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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 | Data Processing Tools</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>Data Processing Tools</span></h2>
<h3 id="ch-calibint">Internal calibration</h3>
<p>To (re)calibrate data using internal calibration standard choose <em>Internal Calibration</em> <span class="hotkey">[Processing → Internal Calibration…]</span> <img src="figures/icon_calib_int.png" alt="icon" class="icon" /> from application main menu. In the top right peaklist click to the peak you want to use and type reference value. List of predefined reference points can be also used. Double-clicking the peak, the <em>skip/use</em> value can be changed.</p>
<p>Calibration type can be set to either <em>Linear fitting</em> or <em>Quadratic fitting</em>. Using <em>Calculate</em> button, relevant constants are calculated and calibration plot can than be seen (<em>View plot</em> button). Press <em>Apply</em> button to recalculate spectrum and/or peaklist data.</p>
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<img src="figures/mproc_calib_int.png" alt="internal calibration dialog" />
<p>Internal calibration dialog.</p>
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<h3 id="ch-calibstat">Statistical calibration</h3>
<p><em>Statistical Calibration</em> <span class="hotkey">[Processing → Statistical calibration…]</span> <img src="figures/icon_calib_stat.png" alt="icon" class="icon" />, sometimes called "self-calibration" is a special method for peptide mass spectra only. It does not need any external reference points since it is based on the fact that monoisotopic masses of peptides are distributed in a very regular way and decimal fraction of peptide mass can be calculated with sufficient accuracy just by multiplying their integral part by factor 1.00048. These calculated values are then used as reference points. Even for this method, linear or quadratic fitting can be used. It is highly recommended to check calibration plot before applying calculation to data.</p>
<p>This calibration type, however, has two main limitations summarised further on. It can be used for peptides only; any non-peptide contamination or modification have disturbing effect and this method can not be used. Double-clicking the peak in list, <em>skip/use</em> value can be changed. Using statistical calibration, only small mass shifts within 0.5 Da can be corrected.</p>
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<img src="figures/mproc_calib_stat.png" alt="statistical calibration dialog" />
<p>Statistical calibration dialog.</p>
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<p>Calibration plot.</p>
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<h3 id="ch-crop">Spectrum crop</h3>
<p>A simple <em>Crop Spectrum</em> tool <span class="hotkey">[Processing → Crop Spectrum…]</span> can be used to choose relevant part of spectrum and/or peaklist and discard the rest. This feature is useful especially in cases of MALDI-TOF MS data to delete unnecessary parts like matrix clusters etc.</p>
<h3 id="ch-undo">Undo processing</h3>
<p>All of the above mentioned function can be undone if the result is not what you want. Simply choose <em>Undo Processing</em> <span class="hotkey">[Processing → Undo Processing]</span> from main menu.</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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<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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