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<div class="title">Calibration </div> </div>
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<div class="textblock"><p>We offer two calibration methods: an internal and an external calibration. Both can handle peak data as well as profile data. If you want to calibrate profile data, a peak picking step is necessary, the important parameters can be set via the ini-file. If you have already picked data, don't forget the '<code>-peak_data</code>' flag.</p>
<p>The external calibration (<b>TOFCalibration</b>) is used to convert flight times into m/z- values with the help of external calibrant spectra containing e.g. a polymer like polylysine. For the calibrant spectra, the calibration constants the machine uses need to be known as well as the expected masses. Then a quadratic function is fitted to convert the flight times into m/z-values.</p>
<p>The internal calibration (<b>InternalCalibration</b>) uses reference masses in the spectra to correct the m/z-values using a linear function.</p>
<p>In a typical setting one would first pick the TOF-data, then perform the TOFCalibration and then the InternalCalibration: </p>
<div class="fragment"><div class="line">PeakPickerWavelet -in raw_tof.mzML -out picked_tof.mzML -ini pp.ini</div>
<div class="line">TOFCalibration -in picked_tof.mzML -out picked.mzML -ext_calibrants ext_cal.mzML</div>
<div class="line"> -ref_masses ext_cal_masses</div>
<div class="line"> -tof_const tof_conv_consts -peak_data</div>
<div class="line">InternalCalibration -in picked.mzML -out picked_calibrated.mzML</div>
<div class="line"> -ref_masses internal_calibrant_masses -peak_data</div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5</font></TD>
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