| OpenMS 2.5.0

MRMAssay.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
33 // --------------------------------------------------------------------------
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
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MRMAssay::ProteinVectorType
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMAssay.h:81
OpenMS::Constants::k
const double k
TargetedExperiment.h
OpenMS::MRMAssay::PeptideVectorType
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMAssay.h:82
OpenMS::MRMAssay
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:68
OpenMS::MRMAssay::PeptideTransitionMapType
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMAssay.h:86
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::SequenceMapT
boost::unordered_map< size_t, ModifiedSequenceMap > SequenceMapT
Stores the ModifiedSequenceMap for all SWATH windows.
Definition: MRMAssay.h:90
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::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
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
ProgressLogger.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::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MRMAssay::CompoundVectorType
std::vector< OpenMS::TargetedExperiment::Compound > CompoundVectorType
Definition: MRMAssay.h:83
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MRMAssay::TransitionVectorType
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMAssay.h:84
LogStream.h
ModificationsDB.h
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::CompoundTransitionMapType
std::map< String, std::vector< const ReactionMonitoringTransition * > > CompoundTransitionMapType
Definition: MRMAssay.h:87
MRMIonSeries.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