OpenMS  2.5.0
MRMAssay.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
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34 
35 #pragma once
36 
37 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
38 #include <OpenMS/CONCEPT/ProgressLogger.h>
39 #include <OpenMS/CONCEPT/LogStream.h>
40 #include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
41 #include <OpenMS/CHEMISTRY/ModificationsDB.h>
42 
43 #include <boost/bind.hpp>
44 #include <boost/lexical_cast.hpp>
45 #include <boost/random/mersenne_twister.hpp>
46 #include <boost/random/uniform_int.hpp>
47 #include <boost/random/variate_generator.hpp>
48 
49 // #define DEBUG_MRMASSAY
50 
51 namespace OpenMS
52 {
68  class OPENMS_DLLAPI MRMAssay :
69  public ProgressLogger
70  {
71 
72 public:
74  MRMAssay(); // empty, no members
76 
78  ~MRMAssay();
80 
81  typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
82  typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
83  typedef std::vector<OpenMS::TargetedExperiment::Compound> CompoundVectorType;
84  typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;
85 
86  typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType;
87  typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > CompoundTransitionMapType;
88 
89  typedef boost::unordered_map<String, std::set<std::string> > ModifiedSequenceMap;
90  typedef boost::unordered_map<size_t, ModifiedSequenceMap> SequenceMapT;
91 
92  typedef std::vector<std::pair<double, std::string> > FragmentSeqMap;
93  typedef boost::unordered_map<size_t, boost::unordered_map<String, FragmentSeqMap > > IonMapT;
94 
95  typedef std::vector<std::pair<std::string, double> > IonSeries;
96  typedef std::map<String, IonSeries > PeptideMapT;
97 
98  typedef boost::unordered_map<String, TargetedExperiment::Peptide> TargetDecoyMapT;
99 
113  void reannotateTransitions(OpenMS::TargetedExperiment& exp,
114  double precursor_mz_threshold,
115  double product_mz_threshold,
116  const std::vector<String>& fragment_types,
117  const std::vector<size_t>& fragment_charges,
118  bool enable_specific_losses,
119  bool enable_unspecific_losses,
120  int round_decPow = -4);
121 
132  void restrictTransitions(OpenMS::TargetedExperiment& exp,
133  double lower_mz_limit, double upper_mz_limit,
134  const std::vector<std::pair<double, double> >& swathes);
135 
144  void detectingTransitions(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);
145 
154  void detectingTransitionsCompound(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);
155 
189  void uisTransitions(OpenMS::TargetedExperiment& exp,
190  const std::vector<String>& fragment_types,
191  const std::vector<size_t>& fragment_charges,
192  bool enable_specific_losses,
193  bool enable_unspecific_losses,
194  bool enable_ms2_precursors,
195  double mz_threshold,
196  const std::vector<std::pair<double, double> >& swathes,
197  int round_decPow = -4,
198  size_t max_num_alternative_localizations = 20,
199  int shuffle_seed = -1,
200  bool disable_decoy_transitions = false);
201 
202 protected:
203 
213  std::vector<std::string> getMatchingPeptidoforms_(const double fragment_ion,
214  const FragmentSeqMap& ions,
215  const double mz_threshold);
216 
225  int getSwath_(const std::vector<std::pair<double, double> >& swathes, const double precursor_mz);
226 
236  bool isInSwath_(const std::vector<std::pair<double, double> >& swathes, const double precursor_mz, const double product_mz);
237 
246  std::string getRandomSequence_(size_t sequence_size, boost::variate_generator<boost::mt19937&, boost::uniform_int<> > pseudoRNG);
247 
256  std::vector<std::vector<size_t> > nchoosekcombinations_(const std::vector<size_t>& n, size_t k);
257 
267  std::vector<OpenMS::AASequence> addModificationsSequences_(const std::vector<OpenMS::AASequence>& sequences,
268  const std::vector<std::vector<size_t> >& mods_combs,
269  const OpenMS::String& modification);
270 
282  std::vector<OpenMS::AASequence> generateTheoreticalPeptidoforms_(const OpenMS::AASequence& sequence);
283 
301  std::vector<OpenMS::AASequence> generateTheoreticalPeptidoformsDecoy_(const OpenMS::AASequence& sequence, const OpenMS::AASequence& decoy_sequence);
302 
316  void generateTargetInSilicoMap_(const OpenMS::TargetedExperiment& exp,
317  const std::vector<String>& fragment_types,
