Free laboratory calculation tool
Peptide Molecular Weight, pI, GRAVY & Molarity Calculator
Calculate theoretical peptide formula and mass, estimated isoelectric point, net charge, and Kyte–Doolittle GRAVY from a sequence, then convert average molecular weight into laboratory amount and molar concentration.
Interactive sequence tool
Peptide molecular weight, pI & charge calculator
Enter an unmodified peptide in standard one-letter amino-acid code. Calculate formula, mass, estimated isoelectric point, net charge, and composition. Spaces, line breaks, hyphens, and a FASTA header are ignored.
Supported residues: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y.
Enter a sequence to calculate its theoretical neutral mass and elemental formula.
Laboratory amount concentration
Convert the sequence mass into molarity.
After entering a valid sequence above, add material mass and final solution volume. The calculator uses the sequence-derived average molecular weight to report amount, mass concentration, and amount concentration.
Enter a valid sequence, positive material mass, and positive final volume to calculate laboratory concentration.
Calculation scope: unmodified linear peptide with free N- and C-termini. The mass calculation adds H₂O to the summed residue composition. Estimated pI and net charge use the displayed EMBOSS default pKa set and Henderson–Hasselbalch fractional charges; different parameter sets or experimental conditions can produce different values. GRAVY is the arithmetic mean of the displayed Kyte–Doolittle residue values and is not, by itself, a solubility or structural measurement. The tool does not include terminal caps, disulfide formation, salts, counterions, adducts, isotope labels, nonstandard residues, post-translational modifications, hydration, or analytical uncertainty. The concentration section is unit conversion for documented in vitro laboratory work only; it does not calculate doses, syringe units, administration volumes, or treatment instructions.
Calculation method
Residue composition plus terminal water.
Each standard amino-acid code maps to the elemental composition of that residue after peptide-bond formation. The calculator sums those residue compositions and adds H₂O to represent a free N-terminal hydrogen and C-terminal hydroxyl group. This is the same terminal-water principle described in the Expasy PeptideMass documentation.
The resulting elemental formula is multiplied by the applicable elemental mass table. Values come from the Unimod symbols and mass reference, which documents both monoisotopic and average elemental masses and their IUPAC basis.
Two mass conventions
Monoisotopic mass and average molecular weight are not interchangeable.
Monoisotopic mass uses the mass of the most abundant natural isotope for each element in the formula. Average molecular weight uses abundance-weighted atomic masses. For a small peptide the difference may be modest; it grows with molecular size and composition.
The calculator reports neutral molecular mass [M]. It does not add or subtract a proton for an ion such as [M+H]⁺ or [M−H]⁻, and it does not calculate charge-state m/z values.
Charge model
Estimated peptide pI and net charge from published pKa values.
The calculator uses Henderson–Hasselbalch fractional charges for the free N-terminus, free C-terminus, and the ionizable side chains of C, D, E, H, K, R, and Y. It estimates pI by finding the pH between 0 and 14 where the modeled net charge is zero.
The parameter values below are the default values published in the EMBOSS Epk.dat documentation. As the IPC benchmark paper explains, different pKa parameter sets and more detailed models can produce different theoretical pI values. This output is therefore a reproducible estimate under a stated model—not a direct measurement.
| Ionizable group | Code | Type | pKa |
|---|---|---|---|
| N-terminus | N-term | Basic | 8.6 |
| C-terminus | C-term | Acidic | 3.6 |
| Cysteine | C | Acidic | 8.5 |
| Aspartic acid | D | Acidic | 3.9 |
| Glutamic acid | E | Acidic | 4.1 |
| Histidine | H | Basic | 6.5 |
| Lysine | K | Basic | 10.8 |
| Arginine | R | Basic | 12.5 |
| Tyrosine | Y | Acidic | 10.1 |
Free termini are included. Terminal blocking groups, covalent modifications, disulfides, and local chemical environment are outside this model.
Sequence hydropathy
Peptide GRAVY from the Kyte–Doolittle scale.
