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<title>mMass - Open Source MS Tool | Documentation | Spectrum Viewer/Analyser</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>Spectrum Viewer/Analyser</span></h2>
<p>The core of the <em>mMass</em> is <em>Mass Spectrum</em> module <span class="hotkey">[Tools → Mass Spectrum]</span> <img src="figures/icon_mspec.png" alt="icon" class="icon" />. This module is not a spectrum viewer only but provides some functions and tools for peaks labeling and spectrum analysis. The module layout consists of main spectrum window and control panel. In the control panel some additional information can bee seen, such as current cursor position <em>(Cursor Info)</em> or list of loaded spectra <em>(Loaded Spectra)</em>, as well as a tool for peak searching <em>(Find Point)</em> and peak labeling setup <em>(Peak Picking)</em>.</p>
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<img src="figures/mspec_layout.png" alt="mass spectrum viewer/analyser" />
<p>Mass spectrum viewer/analyser.</p>
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<h3 id="ch-navigation">Spectrum navigation</h3>
<p>Since most time in data interpretation is spent manipulating spectra (moving, shifting, scaling, zooming etc.), we aimed to make these functions as easy and user friendly as possible.</p>
<ul>
<li><em>Scroll spectrum</em> - to scroll the spectrum use mouse scroll, <span class="hotkey">[Left/Right arrow]</span>, <span class="hotkey">[PageUp/PageDown]</span> or drag x-axis with left-mouse button pressed. To jump to end of the spectrum quickly, press <span class="hotkey">[Home/End]</span> button.</li>
<li><em>Zoom spectrum</em> - to zoom a part of the spectrum select desired area with right-mouse button pressed.</li>
<li><em>Scale x-axis</em> - to continuously scale x-axis drag the axis with right-mouse button pressed, use mouse scroll with <span class="hotkey">[Ctrl + Alt]</span> pressed or use <span class="hotkey">[Ctrl + arrow]</span>.</li>
<li><em>Scale y-axis</em> - to continuously scale y-axis drag the axis with right-mouse button pressed, use mouse scroll with <span class="hotkey">[Shift]</span> pressed or use <span class="hotkey">[Up/Down arrow]</span>.</li>
<li><em>Axis full range</em> - to discard any zoom or shift double-click on appropriate axis.</li>
<li><em>Spectrum full range</em> - to see whole range of the spectrum double-click on spectrum with right-mouse button or press <span class="hotkey">[Ctrl + Home]</span>.</li>
<li><em>User defined range</em> - to specify x-axis and y-axis range manually press <span class="hotkey">[Enter]</span> button and set the values in <em>Spectrum Range</em> dialog.</li>
<li><em>View memory</em> - to go to the previous view of the spectrum use <span class="hotkey">[Backspace]</span> button. This 50-steps view memory is especially useful during peaks labeling to temporarily zoom the peak.</li>
</ul>
<h3 id="ch-options">View options</h3>
<p>Some of the parameters of spectrum view can be set in <em>Spectrum View Options</em> dialog <span class="hotkey">[Spectrum → View Options]</span>. These parameters, however, are used for current document only. To set default view options use application preferences.</p>
<ul>
<li><em>Show label ticks</em> - show vertical line representing peak intensity.</li>
<li><em>Show labels</em> - show peak label.</li>
<li><em>Show annotations</em> - show peak annotation too.</li>
<li><em>Label angle</em> - set label angle to 0, 45 or 90°.</li>
</ul>
<ul>
<li><em>Show grid</em> - show spectrum grid.</li>
<li><em>Show legend</em> - show names of loaded spectra.</li>
<li><em>Show position bar</em> - show current position within whole spectrum.</li>
<li><em>Show gel view</em> - show spectrum represented as a "gel".</li>
<li><em>Gel height</em> - set "gel" height in pixels.</li>
</ul>
<ul>
<li><em>Show cursor tracker</em> - show vertical line representing current cursor position.</li>
<li><em>Show cursor position</em> - show <em>m/z</em> value of current cursor position directly.</li>
<li><em>Show cursor distance</em> - show measured difference between two points directly.</li>
</ul>
<div class="images">
<img src="figures/mspec_view_opt.png" alt="spectrum view options" />
<img src="figures/mspec_view_lbl.png" alt="label view options" />
<p>Spectrum view options.</p>
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<h3 id="ch-label">Peaks labeling</h3>
<p>There are two methods available for peak labelling - <em>Label Point</em> <span class="hotkey">[Spectrum → Label Point]</span> <img src="figures/icon_lbl_point.png" alt="icon" class="icon" />and <em>Label Peak</em> <span class="hotkey">[Spectrum → Label Peak]</span> <img src="figures/icon_lbl_peak.png" alt="icon" class="icon" />.</p>
<p><em>Label Point</em> is the simplest method for peaks labeling. Using left-mouse button, selected point in the spectrum is labeled. Intensity value is interpolated from neighboring spectrum points.</p>
<p>Using left-mouse button and <em>Label Peak</em> tool, selected peak is labeled by centroid method with user definable height. The <em>Height</em> value can be set in the control panel. Intensity value is interpolated from neighboring spectrum points.</p>
<h3 id="ch-delete">Delete label</h3>
<p>Labels can be deleted using left-mouse button and <em>Delete Label</em> tool <span class="hotkey">[Spectrum → Delete Label]</span> <img src="figures/icon_lbl_del.png" alt="icon" class="icon" /> or using <a href="mpeak.html#ch-delete" title="go to chapter">Peaklist Panel</a> tools.</p>
<h3 id="ch-compare">Compare multiple spectra</h3>
<p>To check any differences between mass spectra effectively, up to 9 additional spectra can be loaded simultaneously to currently opened document. To add spectrum, in the control panel press <em>Add Spectrum</em> button, use application menu <span class="hotkey">[Spectrum → Add to Compare…]</span> or drag spectrum file to list of <em>Loaded Spectra</em> (Mac version only). By double-clicking in the name in the list, spectrum can be renamed or shifted on y-axis. Spectrum can be temporarily hidden or removed using the list context menu.</p>
<h3 id="ch-distances">Distance measurement</h3>
<p>One of the most common tasks in mass spectrum analysis is a distance measurement of two peaks. This can be easily done using left-mouse button and <em>Distance Measurement</em> tool <span class="hotkey">[Spectrum → Distance Measurement]</span> <img src="figures/icon_distances.png" alt="icon" class="icon" />. Measured distance is shown in the control panel and, if checked in the <a href="#ch-options" title="go to chapter">Spectrum View Options</a>, the value is shown directly at cursor position as well.</p>
<p>More complex distance analysis is provided in <a href="mdiff.html" title="go to chapter">Check Differences Tool</a>.</p>
<h3 id="ch-findpoint">Find point</h3>
<p>To quickly search for specified <em>m/z</em> value in the spectrum, <em>mMass</em> provides a <em>Find Point</em> tool, located in the control panel. Just specify the <em>m/z</em> value and press <span class="hotkey">[Enter]</span>. Spectrum zooming can be also specified in <em>Zoom</em> combo. Set <em>Current</em> to use current spectrum zoom.</p>
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