OpenMS
IsobaricChannelExtractor.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Stephan Aiche, Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 #include <OpenMS/KERNEL/Peak2D.h>
15 
16 namespace OpenMS
17 {
18  class IsobaricQuantitationMethod;
19  class ConsensusMap;
20  class ConsensusFeature;
21 
43  class OPENMS_DLLAPI IsobaricChannelExtractor :
44  public DefaultParamHandler
45  {
46 public:
52  explicit IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method);
53 
56 
59 
66  void extractChannels(const PeakMap& ms_exp_data, ConsensusMap& consensus_map);
67 
68 private:
76  struct PuritySate_
77  {
82 
87 
93  PuritySate_(const PeakMap& targetExp);
94 
100  void advanceFollowUp(const double rt);
101 
107  bool followUpValid(const double rt) const;
108  };
109 
112 
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118 
121 
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127 
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142 
149  bool isValidPrecursor_(const Precursor& precursor) const;
150 
158 
166  double computePrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PuritySate_& precursor) const;
167 
175  double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PeakMap::SpectrumType& precursor_spec) const;
176 
184  {
185  for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
186  {
187  if (!it->getActivationMethods().empty()) return Precursor::NamesOfActivationMethod[*(it->getActivationMethods().begin())];
188  }
189  return "";
190  }
191 
192 
193 protected:
196 
198  void updateMembers_() override;
199  };
200 } // namespace
201 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:45
A container for consensus elements.
Definition: ConsensusMap.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Extracts individual channels from MS/MS spectra for isobaric labeling experiments.
Definition: IsobaricChannelExtractor.h:45
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:138
const IsobaricQuantitationMethod * quant_method_
The used quantitation method (itraq4plex, tmt6plex,..).
Definition: IsobaricChannelExtractor.h:111
Peak2D::CoordinateType reporter_mass_shift_
Allowed deviation between the expected and observed reporter ion m/z.
Definition: IsobaricChannelExtractor.h:117
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:129
String getActivationMethod_(const PeakMap::SpectrumType &s) const
Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.
Definition: IsobaricChannelExtractor.h:183
double computePrecursorPurity_(const PeakMap::ConstIterator &ms2_spec, const PuritySate_ &precursor) const
Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the ...
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 max_precursor_isotope_deviation_
Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the i...
Definition: IsobaricChannelExtractor.h:135
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:132
Peak2D::IntensityType min_reporter_intensity_
Minimum reporter ion intensity to be considered for quantitation.
Definition: IsobaricChannelExtractor.h:126
String selected_activation_
Used to select only specific types of spectra for the channel extraction.
Definition: IsobaricChannelExtractor.h:114
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:120
bool keep_unannotated_precursor_
Flag if precursor with missing intensity value or missing precursor spectrum should be included or no...
Definition: IsobaricChannelExtractor.h:123
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:32
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:78
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
float IntensityType
Intensity type.
Definition: Peak2D.h:36
double CoordinateType
Coordinate type (of the position)
Definition: Peak2D.h:38
Precursor meta information.
Definition: Precursor.h:35
static const std::string NamesOfActivationMethod[SIZE_OF_ACTIVATIONMETHOD]
Names of activation methods.
Definition: Precursor.h:82
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Small struct to capture the current state of the purity computation.
Definition: IsobaricChannelExtractor.h:77
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:86
PeakMap::ConstIterator precursorScan
Iterator pointing to the potential MS1 precursor scan.
Definition: IsobaricChannelExtractor.h:79
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:81
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:84