Average or monoisotopic mass?

This uses average isotopic masses (what you compare against a gel ladder). Mass spectrometry often uses monoisotopic masses, which are slightly lower; this tool does not compute those.

Does it account for modifications?

No. It assumes an unmodified polypeptide. Disulfide bonds, glycosylation, phosphorylation and other modifications shift the real mass.

Protein molecular weight

Estimate the molecular weight of a protein in Da/kDa from its single-letter amino-acid sequence, using standard average residue masses.

How it works

Formula

MW = Σ(average residue mass) + one water (18.015 Da) for the free N- and C-termini. Residue masses are standard average isotopic values (e.g. Gly 57.0519, Ala 71.0788 Da).

Worked example

Glycylglycine (GG): 2 × 57.0519 + 18.01524 = 132.12 Da — matching the known mass of the dipeptide.

When to use it

To predict where a protein runs on a gel, plan a Western blot ladder, or sanity-check an expression construct’s product size from its translated ORF.

Sensible defaults

The default MAKFGPTDEF is the protein from the ORF-finder example. Paste a translated ORF to get its predicted mass.

Source

Average amino-acid residue masses are the standard biochemistry values (as tabulated by ExPASy / Compute pI/Mw); water = 18.01524 Da.

FAQ

Average or monoisotopic mass?: This uses average isotopic masses (what you compare against a gel ladder). Mass spectrometry often uses monoisotopic masses, which are slightly lower; this tool does not compute those.
Does it account for modifications?: No. It assumes an unmodified polypeptide. Disulfide bonds, glycosylation, phosphorylation and other modifications shift the real mass.