OpenMS  3.0.0
MRMIonSeries.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
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34 
35 #pragma once
36 
39 #include <unordered_map>
40 
41 // #define DEBUG_MRMIONSERIES
42 
43 namespace OpenMS
44 {
45 
67  class OPENMS_DLLAPI MRMIonSeries
68  {
69 private:
70  TargetedExperiment::Interpretation annotationToCVTermList_(const String& annotation);
71 
72  void annotationToCV_(ReactionMonitoringTransition& tr);
73 
74 public:
76  MRMIonSeries();
78 
80  ~MRMIonSeries();
82 
83  typedef std::unordered_map<String, double> IonSeries;
84 
94  std::pair<String, double> getIon(IonSeries& ionseries, const String& ionid);
95 
106  std::pair<String, double> annotateIon(const IonSeries& ionseries, const double ProductMZ, const double mz_threshold);
107 
115  void annotateTransitionCV(ReactionMonitoringTransition& tr, const String& annotation);
116 
133  void annotateTransition(ReactionMonitoringTransition& tr,
134  const TargetedExperiment::Peptide& peptide,
135  const double precursor_mz_threshold,
136  const double product_mz_threshold,
137  const bool enable_reannotation,
138  const std::vector<String>& fragment_types,
139  const std::vector<size_t>& fragment_charges,
140  const bool enable_specific_losses,
141  const bool enable_unspecific_losses,
142  const int round_decPow = -4);
143 
156  IonSeries getIonSeries(const AASequence& sequence,
157  size_t precursor_charge,
158  const std::vector<String>& fragment_types,
159  const std::vector<size_t>& fragment_charges,
160  const bool enable_specific_losses,
161  const bool enable_unspecific_losses,
162  const int round_decPow = -4);
163  };
164 }
165 
TargetedExperiment.h
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:358
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MRMIonSeries::IonSeries
std::unordered_map< String, double > IonSeries
An MRM ion series which maps: "ion_type" -> "fragment m/z".
Definition: MRMIonSeries.h:83
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
MathFunctions.h
OpenMS::MRMIonSeries
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.
Definition: MRMIonSeries.h:67
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::TargetedExperimentHelper::Interpretation
Product ion interpretation.
Definition: TargetedExperimentHelper.h:503