Peptide Net Charge Calculator
Paste a peptide sequence, set the pH and terminal forms, and get its estimated net charge in elementary charge units (e) and its theoretical isoelectric point (pI).
Net charge and isoelectric point
Enter a sequence or select Try HKE to see how charge changes with pH.
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Select a point on the curve plot or adjust the slider to set the pH.
Where the charge comes from
Choose a region of the diagram to inspect the charge contributions of its ionizable groups.
Charge contribution table
| Group | Count | pKa | Charge (e) |
|---|---|---|---|
| Peptide net charge | |||
Compare all four terminal forms
Choose a row to apply that form. The pH and pKa scale stay fixed.
| Terminal form | Net charge (e) | pI |
|---|---|---|
How to calculate peptide net charge and pI
The calculator adds a fractional charge for each ionizable group present at the selected pH and reports the theoretical pI as the pH where that sum equals zero.
Identify the ionizable groups
The calculator counts the free N-terminal amine, the free C-terminal carboxyl, and each ionizable side chain in the sequence. Selecting an N-acetyl or C-amide cap removes that terminal group from the count.
Calculate each group’s charge at the selected pH
Each group contributes a fractional charge set by the pH and its pKa, and at a pH equal to the pKa it contributes half of its full charge magnitude.
Charge per group in elementary charge units (e) Group type Modeled groups Charge per group Basic Free N-terminus, His, Lys, Arg +1 ÷ (1 + 10pH − pKa) Acidic Free C-terminus, Cys, Asp, Glu, Tyr −1 ÷ (1 + 10pKa − pH) Find the zero crossing
The isoelectric point is the pH where the net charge curve reaches zero, and the calculator locates it by bisection between pH 0 and 14. If the net charge keeps one sign across pH 0 to 14, the curve has no zero crossing in this range, and this can happen even when the peptide has both positively and negatively charged groups. If the peptide has no modeled ionizable groups, the net charge is zero at every pH and there is no unique pI.
Worked example with HKE
At pH 7.4 on the IPC peptide scale, N-acetyl removes the positive terminal amine and moves HKE from +0.03 e and pI 7.77 down to −0.96 e and pI 5.17, while C-amide removes the negative terminal carboxyl and moves it up to +1.03 e and pI 10.04.
| Terminal form | pKa scale | Net charge (e) | pI |
|---|---|---|---|
| Free ends | IPC peptide | +0.03 | 7.77 |
| N-acetyl | IPC peptide | −0.96 | 5.17 |
| C-amide | IPC peptide | +1.03 | 10.04 |
| Both capped | IPC peptide | +0.04 | 8.27 |
| Free ends | EMBOSS | +0.05 | 7.55 |
Model assumptions
This theoretical model covers standard linear peptides with free Cys thiols and fixed published pKa values. The supported N-acetyl and C-amide caps each remove one terminal group from the sum. Cyclic, disulfide-linked or otherwise modified peptides need a structure-aware model. Results are theoretical estimates.
Peptide charge and pI FAQs
Which amino and carboxyl groups still count after peptide bonds form?
This model counts the free N-terminal amine, the free C-terminal carboxyl and the ionizable side chains. Amino and carboxyl groups joined in peptide bonds are excluded from the model over the working pH range, so the sum treats the sequence as one chain with two ends. A capped end is also excluded.
Why do equal numbers of basic and acidic side chains give a nonzero net charge?
Each group contributes a fraction of a charge set by its pKa and the pH. On the IPC peptide scale, His has a pKa of 6.018 and contributes about +0.04 at pH 7.4, while Lys and Arg each contribute close to +1. The total also includes any free ends. Three basic and three acidic side chains therefore rarely sum to exactly zero.
Why does averaging two pKa values give a different pI than this calculator?
This calculator finds the pH where the full modeled charge sum equals zero. Averaging two pKa values is a shortcut that holds only when two groups decide the crossing. More ionizable groups, a different pKa scale or capped ends move the zero point, which is why two calculators can report different pI values for the same sequence.
Can the pH and pI tell you how large the charge is?
The pH relative to the pI gives the sign of the charge. When the model has a crossing, the net charge is positive below the pI and negative above it. The magnitude comes from evaluating the full group sum at that pH, which the result and curve show.
What does end capping change for a short peptide?
For the supported caps, N-acetyl removes the free terminal amine contribution and C-amide removes the free terminal carboxyl contribution. All other pKa values stay fixed in this model. The comparison table shows charge and pI for all four terminal forms at the same pH and scale and flags any form with no unique pI.
Can the predicted solution charge tell me the ESI charge state?
The predicted solution charge and the ESI charge state are separate quantities. Solution net charge is the average across all molecules in solution at the selected pH. The charge-state distribution seen in electrospray ionization is a measured result that depends on solution and instrument conditions. For theoretical m/z values at specific charge states, use the molecular weight calculator.
