenty common amino acids, removes spaces and hyphens, and reports the resulting estimate in daltons and kilodaltons. A dalton is approximately the mass of one hydrogen atom, while one kilodalton equals one thousand daltons. The result is useful when choosing electrophoresis conditions, checking an expected band on a western blot, planning purification, or comparing a translated sequence with a known protein. The calculation uses average isotopic residue masses rather than monoisotopic masses. Average mass is normally the practical choice for intact proteins and routine SDS-PAGE comparisons because a macromolecule contains a natural mixture of isotopes. Monoisotopic mass instead uses the lightest common isotope of every atom and is often preferred for accurately resolved small peptides in mass spectrometry. Because these conventions differ, a value from this calculator may not exactly match software configured for monoisotopic mass. Sequence alone does not describe every chemical contribution to a real sample. Signal peptide cleavage, initiator methionine removal, disulfide formation, glycosylation, phosphorylation, acetylation, bound cofactors, affinity tags, and other post-translational modifications can change the observed mass. The displayed estimate assumes an unmodified, neutral polypeptide with free amino and carboxyl termini. It also treats every entered letter as one incorporated residue and adds one terminal water molecule to restore the complete-chain composition. Use the output as a reproducible theoretical reference rather than a guarantee of migration or measured mass. Apparent SDS-PAGE size can differ because of protein shape, charge, detergent binding, aggregation, or unusual amino acid composition. For experimental planning, compare the calculated value with the construct actually expressed, including tags and linkers, and account separately for any known processing or covalent modification.