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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 #include <OpenMS/KERNEL/Peak2D.h>
42 
43 namespace OpenMS
44 {
45  class IsobaricQuantitationMethod;
46  class ConsensusMap;
47  class ConsensusFeature;
48 
70  class OPENMS_DLLAPI IsobaricChannelExtractor :
71  public DefaultParamHandler
72  {
73 public:
79  explicit IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method);
80 
83 
86 
93  void extractChannels(const PeakMap& ms_exp_data, ConsensusMap& consensus_map);
94 
95 private:
103  struct PuritySate_
104  {
109 
114 
120  PuritySate_(const PeakMap& targetExp);
121 
127  void advanceFollowUp(const double rt);
128 
134  bool followUpValid(const double rt);
135  };
136 
139 
142 
145 
148 
151 
154 
157 
160 
163 
166 
168  void registerChannelsInOutputMap_(ConsensusMap& consensus_map);
169 
176  bool isValidPrecursor_(const Precursor& precursor) const;
177 
184  bool hasLowIntensityReporter_(const ConsensusFeature& cf) const;
185 
193  double computePrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PuritySate_& pState) const;
194 
202  double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PeakMap::SpectrumType& precursor_spec) const;
203 
211  {
212  for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
213  {
214  if (!it->getActivationMethods().empty()) return Precursor::NamesOfActivationMethod[*(it->getActivationMethods().begin())];
215  }
216  return "";
217  }
218 
219 
220 protected:
222  void setDefaultParams_();
223 
225  void updateMembers_();
226  };
227 } // namespace
228 
229 #endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICCHANNELEXTRACTOR_H
const PeakMap & baseExperiment
reference to the experiment to analyze
Definition: IsobaricChannelExtractor.h:113
A more convenient string class.
Definition: String.h:57
Precursor meta information.
Definition: Precursor.h:58
Peak2D::IntensityType min_reporter_intensity_
Minimum reporter ion intensity to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:153
bool remove_low_intensity_quantifications_
Flag if complete quantification should be discarded if a single reporter ion has an intensity below t...
Definition: IsobaricChannelExtractor.h:156
double max_precursor_isotope_deviation_
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the i...
Definition: IsobaricChannelExtractor.h:162
String selected_activation_
Used to select only specific types of spectra for the channel extraction.
Definition: IsobaricChannelExtractor.h:141
Small struct to capture the current state of the purity computation.
Definition: IsobaricChannelExtractor.h:103
A container for consensus elements.
Definition: ConsensusMap.h:72
double min_precursor_purity_
Minimum precursor purity to accept the spectrum for quantitation.
Definition: IsobaricChannelExtractor.h:159
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
PeakMap::ConstIterator followUpScan
Iterator pointing to the potential follow up MS1 scan.
Definition: IsobaricChannelExtractor.h:108
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:85
String getActivationMethod_(const PeakMap::SpectrumType &s) const
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.
Definition: IsobaricChannelExtractor.h:210
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Definition: IsobaricChannelExtractor.h:70
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Peak2D::CoordinateType reporter_mass_shift_
Allowed deviation between the expected and observed reporter ion m/z.
Definition: IsobaricChannelExtractor.h:144
bool keep_unannotated_precursor_
Flag if precursor with missing intensity value or missing precursor spectrum should be included or no...
Definition: IsobaricChannelExtractor.h:150
PeakMap::ConstIterator precursorScan
Iterator pointing to the potential MS1 precursor scan.
Definition: IsobaricChannelExtractor.h:106
Peak2D::IntensityType min_precursor_intensity_
Minimum intensity of the precursor to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:147
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:118
bool interpolate_precursor_purity_
Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan.
Definition: IsobaricChannelExtractor.h:165
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:55
const IsobaricQuantitationMethod * quant_method_
The used quantitation method (itraq4plex, tmt6plex,..).
Definition: IsobaricChannelExtractor.h:138
bool hasFollowUpScan
Indicates if a follow up scan was found.
Definition: IsobaricChannelExtractor.h:111
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:65

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:01 using doxygen 1.8.13