Expasy ProtParam defines GRAVY as the sum of the hydropathy values of all amino acids divided by sequence length. This calculator applies the 20 values published in the Expasy Kyte–Doolittle scale.
A higher or lower arithmetic mean describes the sequence under this scale; it does not by itself establish solubility, conformation, membrane association, aggregation, or behavior in a particular solvent. The original scale is described by Kyte and Doolittle (1982).
| 1-letter | 3-letter | Amino acid | Hydropathy |
|---|---|---|---|
| A | Ala | Alanine | 1.8 |
| C | Cys | Cysteine | 2.5 |
| D | Asp | Aspartic acid | -3.5 |
| E | Glu | Glutamic acid | -3.5 |
| F | Phe | Phenylalanine | 2.8 |
| G | Gly | Glycine | -0.4 |
| H | His | Histidine | -3.2 |
| I | Ile | Isoleucine | 4.5 |
| K | Lys | Lysine | -3.9 |
| L | Leu | Leucine | 3.8 |
| M | Met | Methionine | 1.9 |
| N | Asn | Asparagine | -3.5 |
| P | Pro | Proline | -1.6 |
| Q | Gln | Glutamine | -3.5 |
| R | Arg | Arginine | -4.5 |
| S | Ser | Serine | -0.8 |
| T | Thr | Threonine | -0.7 |
| V | Val | Valine | 4.2 |
| W | Trp | Tryptophan | -0.9 |
| Y | Tyr | Tyrosine | -1.3 |
Amount concentration
Laboratory molarity from sequence-derived mass.
IUPAC defines amount concentration as the amount of a constituent divided by the volume of the mixture. The calculator first converts material mass to amount of substance with n = mass ÷ molecular weight, then applies c = n ÷ final volume.
Final volume—not merely solvent added—is the controlling volume. The calculated molecular weight assumes the exact unmodified sequence and free termini described above; a different molecular form, counterion, modification, or hydrate requires its applicable molecular weight.
Reference dataset
Amino-acid residue mass table.
These are residue formulas and masses after removal of H₂O from each free amino acid—the form summed inside a peptide chain. Add one terminal H₂O to the total residue composition for an unmodified linear peptide with free N- and C-termini.
| 1-letter | 3-letter | Amino acid | Residue formula | Monoisotopic (Da) | Average (Da) |
|---|---|---|---|---|---|
| A | Ala | Alanine | C3H5NO | 71.03711 | 71.0779 |
| C | Cys | Cysteine | C3H5NOS | 103.00918 | 103.1429 |
| D | Asp | Aspartic acid | C4H5NO3 | 115.02694 | 115.0874 |
| E | Glu | Glutamic acid | C5H7NO3 | 129.04259 | 129.1140 |
| F | Phe | Phenylalanine | C9H9NO | 147.06841 | 147.1739 |
| G | Gly | Glycine | C2H3NO | 57.02146 | 57.0513 |
| H | His | Histidine | C6H7N3O | 137.05891 | 137.1393 |
| I | Ile | Isoleucine | C6H11NO | 113.08406 | 113.1576 |
| K | Lys | Lysine | C6H12N2O | 128.09496 | 128.1723 |
| L | Leu | Leucine | C6H11NO | 113.08406 | 113.1576 |
| M | Met | Methionine | C5H9NOS | 131.04048 | 131.1961 |
| N | Asn | Asparagine | C4H6N2O2 | 114.04293 | 114.1026 |
| P | Pro | Proline | C5H7NO | 97.05276 | 97.1152 |
| Q | Gln | Glutamine | C5H8N2O2 | 128.05858 | 128.1292 |
| R | Arg | Arginine | C6H12N4O | 156.10111 | 156.1857 |
| S | Ser | Serine | C3H5NO2 | 87.03203 | 87.0773 |
| T | Thr | Threonine | C4H7NO2 | 101.04768 | 101.1039 |
| V | Val | Valine | C5H9NO | 99.06841 | 99.1311 |
| W | Trp | Tryptophan | C11H10N2O | 186.07931 | 186.2099 |
| Y | Tyr | Tyrosine | C9H9NO2 | 163.06333 | 163.1733 |
Source model: Unimod elemental masses. Values are calculated from the displayed residue formulas; they are not measurements of a physical sample.
