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Protein molecular weight calculator

Molecular weight from a protein sequence, plus mass to moles conversion for that protein.

Molecular weight
How is protein molecular weight calculated from sequence?
Each amino acid in a chain has lost one water to the peptide bonds, so the mass of a protein is the sum of its residue masses plus one water for the two free ends.
MW = Σ (ni × residue massi) + 18.015 Da
The average residue masses are the standard values used by ExPASy ProtParam, for example Gly 57.0519, Ala 71.0788, Leu 113.1594 and Trp 186.2132 Da; the full list is in theamino acid table. The monoisotopic mass uses monoisotopic residue masses and 18.0106 Da for water. Selenocysteine (U) and pyrrolysine (O) are included. B, Z and X have no defined mass and are left out with a warning; a stop sign at the end is ignored.
Worked example
The example is human ubiquitin, 76 residues. The residue masses add up to 8,546.8 Da, and adding water gives an average molecular weight of 8,564.8 Da (8.56 kDa). The monoisotopic mass is 8,559.6 Da. These match the published values for ubiquitin.
How do I convert protein mass to moles?
pmol = µg × 106 / MW  ·  µg = pmol × MW / 106
µM = mg/mL × 106 / MW  ·  mg/mL = µM × MW / 106
Type an amount in the field that appears under the sequence and pick the direction. For ubiquitin, 10 µg is 10 × 106 / 8,564.8 = 1,168 pmol, and a 1 mg/mL solution is 116.8 µM. To measure the concentration of a purified protein from its absorbance, use theA280 protein concentration calculator, which derives the extinction coefficient from the same sequence.
Why does my protein run differently on a gel?
SDS-PAGE separates by size of the SDS-coated chain, not by mass alone. Very acidic or basic proteins, membrane proteins, and glycosylated or phosphorylated proteins often migrate at an apparent weight that differs from the calculated one by 10 % or more. Tags, linkers and uncleaved signal peptides also add mass: a His6 tag adds about 0.84 kDa.
Frequently asked questions
How do I calculate the molecular weight of a protein from its sequence?
Add up the residue masses of all amino acids in the chain and add the mass of one water molecule (18.015 Da) for the free N- and C-terminus. Ubiquitin, with 76 residues, comes to 8,564.8 Da.
What is the difference between average and monoisotopic mass?
Average mass uses the natural isotope mixture of each element and is what matters for weighing, molarity and SDS-PAGE. Monoisotopic mass uses only the lightest isotope of each element (12C, 1H, 14N, 16O, 32S) and is the first peak of the isotope pattern in a high-resolution mass spectrum. For ubiquitin they are 8,564.8 and 8,559.6 Da.
How do I convert µg of protein to pmol?
pmol = µg × 1,000,000 / MW (Da). One µg of a 50 kDa protein is 20 pmol. In the other direction, µg = pmol × MW / 1,000,000.
How do I convert mg/mL to µM?
µM = mg/mL × 1,000,000 / MW (Da). A 1 mg/mL solution of a 50 kDa protein is 20 µM, and 1 mg/mL of ubiquitin (8,564.8 Da) is 116.8 µM.
Does the calculated mass include modifications?
No. It is the mass of the unmodified chain with free termini and reduced cysteines. Subtract 2.016 Da per disulfide bond, add 42.04 Da for N-terminal acetylation and 79.98 Da per phosphate, and remove a signal peptide or initiator methionine from the sequence first if the mature protein lacks it.