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.

Why these two values matter in the lab

Molecular weight

MW in daltons is the first number needed for several routine calculations:

• Molar concentration — To make a 1 mM stock of a 2,500 Da peptide, you dissolve 2.5 mg per mL. MW is the conversion factor between mass and moles.
• SDS-PAGE gel selection — Small peptides (under about 3,000 Da) run off standard SDS-PAGE gels rapidly and often need tricine gels or alternative methods. Knowing MW in advance guides gel choice.
• Mass spectrometry interpretation — The measured m/z of an ion equals (MW + z × 1.008) / z for positive mode electrospray. MW lets you predict which m/z peaks to expect for different charge states.

Isoelectric point (pI)

The pI is the pH at which the peptide has zero net charge. At this pH, solubility is often at a minimum and the peptide migrates to a fixed position in isoelectric focusing (IEF). Key uses:

• Buffer selection for solubility — Dissolving a peptide at its pI often leads to precipitation. Working at a pH at least one unit away from pI (above for acidic peptides, below for basic ones) improves solubility.
• Ion-exchange chromatography — At pH above pI the peptide is net negative and binds anion exchangers; at pH below pI it is net positive and binds cation exchangers. Knowing pI guides which resin and buffer to choose.
• Isoelectric focusing and 2D-PAGE — The pI determines where the peptide or protein focuses on an IPG strip and which strip pH range to select.

pKa table used

The ionisable groups and their approximate pKa values used in this calculator:

Different pKa tables (Lehninger, Bjellqvist, EMBOSS, Dawson) produce slightly different pI values. Differences of 0.3–0.5 pH units between tools are normal and not indicative of an error; they reflect which experimental dataset the pKa values were derived from.