OpenMS  2.8.0
ITRAQLabeler.h
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34 
35 #pragma once
36 
40 
41 // forward decl
42 namespace Eigen
43 {
44  template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
45  class Matrix;
46  using MatrixXd = Matrix<double, -1, -1, 0, -1, -1>;
47  using VectorXd = Matrix<double, -1, 1, 0, -1, 1>;
48 }
49 typedef boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr;
50 
51 namespace OpenMS
52 {
53 
62  class OPENMS_DLLAPI ITRAQLabeler :
63  public BaseLabeler
64  {
65 public:
66 
70 
73 
75  ~ITRAQLabeler() override;
76 
78  static BaseLabeler* create()
79  {
80  return new ITRAQLabeler();
81  }
82 
84  static const String getProductName()
85  {
86  return "itraq";
87  }
88 
89  // redeclaration of virtual methods
90  void preCheck(Param& param) const override;
91 
92  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
93 
94  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
95 
96  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
97 
98  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
99 
100  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
101 
102  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
103 
104  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
105 
106 protected:
107 
112  void addModificationToPeptideHit_(Feature& feature, const String& modification, const Size& pos) const;
113 
121  void labelPeptide_(const Feature& feature, SimTypes::FeatureMapSim& result) const;
122 
123  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
124 
126  void updateMembers_() override;
127 
128  // get the closest RT profile factor of a feature for a given RT
129  double getRTProfileIntensity_(const Feature& f, const double MS2_RT_time) const;
130 
132  EigenMatrixXdPtr getItraqIntensity_(const Feature& f, const double MS2_RT_time) const;
133 
134 
135  // Members:
136 
139 
143 
146 
149 
150  };
151 } // namespace OpenMS
152 
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: ITRAQLabeler.h:49
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:51
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:64
void postRawTandemMSHook(SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
Labeling after Tandem MS (e.g. iTRAQ)
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:69
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:67
void addModificationToPeptideHit_(Feature &feature, const String &modification, const Size &pos) const
Modify the first peptide hit of the feature with a modification at pos.
void postIonizationHook(SimTypes::FeatureMapSimVector &) override
Labeling after ionization.
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:78
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:145
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:142
void labelPeptide_(const Feature &feature, SimTypes::FeatureMapSim &result) const
tag a feature with iTRAQ modifications
void postRTHook(SimTypes::FeatureMapSimVector &) override
Labeling after rt simulation.
void postDigestHook(SimTypes::FeatureMapSimVector &) override
Labeling between digestion and rt simulation.
void setUpHook(SimTypes::FeatureMapSimVector &) override
Hook to prepare the simulation process.
void postRawMSHook(SimTypes::FeatureMapSimVector &) override
Labeling after raw signal generation.
void postDetectabilityHook(SimTypes::FeatureMapSimVector &) override
Labeling after detectability simulation.
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:68
EigenMatrixXdPtr getItraqIntensity_(const Feature &f, const double MS2_RT_time) const
convert meta information from feature into intensity values for iTRAQ
void updateMembers_() override
Synchronize members with param class.
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:138
double getRTProfileIntensity_(const Feature &f, const double MS2_RT_time) const
double y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:148
Feature mergeFeatures_(Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const
ITRAQLabeler()
default constructor
~ITRAQLabeler() override
destructor
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:84
void preCheck(Param &param) const override
Checks the (simulation) params passed if they are consistent with the labeling technique.
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:74
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Management and storage of parameters / INI files.
Definition: Param.h:70
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Definition: IsobaricIsotopeCorrector.h:41
Matrix< double, -1, -1, 0, -1, -1 > MatrixXd
Definition: IsobaricIsotopeCorrector.h:44
Matrix< double, -1, 1, 0, -1, 1 > VectorXd
Definition: IsobaricIsotopeCorrector.h:45
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: MatrixUtils.h:49