Free laboratory calculation tool
Peptide Molecular Weight, m/z, pI, Extinction & Molarity Calculator
Calculate theoretical peptide formula and mass, precursor m/z, supported terminal-cap adjustments, estimated isoelectric point, net charge, ε₂₈₀ extinction coefficient, and Kyte–Doolittle GRAVY, then convert average molecular weight into laboratory molarity.
Interactive sequence tool
Peptide molecular weight, pI & charge calculator
Enter a peptide with standard one-letter codes or separated three-letter amino-acid codes. Calculate formula, mass, precursor m/z, estimated isoelectric point, net charge, extinction coefficient, and composition with free or supported capped termini. Spaces, line breaks, hyphens, and a FASTA header are handled automatically.
Supported formats: one-letter sequence (ACD) or three-letter codes separated by spaces or hyphens (Ala-Cys-Asp).
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: linear peptide with the selected free or supported capped termini. The free-terminal mass model adds H₂O; N-acetylation adds C₂H₂O and C-amidation replaces terminal OH with NH₂. Precursor m/z values add or subtract the displayed number of proton masses and divide by charge magnitude; they are theoretical centroids, not isotope envelopes or observed peaks. Estimated pI and net charge use the displayed EMBOSS default pKa set and Henderson–Hasselbalch fractional charges, excluding a blocked terminal group. GRAVY is the arithmetic mean of the displayed Kyte–Doolittle residue values. ε₂₈₀ uses the Pace tryptophan, tyrosine, and cystine model and may be unreliable for short peptides or sequences without tryptophan. The tool does not include disulfide mass loss, salts, counterions, adducts other than H⁺, isotope labels, nonstandard residues, other 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 explicit terminal chemistry.
Each standard amino-acid code maps to the elemental composition of that residue after peptide-bond formation. With free termini, the calculator sums those residue compositions and adds H₂O for the 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.
Terminal caps
N-acetyl and C-amide choices change mass and charge.
Selecting N-terminal acetylation adds C₂H₂O to the free-terminal peptide formula and removes the model's ionizable N-terminal amino group. Selecting C-terminal amidation replaces terminal OH with NH₂—net HN−O—and removes the model's ionizable C-terminal carboxyl group.
The displayed formula, monoisotopic mass, average molecular weight, precursor m/z, net charge, and estimated pI update together. These choices do not infer any other modification or whether a physical sample actually has the selected terminal chemistry.
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] and theoretical protonated and deprotonated precursor m/z values for charge states 1–5. These values describe the entered sequence under the stated model; they do not predict ion abundance, isotope envelopes, fragmentation, adduct formation, or an instrument result.
Precursor ions
Peptide mass-to-charge values for common charge states.
For a protonated ion at charge n, the calculator adds n proton masses to the neutral monoisotopic peptide mass and divides by n. For a deprotonated ion, it subtracts n proton masses before dividing. The proton mass uses the 2022 CODATA value published by NIST.
IUPAC defines m/z as the dimensionless quantity formed by dividing an ion's mass number by its charge number. The calculator's values are theoretical sequence references. They do not establish which charge states, adducts, isotope peaks, or fragment ions will appear in a measured spectrum.
Absorbance estimate
Sequence-derived molar extinction coefficient at 280 nm.
The ε₂₈₀ estimate follows the sequence model evaluated by Pace and colleagues: 5,500 M⁻¹ cm⁻¹ per tryptophan, 1,490 per tyrosine, and 125 per cystine pair. The calculator reports one value with reduced cysteines and a second scenario with the maximum number of cystine pairs allowed by the entered cysteine count.
A sequence does not establish disulfide connectivity, solvent behavior, or measured absorbance. The approximation may be unreliable for short peptides and for sequences without tryptophan; use an experimentally appropriate coefficient when one has been determined.
Charge model
Estimated peptide pI and net charge from published pKa values.
The calculator uses Henderson–Hasselbalch fractional charges for unblocked termini and the ionizable side chains of C, D, E, H, K, R, and Y. A selected N-acetyl or C-amide cap removes that terminal group from the charge model. It estimates pI only when the modeled charge crosses zero between pH 0 and 14.
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 unless the corresponding supported cap is selected. Other 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 entered sequence and selected terminal chemistry 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 linear sequence and selected terminal chemistry under the stated atomic-mass model? It does not establish that a physical sample contains the sequence, has the selected termini, matches a labeled quantity, or 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
- IUPAC Gold Book: Mass-to-charge ratio
- NIST: 2022 CODATA recommended values of the fundamental physical constants
- Pace et al.: How to measure and predict the molar absorption coefficient of a protein
Registry citation: C Suite: molecular weight calculator (RRID:SCR_028937). The identifier supports citation and discovery; it is not an endorsement or experimental validation. Machine-readable software records: CodeMeta JSON-LD · Citation File Format · bio.tools JSON · software linkset.
Calculator FAQ
Method, formats, and limits.
How is peptide molecular weight calculated from a sequence?
For a 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. If N-acetylation or C-amidation is selected, it applies that explicit elemental adjustment before summing 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?
It supports two explicit terminal choices: N-terminal acetylation and C-terminal amidation. It adjusts elemental formula, mass, pI, and charge for the selected termini. Disulfide mass loss, salts, adducts, isotope labels, nonstandard residues, other post-translational modifications, and counterions remain outside the model.
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 and standard three-letter codes separated by spaces or hyphens. Uppercase and lowercase input are accepted. FASTA headers 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.
How are peptide precursor m/z values calculated?
For each displayed positive charge state, the calculator adds that number of proton masses to the neutral monoisotopic peptide mass and divides by the charge magnitude. For each negative state, it subtracts the proton masses before dividing. The results are theoretical centroids, not measured peaks or isotope envelopes.
How is the peptide extinction coefficient at 280 nm estimated?
The calculator applies the Pace sequence model: 5,500 for each tryptophan, 1,490 for each tyrosine, and 125 for each cystine pair. It reports a reduced-cysteine value and a maximum-paired-cysteine scenario because a sequence alone does not establish disulfide connectivity.