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<meta name="author" content="Created by Martin Strohalm PhD; www.biographics.cz" />
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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 | Application Layout</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>Application Layout</span></h2>
<p>The application layout consists of several parts. Beside common parts like toolbar with selected features or statusbar showing current document information, main part is the document frame. On left hand side there is a <a href="mpeak.html" title="go to chapter">Peaklist Panel</a> - a list of all labeled peaks with values of <em>m/z</em>, <em>intensities</em> and <em>annotations</em>. Rest of the document frame covers currently active module with corresponding control panel on right hand side. In some cases, it can be very helpful to switch the document window to horizontal mode, with the peaklist panel bottom <span class="hotkey">[Config → Peaklist Bottom]</span> <img src="figures/icon_pkl_bottom.png" alt="icon" class="icon" /> or to remove the panel completely <span class="hotkey">[Config → Show Peaklist]</span> <img src="figures/icon_pkl_show.png" alt="icon" class="icon" /> to see the module frame only.</p>
<div class="images">
<img src="figures/mmass_layout.png" alt="main mMass layout" />
<p>Main application layout.</p>
</div>
<h3 id="ch-menu">Main menu</h3>
<ul>
<li><em>File</em> - common functions like <a href="mdoc.html#ch-open" title="go to chapter">Open</a>, Close, <a href="mdoc.html#ch-export" title="go to chapter">Export</a> or <a href="mdoc.html#ch-print" title="go to chapter">Print</a> document.</li>
<li><em>Peaklist</em> - tools for <a href="mpeak.html#ch-select" title="go to chapter">peak selection</a>, <a href="mpeak.html#ch-add" title="go to chapter">adding</a>, <a href="mpeak.html#ch-delete" title="go to chapter">removing</a>, <a href="mpeak.html#ch-edit" title="go to chapter">editing</a>, <a href="mpeak.html#ch-copy" title="go to chapter">copying</a> etc.</li>
<li><em>Spectrum</em> - tools for <a href="mspec.html#ch-label" title="go to chapter">peak labeling</a>, <a href="mspec.html#ch-compare" title="go to chapter">comparing multiple spectra</a>, <a href="mspec.html#ch-options" title="go to chapter">view options</a> etc.</li>
<li><em>Processing</em> - data processing tools like <a href="mproc.html#ch-calibint" title="go to chapter">(re)calibration</a> or <a href="mproc.html#ch-crop" title="go to chapter">spectrum crop</a>.</li>
<li><em>Matching</em> - tools for <a href="mmatch.html" title="go to chapter">matching of the data</a> generated in <a href="mcut.html" title="go to chapter">Protein Digest Tool</a>, <a href="mfrag.html" title="go to chapter">Peptide Fragmentation Tool</a> or the peklists from <a href="mcomp.html" title="go to chapter">Compare Peaklists Tool</a> to current spectrum.</li>
<li><em>Sequence</em> - tools for peptide/protein <a href="mseq.html" title="go to chapter">sequence editing</a> and <a href="mseq.html#ch-searchmass" title="go to chapter">searching</a>.</li>
<li><em>Tools</em> - main application tools.</li>
<li><em>Links</em> - links to the most popular on-line tools for mass spectrometry.</li>
<li><em>Config</em> - applications configuration tools.</li>
</ul>
<h3 id="ch-toolbar">Toolbar</h3>
<ul>
<li><img src="figures/icon_open.png" alt="icon" class="icon" /> <a href="mdoc.html#ch-open" title="go to chapter">Open Document</a> - open existing document.</li>
<li><img src="figures/icon_save.png" alt="icon" class="icon" /> <a href="mdoc.html#ch-save" title="go to chapter">Save Document</a> - save current document.</li>
<li><img src="figures/icon_close.png" alt="icon" class="icon" /> <em>Close Document</em> - close current document.</li>
