Free lab calculator
Peptide net charge and isoelectric point (pI) calculator
By Vitality Chems · Published · updated · vendor-authored explanatory note
Short answer
A peptide's net charge at a given pH is the sum, over every ionizable group, of the fraction that is charged, which the Henderson–Hasselbalch equation gives from each group's pKa. The isoelectric point (pI) is the pH where that sum is zero. This calculator does both for any one-letter sequence, using the EMBOSS pKa set and handling acetylated N-termini, amidated C-termini and disulfide-bonded cysteines; it is for analytical method work such as buffer selection, ion-exchange and HPLC method development.
Catalog materials discussed on this page
Net charge and pI calculator
Henderson–Hasselbalch estimate with the EMBOSS pKa set. For analytical method work: buffer and mobile-phase choice, ion-exchange, and solubility screening in vitro.
- Net charge at pH 7.0
- -2.02
- Estimated pI
- 3.88
- Residues / hydrophobic share
- 15 / 27%
| pH | Net charge |
|---|---|
| 2 | 1.94 |
| 3 | 1.50 |
| 4 | -0.27 |
| 5 | -1.70 |
| 6 | -1.97 |
| 7 | -2.02 |
| 7.4 | -2.06 |
| 8 | -2.20 |
| 9 | -2.73 |
| 10 | -3.10 |
| 11 | -3.61 |
pKa values (EMBOSS Epk.dat): N-terminus 8.6, C-terminus 3.6, Asp 3.9, Glu 4.1, His 6.5, Cys 8.5, Tyr 10.1, Lys 10.8, Arg 12.5.
Embed this calculator
Free for lab sites, course pages and internal wikis. One block of HTML with a small inline script: no iframe, no external requests, no cookies or tracking. It uses the same pKa set as this page. Please keep the attribution line (a branded nofollow link).
How the calculation works
For each basic group (N-terminal amine, Lys, Arg, His) the positive fraction is 1 / (1 + 10^(pH − pKa)). For each acidic group (C-terminal carboxyl, Asp, Glu, free Cys, Tyr) the negative fraction is 1 / (1 + 10^(pKa − pH)). Net charge is the sum of the positive fractions minus the sum of the negative fractions. The pI is found by bisection between pH 0 and 14, since net charge falls steadily as pH rises.
Worked check: glycine alone has only its two termini, so with the EMBOSS values its pI is the midpoint of 8.6 and 3.6, which is 6.1. The calculator returns 6.10.
An acetylated N-terminus or amidated C-terminus removes that terminal charge. Cysteines in disulfide bonds cannot ionize, so enter the number of disulfide bonds to exclude two cysteines per bond. If both termini are capped and the sequence has no ionizable side chains, the peptide has no pI and the calculator says so.
Example results (EMBOSS pKa set)
BPC-157 (GEPPPGKPADDAGLV): estimated pI 3.88, net charge −2.02 at pH 7.0. Selank (TKPRPGP): pI 11.65, net charge +1.98 at pH 7.0. Semax (MEHFPGP): pI 5.36, net charge −0.78 at pH 7.0. These come from the same code that runs on this page, with free termini.
For the TB-500 fragment Ac-LKKTETQ, the two lysines are balanced by Glu and the C-terminal carboxyl across a wide pH range, so its net charge stays within about ±0.15 of zero from pH 5 to 9.5 and the computed pI (about 7.4) sits in a flat region. In that situation small changes in pKa assumptions move the pI noticeably; regard it as approximate.
Limits of any sequence-based pI
Published pKa sets differ, and real pKa values shift with neighbouring residues, temperature, ionic strength and structure. Kozlowski's benchmark of many pKa sets found average errors of about 0.25 pH units for peptides with the best sets, and larger errors for older ones (Kozlowski, 2016). Use the result as a starting point for method development and confirm experimentally where it matters.
Non-standard residues, phosphorylation, lipidation and other modifications are not modelled. Remove or account for them before relying on the number.
Embedding and citing the calculator
The embed code below is a self-contained HTML block that runs the same calculation in the reader's browser. It makes no network requests and sets no cookies. To cite the calculator in a protocol or paper, use: Vitality Chems, "Peptide net charge and isoelectric point (pI) calculator", https://vitalitychems.com/resources/peptide-net-charge-isoelectric-point-calculator, accessed on the date you used it.
Related on Vitality Chems
- Peptide solubility from sequence charge — turn the net charge into a solvent choice.
- Expected m/z calculator — charge states for LC-MS identity checks.
- Peptide molarity calculator — stock concentration from COA values.
- COA checklist embed — another free embeddable reference.
- BPC-157 lot documentation — the default example sequence.
Frequently asked
How do you calculate the isoelectric point of a peptide?
Write the net charge as a function of pH using the Henderson–Hasselbalch equation for every ionizable group (termini plus Asp, Glu, Cys, Tyr, His, Lys, Arg), then find the pH where it equals zero. This calculator does that numerically with the EMBOSS pKa set.
Which pKa values does this calculator use?
The EMBOSS iep defaults: N-terminus 8.6, C-terminus 3.6, Cys 8.5, Asp 3.9, Glu 4.1, His 6.5, Lys 10.8, Arg 12.5, Tyr 10.1.
Does acetylation or amidation change the pI?
Yes. N-terminal acetylation removes a positive charge and lowers the pI; C-terminal amidation removes a negative charge and raises it. Tick the matching boxes, or type Ac- and -NH2 in the sequence.
Why does my result differ from another pI calculator?
Different tools use different pKa sets (EMBOSS, Bjellqvist, Lehninger, IPC and others). Differences of a few tenths of a pH unit are normal for peptides.
Is this calculator for preparing material for use in people or animals?
No. It estimates a physical-chemistry property of a sequence for laboratory method work only.
References
- EMBOSS iep: isoelectric point and charge (documentation and Epk.dat pKa values)pKa set used by this calculator.
- Kozlowski LP. IPC – Isoelectric Point Calculator. Biol Direct. 2016;11:55. PMID 27769290Comparison of pKa sets and expected accuracy for peptides.
- Sigma-Aldrich. Solubility guidelines for peptidesWhy net charge at pH 7 predicts aqueous solubility.
