| OpenMS 2.5.0

MRMIonSeries.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
38 #include <OpenMS/MATH/MISC/MathFunctions.h>
39 #include <boost/unordered_map.hpp>
40 #include <boost/assign.hpp>
41 #include <boost/lexical_cast.hpp>
42
43 // #define DEBUG_MRMIONSERIES
44
45 namespace OpenMS
46 {
47
69 class OPENMS_DLLAPI MRMIonSeries
70 {
71 private:
72 TargetedExperiment::Interpretation annotationToCVTermList_(const String& annotation);
73
74 void annotationToCV_(ReactionMonitoringTransition& tr);
75
76 public:
78 MRMIonSeries();
80
82 ~MRMIonSeries();
84
85 typedef boost::unordered_map<String, double> IonSeries;
86
96 std::pair<String, double> getIon(IonSeries& ionseries, const String& ionid);
97
108 std::pair<String, double> annotateIon(const IonSeries& ionseries, const double ProductMZ, const double mz_threshold);
109
117 void annotateTransitionCV(ReactionMonitoringTransition& tr, const String& annotation);
118
135 void annotateTransition(ReactionMonitoringTransition& tr,
136 const TargetedExperiment::Peptide& peptide,
137 const double precursor_mz_threshold,
138 const double product_mz_threshold,
139 const bool enable_reannotation,
140 const std::vector<String>& fragment_types,
141 const std::vector<size_t>& fragment_charges,
142 const bool enable_specific_losses,
143 const bool enable_unspecific_losses,
144 const int round_decPow = -4);
145
158 IonSeries getIonSeries(const AASequence& sequence,
159 size_t precursor_charge,
160 const std::vector<String>& fragment_types,
161 const std::vector<size_t>& fragment_charges,
162 const bool enable_specific_losses,
163 const bool enable_unspecific_losses,
164 const int round_decPow = -4);
165 };
166 }
167
OpenMS::String
A more convenient string class.
Definition: String.h:58
TargetedExperiment.h
MathFunctions.h
OpenMS::MRMIonSeries::IonSeries
boost::unordered_map< String, double > IonSeries
An MRM ion series which maps: "ion_type" -> "fragment m/z".
Definition: MRMIonSeries.h:85
OpenMS::MRMIonSeries
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.
Definition: MRMIonSeries.h:69
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
OpenMS::TargetedExperimentHelper::Interpretation
Product ion interpretation.
Definition: TargetedExperimentHelper.h:520
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370