<li><img src="figures/icon_prn_spec.png" alt="icon" class="icon" /> <a href="mdoc.html#ch-print" title="go to chapter">Print Spectrum</a> - print current spectrum view.</li>
<li><img src="figures/icon_prn_report.png" alt="icon" class="icon" /> <a href="mdoc.html#ch-print" title="go to chapter">Print Report</a> - print current peaklist and additional document information.</li>
<li><img src="figures/icon_docinfo.png" alt="icon" class="icon" /> <a href="mdoc.html#ch-info" title="go to chapter">Document Information</a> - current document summary and user notes.</li>
</ul>
<ul>
<li><img src="figures/icon_mspec.png" alt="icon" class="icon" /> <a href="mspec.html" title="go to chapter">Mass Spectrum</a> - spectrum viewer/analyser tool.</li>
<li><img src="figures/icon_mseq.png" alt="icon" class="icon" /> <a href="mseq.html" title="go to chapter">Sequence Editor</a> - sequence editing tool.</li>
<li><img src="figures/icon_mcut.png" alt="icon" class="icon" /> <a href="mcut.html" title="go to chapter">Protein Digest</a> - protein digest simulation.</li>
<li><img src="figures/icon_mfrag.png" alt="icon" class="icon" /> <a href="mfrag.html" title="go to chapter">Peptide Fragmentation</a> - peptide fragmentation simulation.</li>
<li><img src="figures/icon_mdiff.png" alt="icon" class="icon" /> <a href="mdiff.html" title="go to chapter">Check Differences</a> - search for specified differences between all the peaks.</li>
<li><img src="figures/icon_mcomp.png" alt="icon" class="icon" /> <a href="mcomp.html" title="go to chapter">Compare Peaklists</a> - compare multiple peaklists with current document.</li>
</ul>
<ul>
<li><img src="figures/icon_lbl_point.png" alt="icon" class="icon" /> <a href="mspec.html#ch-label" title="go to chapter">Label Point</a> - label selected point in the spectrum.</li>
<li><img src="figures/icon_lbl_peak.png" alt="icon" class="icon" /> <a href="mspec.html#ch-label" title="go to chapter">Label Peak</a> - label selected peak in the spectrum.</li>
<li><img src="figures/icon_lbl_del.png" alt="icon" class="icon" /> <a href="mspec.html#ch-delete" title="go to chapter">Delete Label</a> - delete selected peaks in the spectrum.</li>
<li><img src="figures/icon_distances.png" alt="icon" class="icon" /> <a href="mspec.html#ch-distances" title="go to chapter">Distance Measurement</a> - measure distances in the spectrum.</li>
</ul>
<ul>
<li><img src="figures/icon_calib_int.png" alt="icon" class="icon" /> <a href="mproc.html#ch-calibint" title="go to chapter">Internal Calibration</a> - calibrate data using internal calibration points.</li>
<li><img src="figures/icon_calib_stat.png" alt="icon" class="icon" /> <a href="mproc.html#ch-calibstat" title="go to chapter">Statistical Calibration</a> - calibrate data using statistical calibration.</li>
</ul>
<ul>
<li><img src="figures/icon_add_peak.png" alt="icon" class="icon" /> <a href="mpeak.html#ch-add" title="go to chapter">Add Peak</a> - add new peak label manually.</li>
<li><img src="figures/icon_clear_annots.png" alt="icon" class="icon" /> <a href="mpeak.html#ch-clear" title="go to chapter">Clear All Annotations</a> - clear all annotations in current peaklist.</li>
<li><img src="figures/icon_del_peaks.png" alt="icon" class="icon" /> <a href="mpeak.html#ch-delete" title="go to chapter">Delete All Peaks</a> - delete all peaks in current peaklist.</li>
</ul>
<ul>
<li><img src="figures/icon_match.png" alt="icon" class="icon" /> <a href="mmatch.html" title="go to chapter">Match Data</a> - match data from active module to current peaklist.</li>
<li><img src="figures/icon_matchinfo.png" alt="icon" class="icon" /> <a href="mmatch.html#ch-matchinfo" title="go to chapter">Match Info</a> - show summary of the latest match.</li>
<li><img src="figures/icon_annotate.png" alt="icon" class="icon" /> <a href="mmatch.html#ch-annotate" title="go to chapter">Annotate Peaklist</a> - annotate current peaklist based on the latest match.</li>
