Protein Molecular Weight Calculator

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Protein Molecular Weight Calculator

Calculate the molecular weight of a protein or peptide from its one-letter amino acid sequence.

Amino Acid Sequence (one-letter code)

Sequence Format

One-letter code (e.g. ACDEFG) Three-letter code (e.g. Ala-Cys-Asp)

Number of Disulfide Bonds

Calculate Molecular Weight Enter a sequence above and click Calculate.

function proCalc() { // Monoisotopic masses of amino acid residues (Da) const residueMassOne = { 'A': 71.03711, 'R': 156.10111, 'N': 114.04293, 'D': 115.02694, 'C': 103.00919, 'E': 129.04259, 'Q': 128.05858, 'G': 57.02146, 'H': 137.05891, 'I': 113.08406, 'L': 113.08406, 'K': 128.09496, 'M': 131.04049, 'F': 147.06841, 'P': 97.05276, 'S': 87.03203, 'T': 101.04768, 'W': 186.07931, 'Y': 163.06333, 'V': 99.06841, 'U': 150.95363, 'O': 237.14773 };

// Average masses of amino acid residues (Da) const residueMassAvg = { 'A': 71.0788, 'R': 156.1875, 'N': 114.1038, 'D': 115.0886, 'C': 103.1388, 'E': 129.1155, 'Q': 128.1307, 'G': 57.0519, 'H': 137.1411, 'I': 113.1594, 'L': 113.1594, 'K': 128.1741, 'M': 131.1926, 'F': 147.1766, 'P': 97.1167, 'S': 87.0782, 'T': 101.1051, 'W': 186.2132, 'Y': 163.1760, 'V': 99.1326, 'U': 150.0388, 'O': 237.3018 };

// Three-letter to one-letter mapping const threeToOne = { 'ALA':'A','ARG':'R','ASN':'N','ASP':'D','CYS':'C', 'GLU':'E','GLN':'Q','GLY':'G','HIS':'H','ILE':'I', 'LEU':'L','LYS':'K','MET':'M','PHE':'F','PRO':'P', 'SER':'S','THR':'T','TRP':'W','TYR':'Y','VAL':'V', 'SEC':'U','PYL':'O','ASX':'B','GLX':'Z','XLE':'J' };

const format = document.getElementById('pro-format').value; let rawSeq = document.getElementById('pro-sequence').value.trim(); const disulfide = parseInt(document.getElementById('pro-disulfide').value) || 0; const resultDiv = document.getElementById('pro-result');

if (!rawSeq) { resultDiv.innerHTML = 'Please enter an amino acid sequence.'; return; }

let sequence = '';

if (format === 'one') { // Remove whitespace, numbers, asterisks (stop codons), dashes sequence = rawSeq.replace(/[\s\d*-]/g, '').toUpperCase(); // Validate const invalid = []; for (let i = 0; i 0) { resultDiv.innerHTML = 'Invalid characters found: ' + invalid.slice(0,5).join(', ') + (invalid.length > 5 ? '...' : '') + ''; return; } } else { // Three-letter: split by dash, comma, space, or newline const tokens = rawSeq.toUpperCase().split(/[-,\s]+/).filter(t => t.length > 0); for (let i = 0; i Unknown three-letter code: "' + t + '" at position ' + (i+1) + ''; return; } } }

if (sequence.length === 0) { resultDiv.innerHTML = 'No valid amino acids found in the sequence.'; return; }

// Validate disulfide bonds const cysteineCount = (sequence.match(/C/g) || []).length; if (disulfide > Math.floor(cysteineCount / 2)) { resultDiv.innerHTML = 'Number of disulfide bonds (' + disulfide + ') exceeds maximum possible (' + Math.floor(cysteineCount/2) + ') for ' + cysteineCount + ' cysteine residues.'; return; }

// Calculate molecular weight // MW = sum of residue masses + water (18.01524 for monoisotopic, 18.0153 for average) // Each disulfide bond removes 2H (2 * 1.00794 average, 2 * 1.007825 monoisotopic)

let monoMW = 0; let avgMW = 0; const composition = {};

for (let i = 0; i ' + '' + 'Sequence Length' + sequence.length + ' residues' + 'Average Molecular Weight' + avgMW.toFixed(2) + ' Da  |  ' + (avgMW/1000).toFixed(4) + ' kDa' + 'Monoisotopic Molecular Weight' + monoMW.toFixed(4) + ' Da' + 'Disulfide Bonds' + disulfide + ' (−' + (disulfide * 2 * 1.00794).toFixed(4) + ' Da)' + 'Extinction Coeff. ε₂₈₀ (oxidized)' + extCoeff.toLocaleString() + ' M⁻¹cm⁻¹' + 'Extinction Coeff. ε₂₈₀ (reduced)' + extCoeffRed.toLocaleString() + ' M⁻¹cm⁻¹' + (extCoeff > 0 ? 'A₂₈₀ (1 mg/mL, oxidized)' + (extCoeff / avgMW).toFixed(4) + '' : '') + 'Amino Acid Composition' + compStr.trim() + '' + ''; }

#### Formula

Average Molecular Weight:

MW = Σ(residue average masses) + H₂O − (2 × nSS × MH)

where H₂O = 18.01524 Da accounts for the free N- and C-termini, and each disulfide bond removes 2 hydrogen atoms (2 × 1.00794 Da).

Monoisotopic Molecular Weight:

MWmono = Σ(residue monoisotopic masses) + 18.01056 − (2 × nSS × 1.007825)

Molar Extinction Coefficient at 280 nm (Pace et al.):

ε₂₈₀ = (nTrp × 5500) + (nTyr × 1490) + (nSS × 125)   [M⁻¹cm⁻¹]

Absorbance at 280 nm (1 mg/mL):

A₂₈₀ = ε₂₈₀ / MWavg

#### Assumptions & References

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