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MRMAssay.h
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1// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2// SPDX-License-Identifier: BSD-3-Clause
3//
4// --------------------------------------------------------------------------
5// $Maintainer: George Rosenberger $
6// $Authors: George Rosenberger $
7// --------------------------------------------------------------------------
8
9#pragma once
10
11#include <functional>
12#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
13#include <OpenMS/CONCEPT/ProgressLogger.h>
14#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
15#include <OpenMS/CHEMISTRY/ModificationsDB.h>
16#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
17
18
19// #define DEBUG_MRMASSAY
20
21namespace OpenMS
22{
38 class OPENMS_DLLAPI MRMAssay :
39 public ProgressLogger
40 {
41
42public:
44
45 MRMAssay(); // empty, no members
46
48 ~MRMAssay() override;
50
51 typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
52 typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
53 typedef std::vector<OpenMS::TargetedExperiment::Compound> CompoundVectorType;
54 typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;
55
56 typedef std::map<std::string, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType;
57 typedef std::map<std::string, std::vector<const ReactionMonitoringTransition*> > CompoundTransitionMapType;
58
59 typedef std::map<std::string, std::set<std::string> > ModifiedSequenceMap;
60 typedef std::map<size_t, ModifiedSequenceMap> SequenceMapT;
61
62 typedef std::vector<std::pair<double, std::string> > FragmentSeqMap;
63 typedef std::map<size_t, std::map<std::string, FragmentSeqMap > > IonMapT;
64
65 typedef std::vector<std::pair<std::string, double> > IonSeries;
66 typedef std::map<std::string, IonSeries > PeptideMapT;
67
68 typedef std::map<std::string, TargetedExperiment::Peptide> TargetDecoyMapT;
69
83 void reannotateTransitions(OpenMS::TargetedExperiment& exp,
84 double precursor_mz_threshold,
85 double product_mz_threshold,
86 const std::vector<std::string>& fragment_types,
87 const std::vector<size_t>& fragment_charges,
88 bool enable_specific_losses,
89 bool enable_unspecific_losses,
90 int round_decPow = -4);
91
102 void restrictTransitions(OpenMS::TargetedExperiment& exp,
103 double lower_mz_limit, double upper_mz_limit,
104 const std::vector<std::pair<double, double> >& swathes);
105
114 void detectingTransitions(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);
115
149 void uisTransitions(OpenMS::TargetedExperiment& exp,
150 const std::vector<std::string>& fragment_types,
151 const std::vector<size_t>& fragment_charges,
152 bool enable_specific_losses,
153 bool enable_unspecific_losses,
154 bool enable_ms2_precursors,
155 double mz_threshold,
156 const std::vector<std::pair<double, double> >& swathes,
157 int round_decPow = -4,
158 size_t max_num_alternative_localizations = 20,
159 int shuffle_seed = 1,
160 bool disable_decoy_transitions = false);
161
170 void filterMinMaxTransitionsCompound(OpenMS::TargetedExperiment& exp, int min_transitions, int max_transitions);
171
185 void filterUnreferencedDecoysCompound(OpenMS::TargetedExperiment &exp);
186
187 // =====================================================================
188 // Light (memory-efficient) versions of the above methods
189 // =====================================================================
190
206 void reannotateTransitionsLight(OpenSwath::LightTargetedExperiment& exp,
207 double precursor_mz_threshold,
