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IsobaricChannelExtractor.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Stephan Aiche, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/KERNEL/Peak2D.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/KERNEL/StandardTypes.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
81 IsobaricChannelExtractor(const IsobaricChannelExtractor& other);
82
84 IsobaricChannelExtractor& operator=(const IsobaricChannelExtractor& rhs);
85
92 void extractChannels(const PeakMap& ms_exp_data, ConsensusMap& consensus_map);
93
94 private:
102 struct PuritySate_
103 {
105 PeakMap::ConstIterator precursorScan;
107 PeakMap::ConstIterator followUpScan;
108
110 bool hasFollowUpScan;
112 const PeakMap& baseExperiment;
113
119 PuritySate_(const PeakMap& targetExp);
120
126 void advanceFollowUp(const double rt);
127
133 bool followUpValid(const double rt);
134 };
135
137 const IsobaricQuantitationMethod* quant_method_;
138
140 String selected_activation_;
141
143 Peak2D::CoordinateType reporter_mass_shift_;
144
146 Peak2D::IntensityType min_precursor_intensity_;
147
149 bool keep_unannotated_precursor_;
150
152 Peak2D::IntensityType min_reporter_intensity_;
153
155 bool remove_low_intensity_quantifications_;
156
158 double min_precursor_purity_;
159
161 double max_precursor_isotope_deviation_;
162
164 bool interpolate_precursor_purity_;
165
167 void registerChannelsInOutputMap_(ConsensusMap& consensus_map);
168
175 bool isValidPrecursor_(const Precursor& precursor) const;
176
183 bool hasLowIntensityReporter_(const ConsensusFeature& cf) const;
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
209 String getActivationMethod_(const PeakMap::SpectrumType& s) const
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:
221 void setDefaultParams_();
222
224 void updateMembers_() override;
225 };
226 } // namespace
227
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
OpenMS::IsobaricChannelExtractor::min_reporter_intensity_
Peak2D::IntensityType min_reporter_intensity_
Minimum reporter ion intensity to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:152
OpenMS::Precursor::NamesOfActivationMethod
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:94
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::IsobaricChannelExtractor::PuritySate_::followUpScan
PeakMap::ConstIterator followUpScan
Iterator pointing to the potential follow up MS1 scan.
Definition: IsobaricChannelExtractor.h:107
OpenMS::Precursor
Precursor meta information.
Definition: Precursor.h:57
OpenMS::IsobaricChannelExtractor::min_precursor_intensity_
Peak2D::IntensityType min_precursor_intensity_
Minimum intensity of the precursor to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:146
OpenMS::IsobaricChannelExtractor::PuritySate_::baseExperiment
const PeakMap & baseExperiment
reference to the experiment to analyze
Definition: IsobaricChannelExtractor.h:112
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::IsobaricChannelExtractor::selected_activation_
String selected_activation_
Used to select only specific types of spectra for the channel extraction.
Definition: IsobaricChannelExtractor.h:140
StandardTypes.h
OpenMS::IsobaricChannelExtractor::quant_method_
const IsobaricQuantitationMethod * quant_method_
The used quantitation method (itraq4plex, tmt6plex,..).
Definition: IsobaricChannelExtractor.h:137
OpenMS::IsobaricChannelExtractor::PuritySate_
Small struct to capture the current state of the purity computation.
Definition: IsobaricChannelExtractor.h:102
OpenMS::IsobaricChannelExtractor::max_precursor_isotope_deviation_
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
OpenMS::IsobaricQuantitationMethod
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:54
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::IsobaricChannelExtractor::getActivationMethod_
String getActivationMethod_(const PeakMap::SpectrumType &s) const
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.
Definition: IsobaricChannelExtractor.h:209
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::IsobaricChannelExtractor::PuritySate_::precursorScan
PeakMap::ConstIterator precursorScan
Iterator pointing to the potential MS1 precursor scan.
Definition: IsobaricChannelExtractor.h:105
OpenMS::IsobaricChannelExtractor::remove_low_intensity_quantifications_
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
OpenMS::IsobaricChannelExtractor::PuritySate_::hasFollowUpScan
bool hasFollowUpScan
Indicates if a follow up scan was found.
Definition: IsobaricChannelExtractor.h:110
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Peak2D.h
OpenMS::IsobaricChannelExtractor::interpolate_precursor_purity_
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:164
MSExperiment.h
OpenMS::IsobaricChannelExtractor
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Definition: IsobaricChannelExtractor.h:69
DefaultParamHandler.h
OpenMS::IsobaricChannelExtractor::min_precursor_purity_
double min_precursor_purity_
Minimum precursor purity to accept the spectrum for quantitation.
Definition: IsobaricChannelExtractor.h:158
double
float
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::IsobaricChannelExtractor::reporter_mass_shift_
Peak2D::CoordinateType reporter_mass_shift_
Allowed deviation between the expected and observed reporter ion m/z.
Definition: IsobaricChannelExtractor.h:143
OpenMS::IsobaricChannelExtractor::keep_unannotated_precursor_
bool keep_unannotated_precursor_
Flag if precursor with missing intensity value or missing precursor spectrum should be included or no...
Definition: IsobaricChannelExtractor.h:149