Peptide Calculator
FREE TOOLEnter standard single-letter codes. Spaces, numbers, and FASTA headers are ignored automatically.
🔗 Peptide Properties
Grand Average Hydropathy (GRAVY) Index
−4.5
+4.5
Net Charge vs pH (pH 0–14)
Charge at a Specific pH
Amino Acid Composition
| AA | Name | Count | % | Contribution to MW (Da) |
|---|
Introduction
Designing, ordering, or QC-checking a peptide starts with a handful of numbers: its mass, its charge at a given pH, and how well it will dissolve. This calculator turns a single-letter amino acid sequence into those numbers instantly — molecular weight, isoelectric point, net charge across the full pH range, hydrophobicity, extinction coefficient, and full residue composition — so you can plan synthesis, purification, and formulation before you ever touch the bench.
About the Tool
The Peptide Calculator accepts any sequence written in standard single-letter amino acid codes and returns its molecular weight in Da and kDa, isoelectric point (pI), net charge at pH 7.4 plus a full charge-versus-pH curve, GRAVY hydrophobicity index, UV extinction coefficient at 280 nm, and a residue-by-residue amino acid composition table. It also supports the two most common synthetic capping modifications — N-acetylation and C-amidation — so predictions stay accurate for capped peptides, not just unmodified ones. Peptide chemists use it to predict a target's expected mass before mass spectrometry QC, synthesis labs use it to anticipate charge and solubility behavior in buffer, and researchers use it to screen candidate sequences before committing to synthesis.
Understanding the Inputs
Peptide sequence: paste your sequence using the 20 standard single-letter amino acid codes (A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V). Numbers, spaces, and FASTA header lines (lines starting with >) are stripped automatically; any other character is flagged as invalid, excluded from the calculation, and listed in the result note so you know exactly what was ignored.
N-terminus modification: leave at the default Free NH₂ setting for a peptide with an unmodified amine. Select Acetylated if your peptide was capped with an acetyl group during synthesis — this adds 42.011 Da and removes the terminal amine's positive charge contribution.
C-terminus modification: leave at the default Free COOH setting, or select Amidated if the C-terminal carboxyl was replaced with an amide — this subtracts 0.984 Da and removes that terminus's negative charge contribution. Match both selections to your actual peptide; check the certificate of analysis for synthetic peptides, since the termini can be a large share of a short peptide's total charge.
The Formulas Behind the Results
Molecular weight is calculated by summing the average residue mass of every amino acid in the sequence, then adding one water molecule (18.015 Da) to account for the free termini. Selecting N-acetylation adds 42.011 Da, and C-amidation subtracts 0.984 Da, reflecting the actual mass change of those chemical modifications. Isoelectric point and net charge both use the Henderson–Hasselbalch equation: for each ionizable group, the fractional positive or negative charge at a given pH is calculated from its pKa, and these are summed across the whole sequence — the pI is the pH where that sum crosses zero. The GRAVY index averages the Kyte–Doolittle hydropathy value of every residue, and the extinction coefficient at 280 nm sums the contribution of Trp (5500 M⁻¹cm⁻¹) and Tyr (1490 M⁻¹cm⁻¹) residues following the Pace et al. 1995 method.
Fractional charge(pH) = 1 / (1 + 10^±(pH − pKa))
GRAVY = Σ(hydropathy) / number of residues
ε₂₈₀ = (Trp count × 5500) + (Tyr count × 1490)
Worked Example
Sample Input
Sequence AYGK (Ala–Tyr–Gly–Lys), both termini left at their free/unmodified default.
Step-by-Step Calculation
- Molecular weight — sum the residue masses (A 71.0788 + Y 163.1760 + G 57.0519 + K 128.1741 = 419.4808 Da) and add water (18.0153 Da) for the free termini: 419.4808 + 18.0153 = 437.4961 Da.
- GRAVY — average the Kyte–Doolittle values (A 1.8, Y −1.3, G −0.4, K −3.9): (1.8 − 1.3 − 0.4 − 3.9) / 4 = −0.95.
- Extinction coefficient — one Tyr and zero Trp: (1 × 1490) + (0 × 5500) = 1490 M⁻¹cm⁻¹.
- Net charge at pH 7.4 — sum the fractional charge of every ionizable group (free N-terminus, free C-terminus, and the Lys and Tyr side chains) using their pKa values: positive contributions from the N-terminus (≈0.80) and Lys (≈1.00) total ≈1.80; negative contributions from the C-terminus (≈1.00) and Tyr (≈0.00, since pH 7.4 is far below its pKa of 10.1) total ≈1.00. Net charge ≈ 1.80 − 1.00 = +0.80.