208 double product_mz_threshold,
209 const std::vector<std::string>& fragment_types,
210 const std::vector<size_t>& fragment_charges,
211 bool enable_specific_losses,
212 bool enable_unspecific_losses,
213 int round_decPow = -4);
214
226 void restrictTransitionsLight(OpenSwath::LightTargetedExperiment& exp,
227 double lower_mz_limit,
228 double upper_mz_limit,
229 const std::vector<std::pair<double, double> >& swathes);
230
241 void detectingTransitionsLight(OpenSwath::LightTargetedExperiment& exp,
242 int min_transitions,
243 int max_transitions);
244
264 void uisTransitionsLight(OpenSwath::LightTargetedExperiment& exp,
265 const std::vector<std::string>& fragment_types,
266 const std::vector<size_t>& fragment_charges,
267 bool enable_specific_losses,
268 bool enable_unspecific_losses,
269 bool enable_ms2_precursors,
270 double mz_threshold,
271 const std::vector<std::pair<double, double> >& swathes,
272 int round_decPow = -4,
273 size_t max_num_alternative_localizations = 20,
274 int shuffle_seed = 1,
275 bool disable_decoy_transitions = false);
276
277protected:
278
289 std::vector<std::string> getMatchingPeptidoforms_(const double fragment_ion,
290 const FragmentSeqMap& ions,
291 const double mz_threshold);
292
301 int getSwath_(const std::vector<std::pair<double, double> >& swathes, const double precursor_mz);
302
312 bool isInSwath_(const std::vector<std::pair<double, double> >& swathes, const double precursor_mz, const double product_mz);
313
324 std::string getRandomSequence_(size_t sequence_size, const std::function<int()>& pseudoRNG);
325
334 std::vector<std::vector<size_t> > nchoosekcombinations_(const std::vector<size_t>& n, size_t k);
335
345 std::vector<OpenMS::AASequence> addModificationsSequences_(const std::vector<OpenMS::AASequence>& sequences,
346 const std::vector<std::vector<size_t> >& mods_combs,
347 const std::string& modification);
348
360 std::vector<OpenMS::AASequence> generateTheoreticalPeptidoforms_(const OpenMS::AASequence& sequence);
361
379 std::vector<OpenMS::AASequence> generateTheoreticalPeptidoformsDecoy_(const OpenMS::AASequence& sequence, const OpenMS::AASequence& decoy_sequence);
380
394 void generateTargetInSilicoMap_(const OpenMS::TargetedExperiment& exp,
395 const std::vector<std::string>& fragment_types,
396 const std::vector<size_t>& fragment_charges,
397 bool enable_specific_losses,
398 bool enable_unspecific_losses,
399 bool enable_ms2_precursors,
400 const std::vector<std::pair<double, double> >& swathes,
401 int round_decPow,
402 size_t max_num_alternative_localizations,
403 SequenceMapT& TargetSequenceMap,
404 IonMapT& TargetIonMap,
405 PeptideMapT& TargetPeptideMap);
406
416 void generateDecoySequences_(const SequenceMapT& TargetSequenceMap,
417 std::map<std::string, std::string>& DecoySequenceMap,
418 int shuffle_seed);
419
431 void generateDecoyInSilicoMap_(const OpenMS::TargetedExperiment& exp,
432 const std::vector<std::string>& fragment_types,
433 const std::vector<size_t>& fragment_charges,
434 bool enable_specific_losses,
435 bool enable_unspecific_losses,
436 bool enable_ms2_precursors,
437 const std::vector<std::pair<double, double> >& swathes,
438 int round_decPow,
439 TargetDecoyMapT& TargetDecoyMap,
440 PeptideMapT& TargetPeptideMap,
441 std::map<std::string, std::string>& DecoySequenceMap,
442 IonMapT& DecoyIonMap,
443 PeptideMapT& DecoyPeptideMap);
444
463 void generateTargetAssays_(const OpenMS::TargetedExperiment& exp,
464 TransitionVectorType& transitions,
465 double mz_threshold,
466 const std::vector<std::pair<double, double> >& swathes,
