Protein Molecular Weight Calculator

A polypeptide's mass is the sum of its residue masses plus one water molecule at 18.015 Da. Each peptide bond forms by releasing water, so the residues in a chain are lighter than the free amino acids; the single water added back accounts for the extra hydrogen at the free N-terminus and the extra hydroxyl at the C-terminus. Residue masses span a wide range, from glycine at 57.05 Da to tryptophan at 186.21 Da, but averaged over typical proteomes the mean lands near 110 Da, which is why multiplying residue count by 110 gives a usable first estimate. The values used here are average masses, weighted by natural isotope abundance. High-resolution mass spectrometry instead reports monoisotopic masses, where glycine is 57.0215 Da; the two scales diverge by roughly 0.05 percent, about 25 Da on a 50 kDa protein. The same sequence supports a second useful quantity. Under the method of Pace and colleagues, the molar extinction coefficient at 280 nm is approximated as 5,500 per tryptophan, 1,490 per tyrosine, and 125 per cystine, so absorbance at 280 nm converts to concentration through the Beer-Lambert law. Proteins containing neither tryptophan nor tyrosine absorb too weakly for that approach to be reliable. Several effects place calculated and observed masses apart: N-linked glycosylation can add 2 to 30 kDa, each phosphorylation site adds about 79.97 Da, every disulfide bond subtracts 2.016 Da, and signal peptide cleavage removes 15 to 30 residues. Apparent mass on SDS-PAGE routinely differs from the calculated value by 5 to 20 percent.

The mass unit itself carries the name of John Dalton, the English chemist whose early nineteenth century atomic theory established relative atomic weights. The notion that a protein possesses one definite mass rather than being an ill-defined colloid was settled by Frederick Sanger, who determined the complete amino acid sequence of bovine insulin at Cambridge over the early 1950s and received the 1958 Nobel Prize in Chemistry for it. Sequencing at scale became practical after Pehr Edman introduced his stepwise N-terminal degradation chemistry around 1950 and, with Geoffrey Begg, an automated sequencer in 1967. Once a sequence was known, its mass could simply be summed from tabulated residue values. Measuring protein mass directly took longer. Soft ionization methods that could lift an intact protein into the gas phase arrived in the late 1980s: matrix-assisted laser desorption ionization from the work of Michael Karas and Franz Hillenkamp, and electrospray ionization from John Fenn's laboratory. Fenn shared the 2002 Nobel Prize in Chemistry with Koichi Tanaka for that advance. Sequence-based calculation became routine in parallel as sequence databases grew. Pace, Vajdos, Fee, Grimsley and Gray published their widely used extinction coefficient estimates in Protein Science in 1995, and the ExPASy ProtParam tool at the Swiss Institute of Bioinformatics made theoretical mass, isoelectric point and extinction coefficient standard outputs for any submitted sequence.