This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More...
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
Public Member Functions | |
| PeakPickerHiRes () | |
| Constructor. | |
| virtual | ~PeakPickerHiRes () |
| Destructor. | |
| template<typename PeakType > | |
| void | pick (const MSSpectrum< PeakType > &input, MSSpectrum< PeakType > &output) const |
| Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. | |
| template<typename PeakType > | |
| void | pickExperiment (const MSExperiment< PeakType > &input, MSExperiment< PeakType > &output) const |
| Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. | |
Protected Member Functions | |
| void | updateMembers_ () |
Protected Attributes | |
| double | signal_to_noise_ |
Detailed Description
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width.
This peak-picking algorithm detects ion signals in raw data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline.
So far, this peak picker was mainly tested on high resolution data. With appropriate preprocessing steps (e.g. noise reduction and baseline subtraction), it might be also applied to low resolution data.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| signal_to_noise | float | 1 | min: 0 | Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!) |
| ms1_only | string | false | true, false | If true, peak picking is only applied to MS1 scans. Other scans are copied to the output without changes. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
- Note:
- The peaks must be sorted according to ascending m/z!
Constructor & Destructor Documentation
| PeakPickerHiRes | ( | ) |
Constructor.
| virtual ~PeakPickerHiRes | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| void pick | ( | const MSSpectrum< PeakType > & | input, | |
| MSSpectrum< PeakType > & | output | |||
| ) | const [inline] |
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum.
References MSSpectrum< PeakT >::clear(), MSSpectrum< PeakT >::getMSLevel(), MSSpectrum< PeakT >::getName(), MSSpectrum< PeakT >::getRT(), SignalToNoiseEstimator< Container >::getSignalToNoise(), SignalToNoiseEstimator< Container >::init(), OpenMS::Constants::k, SpectrumSettings::PEAKS, Peak2D::setIntensity(), MSSpectrum< PeakT >::setMSLevel(), Peak2D::setMZ(), MSSpectrum< PeakT >::setName(), MSSpectrum< PeakT >::setRT(), and SpectrumSettings::setType().
| void pickExperiment | ( | const MSExperiment< PeakType > & | input, | |
| MSExperiment< PeakType > & | output | |||
| ) | const [inline] |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.
References MSExperiment< PeakT, ChromatogramPeakT >::clear().
| void updateMembers_ | ( | ) | [protected] |
Member Data Documentation
double signal_to_noise_ [protected] |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:57 using doxygen 1.7.1 |