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<title>mMass - Open Source MS Tool | Documentation | Sequence Editor</title>
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<h2><span>Sequence Editor</span></h2>
<p>For some <em>mMass</em> modules and tools like <a href="mcut.html" title="go to chapter">Protein Digest</a> or <a href="mfrag.html" title="go to chapter">Peptide Fragmentation</a> it is essential to have a peptide or protein sequence defined. <em>mMass</em> therefore offers a simple internal <em>Sequence Editor</em> <span class="hotkey">[Tools → Sequence Editor]</span> <img src="figures/icon_mseq.png" alt="icon" class="icon" />. Sequence can be written manually or imported from ASCII, FASTA or <em>mMass</em> documents and any post-translational modification can be set to a single amino acid or to selected type. Some relevant sequence information are shown in the module control panel. There are also three additional tools available for sequence filtering, converting and searching of a sub-sequence by specified mass or by sequence pattern using regular expression syntax.</p>
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<img src="figures/mseq_layout.png" alt="sequence editor" />
<p>Sequence editor.</p>
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<h3 id="ch-edit">Sequence editing</h3>
<p>You can write your sequence manually or import from ASCII, FASTA and <em>mMass</em> documents <span class="hotkey">[Sequence → Import Sequence…]</span> <img src="figures/icon_imp_seq.png" alt="icon" class="icon" />. The editor automatically checks validity of your input and does not allow you to write or import any non-amino acid character to sequence window. When the sequence is imported or copied from clipboard some characters are removed without any notice (like whitespaces etc.). If the sequence contains other non-valid characters, these are removed too and shown in a warning dialog. This filtering is especially useful when you copy/paste your sequence from the internet sources where numbers are also included.</p>
<h3 id="ch-modifications">Modifications</h3>
<p>Any post-translational modification can be set to a single amino acid or to selected type <span class="hotkey">[Sequence → Modifications…]</span> <img src="figures/icon_modif.png" alt="icon" class="icon" />. There is currently a list of about 90 pre-defined modifications (according to <a href="http://www.unimod.org/" title="protein modifications for mass spectrometry">UNIMOD</a> website); others can be simply defined <span class="hotkey">[Config → Modifications…]</span>.</p>
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<img src="figures/mseq_modifs.png" alt="modifications dialog" />
<p>Modifications dialog.</p>
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<h3 id="ch-convert">Sequence Converter</h3>
<p>As a part of the <em>Sequence Editor</em> there is a simple <em>Sequence Converter</em> also available <span class="hotkey">[Tools → Sequence Converter…]</span>. Using this converter you can easily convert your sequence from 3-letter to 1-letter representation, filter non-amino acid character or convert a sequence from DNA or RNA to amino acids.</p>
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<img src="figures/mseq_convert.png" alt="sequence converter dialog" />
<p>Sequence converter dialog.</p>
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<h3 id="ch-searchmass">Search for Mass</h3>
<p>Using the <em>Search for Mass</em> tool <span class="hotkey">[Sequence → Search for Mass…]</span> <img src="figures/icon_sr_mass.png" alt="icon" class="icon" /> you can search your sequence for any peptide of specified mass. This tool is very useful for identification of the peaks resulting from non-specific cleavage of protein.</p>
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<img src="figures/mseq_search_mass.png" alt="search for mass dialog" />
<p>Search for mass dialog.</p>
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<h3 id="ch-searchseq">Search for Sequence</h3>
<p>Using the <em>Search for Sequence</em> tool <span class="hotkey">[Sequence → Search for Sequence…]</span> <img src="figures/icon_sr_seq.png" alt="icon" class="icon" /> you can search your sequence for any specified pattern. To define a pattern you can write some sub-sequence or regular expression syntax can be used.</p>
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<img src="figures/mseq_search_seq.png" alt="search for sequence dialog" />
<p>Search for sequence dialog.</p>
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<li><a href="mproc.html" title="Calibration, crop..."><span>Data processing</span></a></li>
<li><a href="mseq.html" title="Sequence editting, modifications, search for mass..."><span>Sequence editor</span></a></li>
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