467 int round_decPow,
468 const PeptideMapT& TargetPeptideMap,
469 const IonMapT& TargetIonMap);
470
477 void generateDecoyAssays_(const OpenMS::TargetedExperiment& exp,
478 TransitionVectorType& transitions,
479 double mz_threshold,
480 const std::vector<std::pair<double, double> >& swathes,
481 int round_decPow,
482 const PeptideMapT& DecoyPeptideMap,
483 TargetDecoyMapT& TargetDecoyMap,
484 const IonMapT& DecoyIonMap,
485 const IonMapT& TargetIonMap);
486
487 // =====================================================================
488 // Light (memory-efficient) versions of IPF helper methods
489 // =====================================================================
490
492 typedef std::map<std::string, OpenSwath::LightCompound> TargetDecoyMapLightT;
493
501 void generateTargetInSilicoMapLight_(const OpenSwath::LightTargetedExperiment& exp,
502 const std::vector<std::string>& fragment_types,
503 const std::vector<size_t>& fragment_charges,
504 bool enable_specific_losses,
505 bool enable_unspecific_losses,
506 bool enable_ms2_precursors,
507 const std::vector<std::pair<double, double> >& swathes,
508 int round_decPow,
509 size_t max_num_alternative_localizations,
510 SequenceMapT& TargetSequenceMap,
511 IonMapT& TargetIonMap,
512 PeptideMapT& TargetPeptideMap);
513
521 void generateDecoyInSilicoMapLight_(const OpenSwath::LightTargetedExperiment& exp,
522 const std::vector<std::string>& fragment_types,
523 const std::vector<size_t>& fragment_charges,
524 bool enable_specific_losses,
525 bool enable_unspecific_losses,
526 bool enable_ms2_precursors,
527 const std::vector<std::pair<double, double> >& swathes,
528 int round_decPow,
529 TargetDecoyMapLightT& TargetDecoyMap,
530 const PeptideMapT& TargetPeptideMap,
531 const std::map<std::string, std::string>& DecoySequenceMap,
532 IonMapT& DecoyIonMap,
533 PeptideMapT& DecoyPeptideMap);
534
542 void generateTargetAssaysLight_(const OpenSwath::LightTargetedExperiment& exp,
543 std::vector<OpenSwath::LightTransition>& transitions,
544 double mz_threshold,
545 const std::vector<std::pair<double, double> >& swathes,
546 int round_decPow,
547 const PeptideMapT& TargetPeptideMap,
548 const IonMapT& TargetIonMap);
549
557 void generateDecoyAssaysLight_(const OpenSwath::LightTargetedExperiment& exp,
558 std::vector<OpenSwath::LightTransition>& transitions,
559 double mz_threshold,
560 const std::vector<std::pair<double, double> >& swathes,
561 int round_decPow,
562 const PeptideMapT& DecoyPeptideMap,
563 const TargetDecoyMapLightT& TargetDecoyMap,
564 const IonMapT& DecoyIonMap,
565 const IonMapT& TargetIonMap);
566
567 };
568}
OpenMS::AASequence
Definition AASequence.h:96
OpenMS::MRMAssay
Generate assays from a TargetedExperiment.
Definition MRMAssay.h:40
OpenMS::MRMAssay::generateTargetAssays_
void generateTargetAssays_(const OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow, const PeptideMapT &TargetPeptideMap, const IonMapT &TargetIonMap)
Generate target identification transitions.
OpenMS::MRMAssay::restrictTransitionsLight
void restrictTransitionsLight(OpenSwath::LightTargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, const std::vector< std::pair< double, double > > &swathes)
Restrict and filter transitions in a LightTargetedExperiment.
OpenMS::MRMAssay::CompoundVectorType
std::vector< OpenMS::TargetedExperiment::Compound > CompoundVectorType
Definition MRMAssay.h:53
OpenMS::MRMAssay::detectingTransitions
void detectingTransitions(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)
Select detecting fragment ions.
