OpenMS
IsobaricChannelExtractor.h
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32 // $Authors: Stephan Aiche, Chris Bielow $
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34 
35 #pragma once
36 
38 #include <OpenMS/KERNEL/Peak2D.h>
41 
42 namespace OpenMS
43 {
44  class IsobaricQuantitationMethod;
45  class ConsensusMap;
46  class ConsensusFeature;
47 
69  class OPENMS_DLLAPI IsobaricChannelExtractor :
70  public DefaultParamHandler
71  {
72 public:
78  explicit IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method);
79 
82 
85 
92  void extractChannels(const PeakMap& ms_exp_data, ConsensusMap& consensus_map);
93 
94 private:
102  struct PuritySate_
103  {
108 
113 
119  PuritySate_(const PeakMap& targetExp);
120 
126  void advanceFollowUp(const double rt);
127 
133  bool followUpValid(const double rt) const;
134  };
135 
138 
141 
144 
147 
150 
153 
156 
159 
162 
165 
168 
175  bool isValidPrecursor_(const Precursor& precursor) const;
176 
184 
192  double computePrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PuritySate_& pState) const;
193 
201  double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PeakMap::SpectrumType& precursor_spec) const;
202 
210  {
211  for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
212  {
213  if (!it->getActivationMethods().empty()) return Precursor::NamesOfActivationMethod[*(it->getActivationMethods().begin())];
214  }
215  return "";
216  }
217 
218 
219 protected:
222 
224  void updateMembers_() override;
225  };
226 } // namespace
227 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:71
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Definition: IsobaricChannelExtractor.h:71
bool hasLowIntensityReporter_(const ConsensusFeature &cf) const
Checks whether the given ConsensusFeature contains a channel that is below the given intensity thresh...
double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator &ms2_spec, const PeakMap::SpectrumType &precursor_spec) const
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference...
bool interpolate_precursor_purity_
Flag if precursor purity will solely be computed based on the precursor scan (false),...
Definition: IsobaricChannelExtractor.h:164
const IsobaricQuantitationMethod * quant_method_
The used quantitation method (itraq4plex, tmt6plex,..).
Definition: IsobaricChannelExtractor.h:137
Peak2D::CoordinateType reporter_mass_shift_
Allowed deviation between the expected and observed reporter ion m/z.
Definition: IsobaricChannelExtractor.h:143
void extractChannels(const PeakMap &ms_exp_data, ConsensusMap &consensus_map)
Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map...
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:155
String getActivationMethod_(const PeakMap::SpectrumType &s) const
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.
Definition: IsobaricChannelExtractor.h:209
IsobaricChannelExtractor(const IsobaricQuantitationMethod *const quant_method)
C'tor to create a new channel extractor for the given quantitation method.
void setDefaultParams_()
implemented for DefaultParamHandler
double computePrecursorPurity_(const PeakMap::ConstIterator &ms2_spec, const PuritySate_ &pState) const
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the ...
double max_precursor_isotope_deviation_
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the i...
Definition: IsobaricChannelExtractor.h:161
IsobaricChannelExtractor & operator=(const IsobaricChannelExtractor &rhs)
Assignment operator.
IsobaricChannelExtractor(const IsobaricChannelExtractor &other)
Copy c'tor.
double min_precursor_purity_
Minimum precursor purity to accept the spectrum for quantitation.
Definition: IsobaricChannelExtractor.h:158
Peak2D::IntensityType min_reporter_intensity_
Minimum reporter ion intensity to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:152
String selected_activation_
Used to select only specific types of spectra for the channel extraction.
Definition: IsobaricChannelExtractor.h:140
bool isValidPrecursor_(const Precursor &precursor) const
Checks if the given precursor fulfills all constraints for extractions.
void updateMembers_() override
implemented for DefaultParamHandler
Peak2D::IntensityType min_precursor_intensity_
Minimum intensity of the precursor to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:146
bool keep_unannotated_precursor_
Flag if precursor with missing intensity value or missing precursor spectrum should be included or no...
Definition: IsobaricChannelExtractor.h:149
void registerChannelsInOutputMap_(ConsensusMap &consensus_map)
add channel information to the map after it has been filled
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:58
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:105
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
float IntensityType
Intensity type.
Definition: Peak2D.h:62
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:64
Precursor meta information.
Definition: Precursor.h:61
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:106
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Small struct to capture the current state of the purity computation.
Definition: IsobaricChannelExtractor.h:103
void advanceFollowUp(const double rt)
Searches the experiment for the next MS1 spectrum with a retention time bigger then rt.
const PeakMap & baseExperiment
reference to the experiment to analyze
Definition: IsobaricChannelExtractor.h:112
PeakMap::ConstIterator precursorScan
Iterator pointing to the potential MS1 precursor scan.
Definition: IsobaricChannelExtractor.h:105
PuritySate_(const PeakMap &targetExp)
C'tor taking the experiment that will be analyzed.
PeakMap::ConstIterator followUpScan
Iterator pointing to the potential follow up MS1 scan.
Definition: IsobaricChannelExtractor.h:107
bool followUpValid(const double rt) const
Check if the currently selected follow up scan has a retention time bigger then the given value.
bool hasFollowUpScan
Indicates if a follow up scan was found.
Definition: IsobaricChannelExtractor.h:110