Protein Molecular Weight Calculator

This protein molecular weight calculator turns a raw or FASTA amino acid sequence into an instant molecular weight in daltons (Da) or kilodaltons (kDa) — plus residue count and estimated extinction coefficient at A280. Use this protein molecular weight calculator before running gels, dilutions, or concentration conversions.

Enter Sequence

Amino acid sequence (raw or FASTA)

FASTA header lines (starting with <code>></code>) are ignored automatically.</div>
    </div>

<div class="pmw-row">
      <div class="pmw-field">
        <label for="pmw-tag">Add tag / epitope</label>
        <select id="pmw-tag">
          <option value="none">None</option>
          <option value="His6">His6 (HHHHHH)</option>
          <option value="FLAG">FLAG (DYKDDDDK)</option>
          <option value="cmyc">c-Myc (EQKLISEEDL)</option>
          <option value="HA">HA (YPYDVPDYA)</option>
          <option value="V5">V5 (GKPIPNPLLGLDST)</option>
          <option value="STag">S-Tag (KETAAAKFERQHMDS)</option>
          <option value="T7">T7 (MASMTGGQQMG)</option>
          <option value="ProteinC">Protein C (EDQVDPRLIDGK)</option>
          <option value="GFP">GFP (~26.9 kDa, fixed)</option>
          <option value="GST">GST (~26.0 kDa, fixed)</option>
        </select>
      </div>
      <div class="pmw-field">
        <label for="pmw-copies">Copies to add</label>
        <select id="pmw-copies">
          <option>1</option><option>2</option><option>3</option><option>4</option><option>5</option>
        </select>
      </div>
    </div>

<div class="pmw-actions">
      <button class="pmw-btn pmw-btn-primary" id="pmw-calc-btn" type="button">Calculate Molecular Weight</button>
      <button class="pmw-btn pmw-btn-ghost" id="pmw-reset-btn" type="button">Reset</button>
    </div>
    <div class="pmw-warn" id="pmw-warn"></div>
  </div>

<div class="pmw-card">
    <h2>Result</h2>
    <div class="pmw-result-mw">
      <div class="pmw-num" id="pmw-mw-value">—</div>
      <div class="pmw-unit" id="pmw-mw-unit">Da · paste a sequence to calculate</div>
    </div>
    <div class="pmw-stats">
      <div class="pmw-stat"><div class="pmw-stat-label">Molecular weight (kDa)</div><div class="pmw-stat-value" id="pmw-stat-kda">—</div></div>
      <div class="pmw-stat"><div class="pmw-stat-label">Residue count</div><div class="pmw-stat-value" id="pmw-stat-len">—</div></div>
      <div class="pmw-stat"><div class="pmw-stat-label">Ext. coefficient (A280)</div><div class="pmw-stat-value" id="pmw-stat-ext">—</div></div>
      <div class="pmw-stat"><div class="pmw-stat-label">Isoelectric hint</div><div class="pmw-stat-value" id="pmw-stat-pi">—</div></div>
    </div>
    <div class="pmw-copybar">
      <button type="button" id="pmw-copy-da">Copy Da</button>
      <button type="button" id="pmw-copy-kda">Copy kDa</button>
    </div>
  </div>
</section>

<section class="pmw-ladder-wrap">
  <h2>Sequence Track</h2>
  <div class="pmw-ladder" id="pmw-ladder"><span class="pmw-empty">Your sequence will appear here as a color-coded residue track.</span></div>
  <div class="pmw-legend">
    <span><i style="background:#146356"></i>Nonpolar (A,V,L,I,M,P,G)</span>
    <span><i style="background:#3A6EA5"></i>Aromatic (F,W,Y)</span>
    <span><i style="background:#6B7A76"></i>Polar (S,T,C,N,Q)</span>
    <span><i style="background:#B3541E"></i>Acidic (D,E)</span>
    <span><i style="background:#7A4FA3"></i>Basic (K,R,H)</span>
  </div>
</section>