OpenMS::MRMAssay::PeptideTransitionMapType
std::map< std::string, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition MRMAssay.h:56
OpenMS::MRMAssay::uisTransitionsLight
void uisTransitionsLight(OpenSwath::LightTargetedExperiment &exp, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=1, bool disable_decoy_transitions=false)
Annotate UIS / site-specific transitions (light version)
OpenMS::MRMAssay::generateTargetInSilicoMapLight_
void generateTargetInSilicoMapLight_(const OpenSwath::LightTargetedExperiment &exp, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, const std::vector< std::pair< double, double > > &swathes, int round_decPow, size_t max_num_alternative_localizations, SequenceMapT &TargetSequenceMap, IonMapT &TargetIonMap, PeptideMapT &TargetPeptideMap)
Generate target in silico map (light version)
OpenMS::MRMAssay::generateDecoyAssaysLight_
void generateDecoyAssaysLight_(const OpenSwath::LightTargetedExperiment &exp, std::vector< OpenSwath::LightTransition > &transitions, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow, const PeptideMapT &DecoyPeptideMap, const TargetDecoyMapLightT &TargetDecoyMap, const IonMapT &DecoyIonMap, const IonMapT &TargetIonMap)
Generate decoy assays (light version)
OpenMS::MRMAssay::generateTargetAssaysLight_
void generateTargetAssaysLight_(const OpenSwath::LightTargetedExperiment &exp, std::vector< OpenSwath::LightTransition > &transitions, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow, const PeptideMapT &TargetPeptideMap, const IonMapT &TargetIonMap)
Generate target identification transitions (light version)
OpenMS::MRMAssay::restrictTransitions
void restrictTransitions(OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, const std::vector< std::pair< double, double > > &swathes)
Restrict and filter transitions in a TargetedExperiment.
OpenMS::MRMAssay::generateDecoySequences_
void generateDecoySequences_(const SequenceMapT &TargetSequenceMap, std::map< std::string, std::string > &DecoySequenceMap, int shuffle_seed)
Generate decoy sequences.
OpenMS::MRMAssay::nchoosekcombinations_
std::vector< std::vector< size_t > > nchoosekcombinations_(const std::vector< size_t > &n, size_t k)
Computes all N choose K combinations.
OpenMS::MRMAssay::SequenceMapT
std::map< size_t, ModifiedSequenceMap > SequenceMapT
Stores the ModifiedSequenceMap for all SWATH windows (uses std::map for deterministic iteration order...
Definition MRMAssay.h:60
OpenMS::MRMAssay::IonMapT
std::map< size_t, std::map< std::string, FragmentSeqMap > > IonMapT
Stores a mapping : "unmodified sequence" -> FragmentSeqMap for all SWATH windows (uses std::map for d...
Definition MRMAssay.h:63
OpenMS::MRMAssay::getSwath_
int getSwath_(const std::vector< std::pair< double, double > > &swathes, const double precursor_mz)
Get swath index (precursor isolation window ordinal) for a particular precursor.
OpenMS::MRMAssay::generateDecoyInSilicoMapLight_
void generateDecoyInSilicoMapLight_(const OpenSwath::LightTargetedExperiment &exp, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, const std::vector< std::pair< double, double > > &swathes, int round_decPow, TargetDecoyMapLightT &TargetDecoyMap, const PeptideMapT &TargetPeptideMap, const std::map< std::string, std::string > &DecoySequenceMap, IonMapT &DecoyIonMap, PeptideMapT &DecoyPeptideMap)
Generate decoy in silico map (light version)
OpenMS::MRMAssay::generateTheoreticalPeptidoforms_
std::vector< OpenMS::AASequence > generateTheoreticalPeptidoforms_(const OpenMS::AASequence &sequence)
Generate alternative modified peptide forms according to ModificationsDB.
OpenMS::MRMAssay::PeptideMapT
std::map< std::string, IonSeries > PeptideMapT
Maps a peptide sequence to an ion series: "ion_type" -> "fragment m/z".
Definition MRMAssay.h:66
OpenMS::MRMAssay::getRandomSequence_
std::string getRandomSequence_(size_t sequence_size, const std::function< int()> &pseudoRNG)
Generates random peptide sequence.
OpenMS::MRMAssay::TargetDecoyMapLightT
std::map< std::string, OpenSwath::LightCompound > TargetDecoyMapLightT
Light version of TargetDecoyMapT using LightCompound.
Definition MRMAssay.h:492
OpenMS::MRMAssay::generateDecoyAssays_
void generateDecoyAssays_(const OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow, const PeptideMapT &DecoyPeptideMap, TargetDecoyMapT &TargetDecoyMap, const IonMapT &DecoyIonMap, const IonMapT &TargetIonMap)
Generate decoy assays.
