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<meta name="description" content="Program mMass presents an open source package of simple tools for mass spectrometric data analysis. It consist of several modules and tools for protein sequence handling and mass spectrum interpretation with focus on common proteomic tasks." lang="en" />
<title>mMass - Open Source MS Tool | Documentation | Document Basics</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>Document Basics</span></h2>
<h3 id="ch-new">Make new document</h3>
<p>One of the popular features of <em>mMass</em> is the ability to open a blank document <span class="hotkey">[File → New Document]</span> and create peaklist manually. This feature is particularly useful in those cases where raw data is unavailable, and the user has only a spectrum image or printed list of labelled peaks. Such is often the situation in laboratories that do not have their own instruments and have to send their samples to other laboratories. This feature gives such laboratories the chance to analyse the data themselves. Once the peaklist is <a href="mpeak.html#ch-add" title="go to chapter">prepared</a>, all interpretation tools can be used.</p>
<h3 id="ch-open">Open existing document</h3>
<p>To open existing document choose <em>Open…</em> <span class="hotkey">[File → Open…]</span> <img src="figures/icon_open.png" alt="icon" class="icon" />. You can also choose from <em>Recent Files</em> <span class="hotkey">[File → Recent Files]</span> or drag your file to application window (Windows version only).</p>
<h3 id="ch-save">Save current document</h3>
<p>To save current document to <em>mMass</em> format choose <em>Save</em> <span class="hotkey">[File → Save]</span> <img src="figures/icon_save.png" alt="icon" class="icon" /> or <em>Save As…</em> <span class="hotkey">[File → Save As…]</span>. If you want to save your data to different format choose one of the <em><a href="#ch-export" title="go to chapter">Export</a></em> options <span class="hotkey">[File → Export]</span>.</p>
<h3 id="ch-print">Print spectrum or sample report</h3>
<p>There are to options in <em>mMass</em> to print your data. Choose <em>Print Spectrum</em> <span class="hotkey">[File → Print → Spectrum]</span> <img src="figures/icon_prn_spec.png" alt="icon" class="icon" /> to print current spectrum view or <em>Print Report</em> <span class="hotkey">[File → Print → Report]</span> <img src="figures/icon_prn_report.png" alt="icon" class="icon" /> to print sample report containing annotated peaklist and some additional information about sample measurement and peptide/protein sequence as well.</p>
<h3 id="ch-export">Export data or image</h3>
<p>From any opened document you can easily export data or spectrum image to several formats.</p>
<p>To export spectrum data choose <em>Spectrum Data…</em> <span class="hotkey">[File → Export → Spectrum Data…]</span>. This option saves current spectrum points to simple ASCII file containing <em>m/z</em> and <em>intensity</em> pairs.</p>
<p>To export spectrum image choose <em>Spectrum Image…</em> <span class="hotkey">[File → Export → Spectrum Image…]</span>. This option saves current spectrum view to <acronym title="Portable Network Graphics">PNG</acronym> image. User can specify the image size in pixels.</p>
<p>To export peaklist data choose <em>Peaklist…</em> <span class="hotkey">[File → Export → Peaklist…]</span>. This option saves current peaklist to simple ASCII file containing <em>m/z</em>, <em>intensity</em> and <em>annotations</em>. In application preferences you can specify which values to export and ASCII delimiter as well.</p>
<h3 id="ch-info">Document information</h3>
<p>Dialog window <em>Document Information</em> <span class="hotkey">[File → Information]</span> <img src="figures/icon_docinfo.png" alt="icon" class="icon" /> allows you to add additional notes and it shows some basic information about current document. You can also specify measurement details like <em>Date</em>, <em>Operator name</em>, <em>Contact</em>, <em>Institution</em> and <em>Instrument type</em>. On <em>Notes</em> tab, there is a space for some notes. These information, however, are saved in <em>mMass</em> document format only.</p>
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<p>Document information dialog.</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>
<li><a href="mmass.html" title="Layout, menubar, toolbar, statusbar..."><span>Application layout</span></a></li>
<li><a href="mdoc.html" title="Open, save, print, export, info..."><span>Document basics</span></a></li>
<li><a href="mspec.html" title="Spectrum manipulations, peaks labelling, comparison..."><span>Spectrum viewer</span></a></li>
<li><a href="mpeak.html" title="Peaklist options..."><span>Peaklist panel</span></a></li>
<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>
<li><a href="mcut.html" title="In silicio protein digest..."><span>Protein digest</span></a></li>
<li><a href="mfrag.html" title="In silicio peptide fragmentation..."><span>Peptide fragmentation</span></a></li>
<li><a href="mdiff.html" title="Check differences among all the peaks in peaklist..."><span>Check differences</span></a></li>
<li><a href="mcomp.html" title="Compare multiple peaklists..."><span>Compare peaklists</span></a></li>
<li><a href="mmatch.html" title="Match teoretical data to spectrum..."><span>Data matching</span></a></li>
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