How to Calculate Protein Molecular Weight from Sequence

Calculating protein molecular weight from a sequence is a straightforward summation problem: add up the average residue mass of every amino acid in the chain, then add the mass of one water molecule (18.011 Da) to account for the free H at the N-terminus and OH at the C-terminus. This is exactly how the protein molecular weight calculator above works — it is not an estimate, it is an exact sum based on the primary sequence.

There are two types of mass used in protein chemistry, and knowing which one to use matters. Average mass uses the natural isotopic-abundance-weighted mass of each element and is the correct choice for nearly all everyday biochemistry — buffer prep, gel loading, general protein molecular weight reporting. Monoisotopic mass uses only the most common isotope of each atom (¹²C, ¹H, ¹⁴N, ¹⁶O, ³²S) and is the standard for mass spectrometry, where it corresponds to the sharpest peak in a spectrum. This calculator reports both values simultaneously.

A frequently used shortcut is the 110 Da/residue rule — multiply the number of amino acids by 110 to get a rough protein molecular weight. This approximation is good enough for quick gel-loading estimates or grant-proposal ballpark figures, typically within 5–10% of the true value, but it should never replace a sequence-based calculation when accuracy matters (cloning, mass spec interpretation, molar concentration work).

Protein Size in kDa — Converting Daltons to Kilodaltons

1 kDa (kilodalton) equals exactly 1,000 Da (Dalton). Proteins are conventionally reported in kDa rather than Da simply because it produces more convenient, readable numbers — most proteins fall somewhere between 10 kDa and 500 kDa, so "45 kDa" is easier to work with than "45,000 Da." Both units describe the exact same physical quantity: molecular mass.

Here's how protein molecular weight in kDa maps to real biological structures:

Using the 110 Da/residue rule: a 300-amino-acid protein has an estimated protein molecular weight of 300 × 110 = 33,000 Da, or 33 kDa. Use the kDa converter above to move freely between Da, kDa, and MDa, or estimate molecular weight directly from a residue count.

Amino Acid Molecular Weights — Reference Table

This is the complete reference table of average and monoisotopic residue masses for all 20 standard amino acids, used internally by this protein molecular weight calculator and peptide mass calculator.

This amino acid molecular weight calculator reference table also underlies the polypeptide molecular weight and protein mol wt calculator functions above — every residue mass is applied exactly once per occurrence in your sequence.

Molar Extinction Coefficient at 280 nm

The molar extinction coefficient (ε280) predicts how strongly a protein absorbs ultraviolet light at 280 nm, which is the standard wavelength used to measure protein concentration in a spectrophotometer. The Pace method (Pace et al., 1995) calculates it directly from amino acid composition:

Tryptophan (W) and tyrosine (Y) absorb strongly at 280 nm because of their aromatic ring side chains; cysteine (C) contributes a small amount, historically attributed to disulfide (cystine) bond formation. Once you know ε280 and the protein molecular weight, you can calculate the concentration of any purified protein solution using the Beer-Lambert law: A = ε × c × l, solved for concentration as c = A / (ε × l).

Limitation: a protein with zero tryptophan, tyrosine, and cysteine residues has an ε280 of exactly 0 — meaning A280 cannot detect it at all, regardless of concentration. This is common in short peptides and certain structural proteins, and is why the calculator correctly returns 0 rather than a false positive value in that case.

Worked Examples

Frequently Asked Questions

Related Tools

Also see the DNA Molecular Weight Calculator for nucleic acid mass, and the Reverse Complement Calculator for sequence manipulation tools.