Protein Molecular Weight Calculator
From sequence to mass. Explore your protein’s composition.
Average & monoisotopic mass · Theoretical pI · UV A280
Sequence & Parameters
Result
Average molecular weight
Enable JavaScriptAnalyze a sequence or choose count mode.
Elemental composition
—Sequence-specific properties appear after calculation.
Amino Acid Composition
A sequence is needed to determine amino acid composition.
Residue class composition
Full amino acid composition table
Classes: nonpolar AVILMFWPG; polar uncharged STCYNQ; charged side chains DEKRH. This grouping does not replace pH-dependent ionization. Mass contributions exclude terminal water and disulfide H loss.
| Amino acid | Count | Fraction | Residue contribution (Da) |
|---|
Net Charge & Isoelectric Point
Theoretical curve · terminal-specific Bjellqvist pKa model. At the marked pI, model net charge is zero.
Charge model & assumptions
The model sums Henderson–Hasselbalch charges for free termini and ionizable side chains, then solves charge = 0 by bisection over pH 0–14. pKa: K 10.0, R 12.0, H 5.98; D 4.05, E 4.45, C 9.0, Y 10.0; default N-terminus 7.5 and C-terminus 3.55. N-terminal corrections: A 7.59, M 7.00, S 6.93, P 8.36, T 6.82, V 7.44, E 7.70; C-terminal D 4.55, E 4.75.
Paired disulfide cysteines are excluded from titratable thiols. This is an explicit extension of the reduced-chain model, not a site-specific structure calculation. Ionic strength, local environments, blocked termini and post-translational modifications can alter experimental pI.
Mass Calculation Guide
MW = Σ residue masses + H₂O
- Read the sequenceIdentify canonical amino acids and any selected intrachain disulfide bonds.
- Sum residue massesUse average atomic weights or monoisotopic elemental masses.
- Add terminal waterAdd one H₂O for free termini; subtract two H atoms per disulfide bond.
A280 extinction is not a Bradford assay calibration.
Understanding your result
- Molecular weightAverage mass uses isotope-averaged atomic weights. Monoisotopic mass uses the lightest stable isotopes. Da is a molecular mass unit; the same numeric value expresses molar mass in g/mol.
- Theoretical pIThe pH at which calculated net charge is zero. It is a model estimate, especially for short or very basic peptides.
- UV A280ε280 = 5,500 × Trp + 1,490 × Tyr + 125 × disulfide bonds, in M⁻¹ cm⁻¹. The estimate assumes no additional absorbing chromophores; Trp-free proteins can have appreciable error.
Linear unmodified chain only. Tags must be included in the input sequence. Adducts, isotopic labeling, glycosylation, terminal modifications and multimer formation are not modeled. No mass spectrum, isotope envelope or 3D structure is predicted.
Frequently asked questions
Average vs monoisotopic mass?
Average mass reflects natural isotope abundance. Monoisotopic mass uses the lightest stable isotope of each element, useful when interpreting high-resolution peptide mass data. Measured m/z also depends on charge state and adducts; it is not calculated here.
Why add one water molecule?
Residue formulas have already lost H₂O relative to free amino acids. Adding one terminal H₂O gives the elemental formula for a linear chain with free N- and C-termini. Do not subtract (N − 1) water molecules again from residue masses.
Can this predict a 3D structure?
No. The moving ribbon is an illustrative visual only. These calculations use sequence composition and ionization assumptions, not protein folding or structural prediction.
How are disulfide bonds handled?
Each intrachain disulfide removes two H atoms, adds 125 M⁻¹ cm⁻¹ to the UV estimate, and removes two free cysteine thiols from the charge model. You must specify the bond count; connectivity is not inferred.
Which sequence formats are accepted?
Paste a plain one-letter sequence or one FASTA record. Whitespace, position digits and lower-case letters are normalized. Unknown or modified residues (B, J, O, U, X, Z), gap punctuation, stop marks and multiple records produce an explicit error.
Sources & References
ExPASy / ProtParamProtein properties, UV extinction & calculation methods.
SIB Swiss Institute of BioinformaticsCompute pI/Mw reference documentation.Educational sequence calculations; experimental validation and method assumptions still apply. Reference logos identify sources, not endorsement.
From sequence to mass. Explore your protein’s composition.