<section class="pmw-ref">
  <h2>How This Protein Molecular Weight Calculator Works</h2>
  <p>This protein molecular weight calculator sums the average residue mass of every amino acid in the chain, then adds the mass of one water molecule for the terminal H and OH groups formed when the peptide bond releases water during synthesis.</p>
  <div class="pmw-formula">MW (Da) = Σ (residue mass of each amino acid) + 18.02 (one water molecule)</div>
  <p>Residue mass is the amino acid’s mass minus water, since each peptide bond formed between two amino acids releases one water molecule. Like the reference method described in <a href="https://web.expasy.org/protparam/" target="_blank" rel="noopener noreferrer">ExPASy ProtParam</a>, this protein molecular weight calculator uses average isotopic masses, the standard convention for intact-protein molecular weight (rather than monoisotopic mass, which is used for mass-spec fragment matching).</p>

<h3>Average Residue Masses This Protein Molecular Weight Calculator Uses</h3>
  <table class="pmw-table">
    <thead><tr><th>Amino acid</th><th>Code</th><th>Residue mass (Da)</th><th>Amino acid</th><th>Code</th><th>Residue mass (Da)</th></tr></thead>
    <tbody>
      <tr><td>Glycine</td><td>G</td><td>57.05</td><td>Leucine</td><td>L</td><td>113.16</td></tr>
      <tr><td>Alanine</td><td>A</td><td>71.08</td><td>Isoleucine</td><td>I</td><td>113.16</td></tr>
      <tr><td>Serine</td><td>S</td><td>87.08</td><td>Asparagine</td><td>N</td><td>114.10</td></tr>
      <tr><td>Proline</td><td>P</td><td>97.12</td><td>Aspartate</td><td>D</td><td>115.09</td></tr>
      <tr><td>Valine</td><td>V</td><td>99.13</td><td>Glutamine</td><td>Q</td><td>128.13</td></tr>
      <tr><td>Threonine</td><td>T</td><td>101.11</td><td>Lysine</td><td>K</td><td>128.17</td></tr>
      <tr><td>Cysteine</td><td>C</td><td>103.14</td><td>Glutamate</td><td>E</td><td>129.12</td></tr>
      <tr><td>Methionine</td><td>M</td><td>131.19</td><td>Histidine</td><td>H</td><td>137.14</td></tr>
      <tr><td>Phenylalanine</td><td>F</td><td>147.18</td><td>Arginine</td><td>R</td><td>156.19</td></tr>
      <tr><td>Tyrosine</td><td>Y</td><td>163.18</td><td>Tryptophan</td><td>W</td><td>186.21</td></tr>
    </tbody>
  </table>

<h2>Protein Molecular Weight Calculator: Frequently Asked Questions</h2>
  <div class="pmw-faq">
    <details>
      <summary>What’s the difference between average and monoisotopic molecular weight?</summary>
      <p>Average molecular weight uses the natural isotopic abundance of each element and is the correct value for describing the mass of an intact protein — the number you’ll see on a data sheet or gel standard. Monoisotopic mass uses only the most abundant isotope of each element and is used almost exclusively for interpreting mass spectrometry fragments. This protein molecular weight calculator reports average molecular weight, and you can cross-check results against the <a href="https://www.uniprot.org/" target="_blank" rel="noopener noreferrer">UniProt database</a> for characterized proteins.</p>
    </details>
    <details>
      <summary>Why does adding a His6 or FLAG tag change the molecular weight?</summary>
      <p>A fusion tag is itself a short peptide, so it adds its own residue mass to the total. A His6 tag adds roughly 840 Da; a FLAG tag adds roughly 1,012 Da. Selecting a tag above adds its calculated mass — including copy number — to your sequence’s molecular weight.</p>
    </details>
    <details>
      <summary>Does this account for post-translational modifications?</summary>
      <p>No. This calculator computes the theoretical molecular weight from the primary amino acid sequence only. Modifications such as glycosylation, phosphorylation, or disulfide-bond formation will change the actual measured mass — sometimes substantially — so treat this as a baseline, not a final experimental value.</p>
    </details>
    <details>
      <summary>What do X, B, Z, and U mean in my sequence?</summary>
      <p>These are ambiguity or non-standard codes: X (unknown residue), B (Asx: Asp or Asn), Z (Glx: Glu or Gln), and U (selenocysteine). This calculator skips them in the weight calculation and flags how many were excluded, since their exact mass can’t be determined from the code alone.</p>
    </details>
    <details>
      <summary>How accurate is the extinction coefficient estimate?</summary>
      <p>The estimate uses the standard Pace/Gill method (Trp × 5,500 + Tyr × 1,490 + Cys × 125 M⁻¹cm⁻¹), which assumes all cysteines form cystine bridges. It’s a useful working estimate for A280 protein quantification, but always confirm against a validated tool like ExPASy ProtParam before relying on it for published work.</p>
    </details>
  </div>