- Isoelectric point — the calculator scans pH 0–14 for the point where positive and negative contributions balance. Between pH 8.9 (net ≈ +0.03) and pH 9.0 (net ≈ −0.01) the curve crosses zero, giving pI ≈ 8.97.
Final Result
MW = 437.50 Da (0.4375 kDa) · pI ≈ 8.97 · net charge at pH 7.4 ≈ +0.80 · GRAVY = −0.95 · ε₂₈₀ = 1490 M⁻¹cm⁻¹.
Interpretation
The peptide is mildly hydrophilic (negative GRAVY) and carries a small net positive charge at physiological pH, consistent with a pI close to 9 driven mainly by the single lysine residue. Its low, non-zero extinction coefficient means A280 absorbance can be used to estimate concentration, but with limited sensitivity since it relies on a single tyrosine rather than a tryptophan.
Interpreting Your Results
The molecular weight is your expected target mass for comparison against mass spectrometry. The pI and net charge at pH 7.4 together tell you how the peptide will behave electrically in near-physiological buffer — useful for predicting binding to ion-exchange resin or migration on a native gel. The GRAVY index flags likely solubility behavior: strongly positive values suggest hydrophobic, potentially poorly soluble peptides, while negative values suggest good aqueous solubility. The extinction coefficient lets you convert a measured A280 absorbance reading into peptide concentration via the Beer-Lambert law, provided the peptide contains Trp and/or Tyr. The amino acid composition table breaks down exactly how much each residue contributes to the total mass, which is useful for spotting synthesis errors.
When to Use This Calculator
This tool is most useful right before and after peptide synthesis: use it beforehand to predict the expected molecular weight, charge state, and solubility behavior of a designed sequence, and use it afterward to sanity-check a mass spectrometry result against the theoretical mass. It's also valuable when comparing capped versus uncapped versions of the same peptide, when choosing a buffer pH for storage or chromatography based on the predicted net charge, and when screening candidate peptide sequences for likely solubility problems using the GRAVY score before committing to synthesis.
Scientific Notes & Limitations
This calculator uses average residue masses and a two-state Henderson–Hasselbalch model for each ionizable group; it does not model non-standard or D-amino acids, chemical linkers, disulfide bonds, oxidation, or synthesis byproducts, all of which shift the true values away from what is calculated here. GRAVY reflects only average per-residue hydropathy and ignores charge distribution, secondary structure, and sequence-specific hydrophobic patches, while the ε₂₈₀ value depends entirely on Trp and Tyr content, so peptides without either residue will always show a coefficient of zero. Treat every result as a theoretical starting point to compare against experimental data — mass spectrometry for molecular weight, an orthogonal assay such as BCA or Bradford where UV-active residues are absent — rather than as a substitute for direct measurement.
Practical Tips
- Confirm capping before you calculate: check your certificate of analysis for N-acetylation or C-amidation before running the calculation — both are common in therapeutic and bench-use peptides (oxytocin and vasopressin, for example, are C-terminally amidated in vivo) and will shift MW, charge, and pI if left unselected.
- Use the pH lookup for your actual buffer: rather than relying only on the default pH 7.4 card, enter the pH of your storage buffer or chromatography mobile phase in the Charge at a Specific pH field to get the number that's actually relevant to your experiment.
- Cross-check GRAVY against bench behavior: a strongly positive GRAVY score paired with observed aggregation is a good early signal to reformulate or add a solubilizing tag before scaling up.
- Watch the result note for ignored characters: if your pasted sequence includes non-standard codes, linkers, or stray characters, the note lists exactly what was dropped so you know the result is based on a slightly shorter effective sequence.
Common Mistakes to Avoid
- Leaving termini at their default "free" setting for a capped peptide: most synthetic peptides ordered from a vendor are acetylated, amidated, or both — check your certificate of analysis and select the correct modification, or the MW, charge, and pI will all be off.
- Ignoring invalid characters silently: numbers, FASTA headers, or non-standard residue codes pasted into the sequence box are dropped from the calculation; always check the result note for a list of ignored characters.
- Reading GRAVY as a precise solubility prediction: it is a useful screening heuristic based on average hydropathy, not a guarantee — charge distribution and specific motifs can make a peptide behave differently than its GRAVY score alone would suggest.
- Assuming extinction coefficient of zero means no peptide is present: a zero or very low ε₂₈₀ simply means the peptide lacks Trp/Tyr residues; you'll need an alternative quantification method such as BCA or Bradford instead of UV absorbance.