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IsobaricChannelExtractor.h
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34 
35 #ifndef OPENMS_ANALYSIS_QUANTITATION_ISOBARICCHANNELEXTRACTOR_H
36 #define OPENMS_ANALYSIS_QUANTITATION_ISOBARICCHANNELEXTRACTOR_H
37 
39 
41 
44 
45 namespace OpenMS
46 {
52  class OPENMS_DLLAPI IsobaricChannelExtractor :
53  public DefaultParamHandler
54  {
55 public:
61  IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method);
62 
65 
68 
75  void extractChannels(const MSExperiment<Peak1D>& ms_exp_data, ConsensusMap& consensus_map);
76 
77 private:
80 
83 
86 
89 
92 
95 
98 
101 
104 
106  void registerChannelsInOutputMap_(ConsensusMap& consensus_map);
107 
114  bool isValidPrecursor_(const Precursor& precursor) const;
115 
122  bool hasLowIntensityReporter_(const ConsensusFeature& cf) const;
123 
131  DoubleReal computePrecursorPurity_(const MSExperiment<>::ConstIterator& ms2_spec, const MSExperiment<>::ConstIterator& precursor) const;
132 
142  DoubleReal sumPotentialIsotopePeaks_(const MSExperiment<Peak1D>::ConstIterator& precursor, const Peak1D::CoordinateType& lower_mz_bound, const Peak1D::CoordinateType& upper_mz_bound, Peak1D::CoordinateType theoretical_mz, const Peak1D::CoordinateType isotope_offset) const;
143 
144 protected:
146  void setDefaultParams_();
147 
149  void updateMembers_();
150  };
151 } // namespace
152 
153 #endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICCHANNELEXTRACTOR_H
Real IntensityType
Intensity type.
Definition: Peak2D.h:63
A more convenient string class.
Definition: String.h:56
Precursor meta information.
Definition: Precursor.h:56
Peak2D::IntensityType min_reporter_intensity_
Minimum reporter ion intensity to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:94
bool remove_low_intensity_quantifications_
Flag if complete qunatification should be discarded if a single reporter ion has an intensity below t...
Definition: IsobaricChannelExtractor.h:97
String selected_activation_
Used to select only specific types of spectra for the channel extraction.
Definition: IsobaricChannelExtractor.h:82
DoubleReal min_precursor_purity_
Minimum precursor purity to accept the spectrum for quantitation.
Definition: IsobaricChannelExtractor.h:100
A container for consensus elements.
Definition: ConsensusMap.h:60
DoubleReal max_precursor_isotope_deviation_
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the i...
Definition: IsobaricChannelExtractor.h:103
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Definition: IsobaricChannelExtractor.h:52
Peak2D::CoordinateType reporter_mass_shift_
Allowed deviation between the expected and observed reporter ion m/z.
Definition: IsobaricChannelExtractor.h:85
bool keep_unannotated_precursor_
Flag if precursor with missing intensity value or missing precursor spectrum should be included or no...
Definition: IsobaricChannelExtractor.h:91
Peak2D::IntensityType min_precursor_intensity_
Minimum intensity of the precursor to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:88
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:103
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:51
const IsobaricQuantitationMethod * quant_method_
The used quantitation method (itraq4plex, tmt6plex,..).
Definition: IsobaricChannelExtractor.h:79
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:59

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5