<h2>When to Use a Protein Molecular Weight Calculator</h2>
  <p>Reach for a protein molecular weight calculator whenever you need a quick, sequence-based mass estimate — before running SDS-PAGE against known standards, before setting up a molar dilution series, or before converting a mg/mL stock to µM. For background on how amino acid composition drives protein mass and function, see the <a href="https://www.ncbi.nlm.nih.gov/pmc/" target="_blank" rel="noopener noreferrer">NCBI PMC literature database</a>.</p>
  <p>Working with concentrations instead of raw sequence mass? Use the <a href="https://calculatorprotein.com/protein-concentration-calculator/">protein concentration calculator</a> to convert mg/mL to µM once you have your molecular weight from this protein molecular weight calculator.</p>

<div class="pmw-disclaimer">
    This tool is intended for research, educational, and laboratory-reference use. Results are theoretical estimates based on primary sequence only and do not account for post-translational modifications. Not medical advice.
  </div>
</section>

function calculate(){
    var raw = document.getElementById('pmw-seq').value;
    var seq = cleanSequence(raw);
    var warnEl = document.getElementById('pmw-warn');
    var ladder = document.getElementById('pmw-ladder');
    warnEl.style.display = "none";
    ladder.innerHTML = "";

if (!seq.length){
      document.getElementById('pmw-mw-value').textContent = "—";
      document.getElementById('pmw-mw-unit').textContent = "Da · paste a sequence to calculate";
      document.getElementById('pmw-stat-kda').textContent = "—";
      document.getElementById('pmw-stat-len').textContent = "—";
      document.getElementById('pmw-stat-ext').textContent = "—";
      document.getElementById('pmw-stat-pi').textContent = "—";
      ladder.innerHTML = '<span class="pmw-empty">Your sequence will appear here as a color-coded residue track.</span>';
      return;
    }

var sum = 0, counted = 0, skipped = 0, trp = 0, tyr = 0, cys = 0, acidic = 0, basic = 0;
    for (var i = 0; i < seq.length; i++){
      var ch = seq[i];
      var m = residueMass(ch);
      var chip = document.createElement('span');
      chip.className = 'pmw-chip';
      chip.textContent = ch;
      chip.style.background = m === null ? "#C9CFCD" : colorFor(ch);
      chip.title = ch + (m === null ? " (unknown mass)" : " · " + m.toFixed(2) + " Da residue mass");
      ladder.appendChild(chip);

if (m === null){ skipped++; continue; }
      sum += m; counted++;
      if (ch === "W") trp++;
      if (ch === "Y") tyr++;
      if (ch === "C") cys++;
      if (ch === "D" || ch === "E") acidic++;
      if (ch === "K" || ch === "R" || ch === "H") basic++;
    }

var mw = counted > 0 ? sum + WATER : 0;

// add tag
    var tagKey = document.getElementById('pmw-tag').value;
    var copies = parseInt(document.getElementById('pmw-copies').value, 10) || 1;
    var tag = TAGS[tagKey];
    if (tag && tagKey !== "none"){
      if (tag.fixed !== null){
        mw += tag.fixed * copies;
      } else {
        var tagSum = 0;
        for (var j = 0; j < tag.seq.length; j++){ tagSum += residueMass(tag.seq[j]); }
        mw += (tagSum + WATER * 0) * copies; // tag contributes residues only; parent chain keeps the single terminal water
      }
    }