</ul>
<ul>
<li><img src="figures/icon_mascot_pmf.png" alt="icon" class="icon" /> <a href="mmascot.html" title="go to chapter">Mascot PMF Search</a> - send current peaklist to <a href="http://www.matrixscience.com/search_form_select.html" title="www.matrixscience.com">Mascot server</a>.</li>
<li><img src="figures/icon_mascot_sq.png" alt="icon" class="icon" /> <a href="mmascot.html" title="go to chapter">Mascot Sequence Query</a> - send current peaklist to <a href="http://www.matrixscience.com/search_form_select.html" title="www.matrixscience.com">Mascot server</a>.</li>
<li><img src="figures/icon_mascot_mis.png" alt="icon" class="icon" /> <a href="mmascot.html" title="go to chapter">Mascot MS/MS Ion Search</a> - send current peaklist to <a href="http://www.matrixscience.com/search_form_select.html" title="www.matrixscience.com">Mascot server</a>.</li>
</ul>
<ul>
<li><img src="figures/icon_modif.png" alt="icon" class="icon" /> <a href="mseq.html#ch-modifications" title="go to chapter">Modifications</a> - set modifications to current peptide/protein sequence.</li>
<li><img src="figures/icon_sr_mass.png" alt="icon" class="icon" /> <a href="mseq.html#ch-searchmass" title="go to chapter">Search for Mass</a> - search current sequence for specified peptide mass.</li>
<li><img src="figures/icon_sr_seq.png" alt="icon" class="icon" /> <a href="mseq.html#ch-searchseq" title="go to chapter">Search for Sequence</a> - search current sequence for specified sub-sequence.</li>
<li><img src="figures/icon_imp_seq.png" alt="icon" class="icon" /> <a href="mseq.html#ch-edit" title="go to chapter">Import Sequence</a> - import sequence from file.</li>
</ul>
<ul>
<li><img src="figures/icon_mono.png" alt="icon" class="icon" /> <em>Monoisotopic Mass</em> - use monoisotopic mass for all mMass calculations.</li>
<li><img src="figures/icon_average.png" alt="icon" class="icon" /> <em>Average Mass</em> - use average mass for all mMass calculations.</li>
<li><img src="figures/icon_tolerance.png" alt="icon" class="icon" /> <a href="mmatch.html#ch-tolerance" title="go to chapter">Tolerance</a> - set tolerance value and units for data matching.</li>
</ul>
<ul>
<li><img src="figures/icon_pkl_show.png" alt="icon" class="icon" /> <a href="mpeak.html" title="go to chapter">Show Peaklist</a> - show/hide peaklist panel.</li>
<li><img src="figures/icon_pkl_bottom.png" alt="icon" class="icon" /> <a href="mpeak.html" title="go to chapter">Peaklist Bottom</a> - switch to horizontal layout with peaklist bottom.</li>
<li><img src="figures/icon_preferences.png" alt="icon" class="icon" /> <em>Preferences</em> - application prefernces.</li>
</ul>
<h3 id="ch-stausbar">Statusbar</h3>
<p>Selected information about current document are shown in application statusbar.</p>
<div class="images">
<img src="figures/mmass_statusbar.png" alt="statusbar" />
<p>Application statusbar.</p>
</div>
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<h2><span>Main menu</span></h2>
<ul>
<li><a href="/" title="latest news"><span>News</span></a></li>
<li><a href="features.html" title="mMass main features"><span>Features</span></a></li>
<li><a href="download.html" title="download source files or binary distribution"><span>Download</span></a></li>
<li><href=index.html title="detailed mMass description"><span>Documentation</span></a></li>
<li><a href="message.html" title="send bug report, function request etc."><span>Contact</span></a></li>
</ul>
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<div id="chapters" class="panel">
<h2><span>Chapters</span></h2>
<ul>
<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>
<li><a href="mmascot.html" title="Mascot search tools..."><span>Mascot tools</span></a></li>
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