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<title>mMass - Open Source MS Tool | Documentation | Protein Digest Tool</title>
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<h1><a href="/" title="Homepage"><span>mMass - Open Source Mass Spectrometry Tool</span></a></h1>
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<h2><span>Protein Digest Tool</span></h2>
<p>Many experiments, involving the detection of modifications, protein validation etc., apply the specific enzymatic digestion of a protein with a known sequence. The <em>Protein Digest</em> module <span class="hotkey">[Tools → Protein Digest]</span> <img src="figures/icon_mcut.png" alt="icon" class="icon" /> can be used to generate a list of peptides resulting from <em>in silico</em> enzymatic digestion or <em>in silico</em> chemical digestion of a sequence previously defined using <a href="mseq.html" title="go to chapter">Sequence Editor</a>. The masses of these peptides can then be compared with the current peaklist within a specified tolerance.</p>
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<p>Protein digest tool.</p>
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<h3 id="ch-digest">Digest settings</h3>
<p>In the module control panel some digest options can be set. You can specify used <em>Enzyme</em> or number of missed cleavage sites - <em>Partials</em>. If there are any <a href="mseq.html#ch-modifications" title="go to chapter">modifications</a> in the sequence, all combinations of modifications can be calculated for each peptide - <em>Optional modifications</em>. A <em>Charge</em> state and <em>Mass limits</em> of resulted peptides can be also set.</p>
<h3 id="ch-masstype">Mass type settings</h3>
<p>It is important to set proper mass type for masses calculations - <em>Monoisotopic Mass</em> <span class="hotkey">[Config → Monoisotopic Mass]</span> <img src="figures/icon_mono.png" alt="icon" class="icon" /> or <em>Average Mass</em> <span class="hotkey">[Config → Average Mass]</span> <img src="figures/icon_average.png" alt="icon" class="icon" />. Current mass type is shown in application statusbar.</p>
<h3 id="ch-generate">Generate peptides</h3>
<p>To generate the list of peptide masses press <em>Digest</em> button located in module control panel.</p>
<h3 id="ch-match">Data matching</h3>
<p>See the separate <a href="mmatch.html" title="go to chapter">chapter</a>.</p>
<h3 id="ch-panel">Panel view</h3>
<p>List of all generated peptides can also be viewed in separate panel. To show the panel press <em>Show in panel</em> button. Peptides can be filtered to show missed or matched only or sorted by the range, partials, mass or sequence. The main purpose of this panel, however, is the ability to highlight selected mass in the current spectrum within specified <em>Zoom</em>. Using this feature you can easily find some missed peaks etc.</p>
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<p>Peptides list.</p>
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<h2><span>Chapters</span></h2>
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<li><a href="index.html" title="mMass structure..."><span>Introduction</span></a></li>
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