if (skipped > 0){
      warnEl.style.display = "block";
      warnEl.textContent = skipped + " character(s) were not recognized standard amino acids (e.g. X, B, Z, U) and were excluded from the weight calculation.";
    }

var kda = mw / 1000;
    var ext = trp * 5500 + tyr * 1490 + Math.floor(cys / 2) * 125;

document.getElementById('pmw-mw-value').textContent = mw.toLocaleString(undefined, {maximumFractionDigits: 2});
    document.getElementById('pmw-mw-unit').textContent = "Da (daltons)";
    document.getElementById('pmw-stat-kda').textContent = kda.toFixed(2) + " kDa";
    document.getElementById('pmw-stat-len').textContent = counted + (skipped ? " (+" + skipped + " unresolved)" : "") + " aa";
    document.getElementById('pmw-stat-ext').textContent = ext.toLocaleString() + " M⁻¹cm⁻¹";

var netCharge = basic - acidic;
    var piHint = netCharge > 2 ? "Likely basic (pI > 7)" : netCharge < -2 ? "Likely acidic (pI < 7)" : "Likely neutral range";
    document.getElementById('pmw-stat-pi').textContent = piHint;

window.pmwLastResult = { da: mw, kda: kda };
  }

function copyToClipboard(text){
    if (navigator.clipboard && navigator.clipboard.writeText){
      navigator.clipboard.writeText(text);
    }
  }

calculate();
})();
</script>
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        alt="Shady Elbody"
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<p style="font-size:11px;font-weight:700;text-transform:uppercase;letter-spacing:1px;color:#2E5FA3;margin:0 0 4px 0;padding:0;">
        Reviewed & Written by
      </p>

<h3 style="font-size:20px;font-weight:700;color:#1a1a2e;margin:0 0 4px 0;padding:0;line-height:1.2;">
        Shady Elbody
      </h3>

<p style="font-size:13px;color:#555;margin:0 0 10px 0;padding:0;line-height:1.5;">
        SEO Specialist · Protein Nutrition Researcher · Founder, CalculatorProtein.com
      </p>

<p style="font-size:14px;line-height:1.6;color:#333;margin:0 0 14px 0;padding:0;">
        Shady Elbody is an SEO specialist and the founder of CalculatorProtein.com,
        a protein calculator resource used by athletes and fitness enthusiasts worldwide.
        He combines deep expertise in search optimisation with evidence-based sports
        nutrition, building every calculator and guide around ACSM, ISSN, and current
        PubMed-indexed research.
      </p>

<div style="display:flex;gap:12px;flex-wrap:wrap;margin-bottom:10px;">

<a href="https://www.linkedin.com/in/shady-el-body/" target="_blank" rel="noopener noreferrer"
           style="display:inline-flex;align-items:center;gap:6px;font-size:13px;font-weight:600;color:#2E5FA3;text-decoration:none;">
          <svg width="15" height="15" viewBox="0 0 24 24" fill="#2E5FA3" style="flex-shrink:0;"><path d="M20.447 20.452h-3.554v-5.569c0-1.328-.027-3.037-1.852-3.037-1.853 0-2.136 1.445-2.136 2.939v5.667H9.351V9h3.414v1.561h.046c.477-.9 1.637-1.85 3.37-1.85 3.601 0 4.267 2.37 4.267 5.455v6.286zM5.337 7.433a2.062 2.062 0 01-2.063-2.065 2.064 2.064 0 112.063 2.065zm1.782 13.019H3.555V9h3.564v11.452zM22.225 0H1.771C.792 0 0 .774 0 1.729v20.542C0 23.227.792 24 1.771 24h20.451C23.2 24 24 23.227 24 22.271V1.729C24 .774 23.2 0 22.222 0h.003z"/></svg>
          LinkedIn
        </a>

<a href="https://calculatorprotein.com/about/" rel="author"
           style="display:inline-flex;align-items:center;gap:6px;font-size:13px;font-weight:600;color:#2E5FA3;text-decoration:none;">
          Author Page
        </a>

</div>

<p style="font-size:12px;color:#999;margin:0;padding:0;">
        <time datetime="2026-04-08">Last reviewed: April 2026</time>
      </p>

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