Interpretation boundary
A theoretical mass is not a sample result.
The output answers a defined mathematical question: what mass follows from this unmodified linear sequence under the stated atomic-mass model? It does not establish that a physical sample contains the sequence, that its quantity matches a label, or that it meets a purity specification.
Experimental identity may be supported through mass-spectrometric evidence interpreted against the method and expected charge states. Chromatographic purity, measured quantity, sterility, endotoxin status, counterions, residual solvents, and suitability remain separate questions. See the HPLC vs LC-MS guide and peptide COA guide.
Sources
Mass, charge, and nomenclature references.
- Unimod: Symbols and mass values
- Expasy: PeptideMass documentation
- IUPAC Gold Book: Peptides
- IUPAC Gold Book: Amount concentration
- EMBOSS: iep documentation and default Epk.dat pKa values
- Expasy: Compute pI/Mw documentation
- Kozlowski: IPC—Isoelectric Point Calculator
- Expasy: ProtParam GRAVY documentation
- Expasy: Kyte–Doolittle hydropathy scale
- Kyte and Doolittle: A simple method for displaying hydropathic character
Calculator FAQ
Method, formats, and limits.
How is peptide molecular weight calculated from a sequence?
For an unmodified linear peptide with free termini, the calculator sums the elemental composition of every amino-acid residue and adds H2O for the terminal hydrogen and hydroxyl group. Elemental masses are then summed using either monoisotopic or average atomic masses.
What is the difference between monoisotopic mass and average molecular weight?
Monoisotopic mass uses the mass of the most abundant natural isotope of each element. Average molecular weight uses abundance-weighted average atomic masses. The values diverge as molecular size and elemental composition increase.
Does the calculator include peptide modifications?
No. It assumes the 20 standard amino-acid residues, a linear sequence, and free N- and C-termini. Terminal caps, disulfides, salts, adducts, isotope labels, nonstandard residues, post-translational modifications, and counterions require explicit mass adjustments.
Can theoretical peptide mass verify a laboratory sample?
No. A theoretical mass is a calculation from a stated sequence. It does not measure a sample or establish identity, purity, quantity, sterility, or suitability. Experimental evidence requires an applicable analytical method and record.
What sequence format does the calculator accept?
It accepts standard one-letter codes for the 20 common amino acids. Uppercase and lowercase input are accepted. Spaces, line breaks, hyphens, and a FASTA header are ignored; ambiguous or unsupported residue codes produce an error instead of an estimated result.
How does the calculator convert peptide mass into molarity?
It divides material mass by the sequence-derived average molecular weight to obtain amount of substance, then divides that amount by final solution volume. With mass in milligrams, molecular weight in grams per mole, and final volume in millilitres, the numerical result mass/(molecular weight × volume) is mol per litre.
How are peptide isoelectric point and net charge estimated?
The calculator applies Henderson–Hasselbalch fractional charges to the free N-terminus, free C-terminus, and ionizable C, D, E, H, K, R, and Y side chains using the default pKa values published in the EMBOSS Epk.dat model. Estimated pI is the pH where the modeled net charge reaches zero.
Why can peptide pI calculators return different values?
Estimated pI depends on the selected pKa parameter set, terminal chemistry, modifications, and the physical environment. This calculator publishes its exact pKa values and assumptions so its output can be reproduced, but the estimate is not an experimental measurement.
What does peptide GRAVY mean?
GRAVY is the grand average of hydropathy: the sum of the Kyte–Doolittle hydropathy values for every residue divided by sequence length. It is a sequence-scale descriptor, not a direct measurement of solubility, structure, or membrane association.