| OpenMS 2.5.0

ITRAQLabeler.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
38 #include <OpenMS/DATASTRUCTURES/Utils/MatrixUtils.h>
39 #include <OpenMS/SIMULATION/LABELING/BaseLabeler.h>
40 #include <OpenMS/SIMULATION/SimTypes.h>
41
42 namespace OpenMS
43 {
44
53 class OPENMS_DLLAPI ITRAQLabeler :
54 public BaseLabeler
55 {
56 public:
57
58 typedef ItraqConstants::ChannelInfo ChannelInfo;
59 typedef ItraqConstants::ChannelMapType ChannelMapType;
60 typedef ItraqConstants::IsotopeMatrices IsotopeMatrices;
61
63 ITRAQLabeler();
64
66 ~ITRAQLabeler() override;
67
69 static BaseLabeler* create()
70 {
71 return new ITRAQLabeler();
72 }
73
75 static const String getProductName()
76 {
77 return "itraq";
78 }
79
80 // redeclaration of virtual methods
81 void preCheck(Param& param) const override;
82
83 void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
84
85 void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86
87 void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
88
89 void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
90
91 void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
92
93 void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
94
95 void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
96
97 protected:
98
103 void addModificationToPeptideHit_(Feature& feature, const String& modification, const Size& pos) const;
104
112 void labelPeptide_(const Feature& feature, SimTypes::FeatureMapSim& result) const;
113
114 Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
115
117 void updateMembers_() override;
118
119 // get the closest RT profile factor of a feature for a given RT
120 double getRTProfileIntensity_(const Feature& f, const double MS2_RT_time) const;
121
123 EigenMatrixXdPtr getItraqIntensity_(const Feature& f, const double MS2_RT_time) const;
124
125
126 // Members:
127
129 Int itraq_type_;
130
133 ChannelMapType channel_map_;
134
136 IsotopeMatrices isotope_corrections_;
137
139 double y_labeling_efficiency_;
140
141 };
142 } // namespace OpenMS
143
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::ITRAQLabeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: ITRAQLabeler.h:69
OpenMS::ITRAQLabeler::y_labeling_efficiency_
double y_labeling_efficiency_
efficiency of "Y" labeling
Definition: ITRAQLabeler.h:139
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ITRAQLabeler::itraq_type_
Int itraq_type_
set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ITRAQLabeler.h:129
SimTypes.h
OpenMS::ItraqConstants::ChannelInfo
stores information on an iTRAQ channel
Definition: ItraqConstants.h:61
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::ITRAQLabeler::IsotopeMatrices
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ITRAQLabeler.h:60
OpenMS::EigenMatrixXdPtr
boost::shared_ptr< const Eigen::MatrixXd > EigenMatrixXdPtr
Definition: MatrixUtils.h:49
MatrixUtils.h
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::ItraqConstants::IsotopeMatrices
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:74
OpenMS::ITRAQLabeler::ChannelInfo
ItraqConstants::ChannelInfo ChannelInfo
Definition: ITRAQLabeler.h:58
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ITRAQLabeler
Simulate iTRAQ experiments.
Definition: ITRAQLabeler.h:53
ItraqConstants.h
OpenMS::ITRAQLabeler::channel_map_
ChannelMapType channel_map_
Definition: ITRAQLabeler.h:133
OpenMS::ITRAQLabeler::isotope_corrections_
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ITRAQLabeler.h:136
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
int
OpenMS::ITRAQLabeler::ChannelMapType
ItraqConstants::ChannelMapType ChannelMapType
Definition: ITRAQLabeler.h:59
BaseLabeler.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ITRAQLabeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: ITRAQLabeler.h:75