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OpenMS
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A tool for peak detection in profile data. Executes the peak picking with the algorithm described in described in Lange et al. (2006) Proc. PSB-06.
pot. predecessor tools | → PeakPickerWavelet → | pot. successor tools |
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BaselineFilter | any tool operating on MS peak data (in mzML format) | |
NoiseFilterGaussian | ||
NoiseFilterSGolay |
The conversion of the ''raw'' ion count data acquired by the machine into peak lists for further processing is usually called peak picking. The choice of the algorithm should mainly depend on the resolution of the data. As the name implies, the high_res algorithm is fit for high resolution data whereas in case of low-resoluted data the wavelet algorithm offers the ability to resolve highly convoluted and asymmetric signals, separation of overlapping peaks and nonlinear optimization.
TOPP_example_signalprocessing_parameters is explained in the TOPP tutorial.
The command line parameters of this tool are:
INI file documentation of this tool:
For the parameters of the algorithm section see the algorithm documentation:
PeakPickerCWT
In the following table you, can find example values of the most important algorithm parameters for different instrument types.
These parameters are not valid for all instruments of that type, but can be used as a starting point for finding suitable parameters.
Q-TOF | LTQ Orbitrap | |
signal_to_noise | 2 | 0 |
peak_width ("wavelet" only) | 0.1 | 0.012 |
In order to impove the results of the peak detection on low resolution data NoiseFilterSGolay or NoiseFilterGaussian and BaselineFilter can be applied. For high resolution data this is not necessary.