318  const std::vector<size_t>& fragment_charges,
319  bool enable_specific_losses,
320  bool enable_unspecific_losses,
321  bool enable_ms2_precursors,
322  const std::vector<std::pair<double, double> >& swathes,
323  int round_decPow,
324  size_t max_num_alternative_localizations,
325  SequenceMapT& TargetSequenceMap,
326  IonMapT& TargetIonMap,
327  PeptideMapT& TargetPeptideMap);
328 
338  void generateDecoySequences_(const SequenceMapT& TargetSequenceMap,
339  boost::unordered_map<String, String>& DecoySequenceMap,
340  int shuffle_seed);
341 
353  void generateDecoyInSilicoMap_(const OpenMS::TargetedExperiment& exp,
354  const std::vector<String>& fragment_types,
355  const std::vector<size_t>& fragment_charges,
356  bool enable_specific_losses,
357  bool enable_unspecific_losses,
358  bool enable_ms2_precursors,
359  const std::vector<std::pair<double, double> >& swathes,
360  int round_decPow,
361  TargetDecoyMapT& TargetDecoyMap,
362  PeptideMapT& TargetPeptideMap,
363  boost::unordered_map<String, String>& DecoySequenceMap,
364  IonMapT& DecoyIonMap,
365  PeptideMapT& DecoyPeptideMap);
366 
385  void generateTargetAssays_(const OpenMS::TargetedExperiment& exp,
386  TransitionVectorType& transitions,
387  double mz_threshold,
388  const std::vector<std::pair<double, double> >& swathes,
389  int round_decPow,
390  const PeptideMapT& TargetPeptideMap,
391  const IonMapT& TargetIonMap);
392 
399  void generateDecoyAssays_(const OpenMS::TargetedExperiment& exp,
400  TransitionVectorType& transitions,
401  double mz_threshold,
402  const std::vector<std::pair<double, double> >& swathes,
403  int round_decPow,
404  const PeptideMapT& DecoyPeptideMap,
405  TargetDecoyMapT& TargetDecoyMap,
406  const IonMapT& DecoyIonMap,
407  const IonMapT& TargetIonMap);
408 
409  };
410 }
411 
LogStream.h
TargetedExperiment.h
OpenMS::MRMAssay::PeptideTransitionMapType
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMAssay.h:86
OpenMS::MRMAssay::CompoundVectorType
std::vector< OpenMS::TargetedExperiment::Compound > CompoundVectorType
Definition: MRMAssay.h:83
OpenMS::Constants::k
const double k
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MRMAssay::IonSeries
std::vector< std::pair< std::string, double > > IonSeries
Describes an ion series: "ion_type" -> "fragment m/z".
Definition: MRMAssay.h:95
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MRMAssay::SequenceMapT
boost::unordered_map< size_t, ModifiedSequenceMap > SequenceMapT
Stores the ModifiedSequenceMap for all SWATH windows.
Definition: MRMAssay.h:90
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
OpenMS::MRMAssay::PeptideVectorType
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMAssay.h:82
OpenMS::MRMAssay::ProteinVectorType
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMAssay.h:81
MRMIonSeries.h
OpenMS::MRMAssay::FragmentSeqMap
std::vector< std::pair< double, std::string > > FragmentSeqMap
Describes a fragment sequence map of : "fragment m/z" -> "modified sequence".
Definition: MRMAssay.h:92
OpenMS::MRMAssay::PeptideMapT
std::map< String, IonSeries > PeptideMapT
Maps a peptide sequence to an ion series: "ion_type" -> "fragment m/z".
Definition: MRMAssay.h:96
OpenMS::MRMAssay::CompoundTransitionMapType
std::map< String, std::vector< const ReactionMonitoringTransition * > > CompoundTransitionMapType
Definition: MRMAssay.h:87
ModificationsDB.h
OpenMS::MRMAssay::IonMapT
boost::unordered_map< size_t, boost::unordered_map< String, FragmentSeqMap > > IonMapT
Stores a mapping : "unmodified sequence" -> FragmentSeqMap for all SWATH windows.
Definition: MRMAssay.h:93
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS::MRMAssay
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:68
OpenMS::MRMAssay::TargetDecoyMapT
boost::unordered_map< String, TargetedExperiment::Peptide > TargetDecoyMapT
Maps the peptide id (same for target and decoy) to the decoy peptide object.
Definition: MRMAssay.h:98
OpenMS::MRMAssay::ModifiedSequenceMap
boost::unordered_map< String, std::set< std::string > > ModifiedSequenceMap
Maps an unmodified sequence to all its modified sequences.
Definition: MRMAssay.h:89
OpenMS::MRMAssay::TransitionVectorType
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMAssay.h:84
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