How is peptide molecular weight calculated?

Each residue contributes its average residue mass (the amino acid mass minus one water lost in the peptide bond). The tool sums these and adds back one water (18.015 Da) for the free N- and C-termini. The result is average MW in daltons.

How is the isoelectric point found?

The pI is the pH at which net charge is zero. The calculator sweeps pH from 0 to 14, computing net charge with the Henderson-Hasselbalch equation over the N-terminus, C-terminus, and all ionisable side chains, then bisects to the crossing point.

Which side chains carry charge?

Positive groups are the N-terminus, lysine (K), arginine (R), and histidine (H). Negative groups are the C-terminus, aspartate (D), glutamate (E), cysteine (C), and tyrosine (Y). Each has a characteristic pKa used in the charge sum.

Does this handle modifications or disulfides?

No. It computes the unmodified linear peptide. Phosphorylation, acetylation, amidation, or disulfide bonds change both mass and charge and are not included. Use it as a baseline estimate.

Why does my pI differ slightly from other tools?

Different tools use slightly different pKa tables (EMBOSS, Lehninger, Bjellqvist). pI can vary by a few tenths of a unit depending on the set. This tool uses a common EMBOSS-style table, so expect small differences.

Peptide Molecular Weight & Isoelectric Point Calculator

This tool turns a one-letter amino acid sequence into two of the numbers protein chemists need most: the molecular weight of the peptide and its isoelectric point. It runs entirely in your browser, so sequences never leave the page.

How it works

Molecular weight is the sum of average residue masses plus one water molecule for the terminal groups:

MW = Σ residue_mass(aa) + 18.01528

Each residue mass already has the peptide-bond water removed, so adding a single water back accounts for the free N- and C-termini of the whole chain.

The isoelectric point is the pH where net charge is zero. Net charge at a given pH uses the Henderson-Hasselbalch relation for each ionisable group:

positive group:  charge = 1 / (1 + 10^(pH − pKa))
negative group:  charge = −1 / (1 + 10^(pKa − pH))
net = Σ positive − Σ negative

The calculator bisects pH between 0 and 14 until net charge crosses zero — that crossing pH is the pI.

Notes and tips

The charged groups are the N-terminus and K, R, H (basic) versus the C-terminus and D, E, C, Y (acidic). Sequences rich in K and R have a high pI and migrate as basic proteins; D- and E-rich sequences have a low pI. Remember this is the unmodified linear peptide — amidated C-termini, acetylated N-termini, phosphorylation, and disulfide bonds all shift mass and charge and are not modelled here.