OpenMS::MRMAssay::generateDecoyInSilicoMap_
void generateDecoyInSilicoMap_(const OpenMS::TargetedExperiment &exp, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, const std::vector< std::pair< double, double > > &swathes, int round_decPow, TargetDecoyMapT &TargetDecoyMap, PeptideMapT &TargetPeptideMap, std::map< std::string, std::string > &DecoySequenceMap, IonMapT &DecoyIonMap, PeptideMapT &DecoyPeptideMap)
Generate decoy in silico map.
OpenMS::MRMAssay::TransitionVectorType
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition MRMAssay.h:54
OpenMS::MRMAssay::TargetDecoyMapT
std::map< std::string, TargetedExperiment::Peptide > TargetDecoyMapT
Maps the peptide id (same for target and decoy) to the decoy peptide object.
Definition MRMAssay.h:68
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:62
OpenMS::MRMAssay::PeptideVectorType
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition MRMAssay.h:52
OpenMS::MRMAssay::IonSeries
std::vector< std::pair< std::string, double > > IonSeries
Describes an ion series: "ion_type" -> "fragment m/z".
Definition MRMAssay.h:65
OpenMS::MRMAssay::reannotateTransitionsLight
void reannotateTransitionsLight(OpenSwath::LightTargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow=-4)
Annotates and filters transitions in a LightTargetedExperiment.
OpenMS::MRMAssay::filterMinMaxTransitionsCompound
void filterMinMaxTransitionsCompound(OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)
Filters target and decoy transitions by intensity, only keeping the top N transitions.
OpenMS::MRMAssay::CompoundTransitionMapType
std::map< std::string, std::vector< const ReactionMonitoringTransition * > > CompoundTransitionMapType
Definition MRMAssay.h:57
OpenMS::MRMAssay::detectingTransitionsLight
void detectingTransitionsLight(OpenSwath::LightTargetedExperiment &exp, int min_transitions, int max_transitions)
Select detecting fragment ions in a LightTargetedExperiment.
OpenMS::MRMAssay::reannotateTransitions
void reannotateTransitions(OpenMS::TargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow=-4)
Annotates and filters transitions in a TargetedExperiment.
OpenMS::MRMAssay::MRMAssay
MRMAssay()
Constructor.
OpenMS::MRMAssay::uisTransitions
void uisTransitions(OpenMS::TargetedExperiment &exp, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, const std::vector< std::pair< double, double > > &swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=1, bool disable_decoy_transitions=false)
Annotate UIS / site-specific transitions.
OpenMS::MRMAssay::filterUnreferencedDecoysCompound
void filterUnreferencedDecoysCompound(OpenMS::TargetedExperiment &exp)
Filters decoy transitions, which do not have respective target transition based on the transitionID.
OpenMS::MRMAssay::ProteinVectorType
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition MRMAssay.h:51
OpenMS::MRMAssay::generateTheoreticalPeptidoformsDecoy_
std::vector< OpenMS::AASequence > generateTheoreticalPeptidoformsDecoy_(const OpenMS::AASequence &sequence, const OpenMS::AASequence &decoy_sequence)
Generate alternative modified peptide forms according to ModificationsDB.
OpenMS::MRMAssay::generateTargetInSilicoMap_
void generateTargetInSilicoMap_(const OpenMS::TargetedExperiment &exp, const std::vector< std::string > &fragment_types, const std::vector< size_t > &fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, const std::vector< std::pair< double, double > > &swathes, int round_decPow, size_t max_num_alternative_localizations, SequenceMapT &TargetSequenceMap, IonMapT &TargetIonMap, PeptideMapT &TargetPeptideMap)
Generate target in silico map.
OpenMS::MRMAssay::isInSwath_
bool isInSwath_(const std::vector< std::pair< double, double > > &swathes, const double precursor_mz, const double product_mz)
Check whether the product m/z of a transition falls into the precursor isolation window.
OpenMS::MRMAssay::getMatchingPeptidoforms_
std::vector< std::string > getMatchingPeptidoforms_(const double fragment_ion, const FragmentSeqMap &ions, const double mz_threshold)
Check whether fragment ion are unique ion signatures in vector within threshold and return matching p...
OpenMS::MRMAssay::ModifiedSequenceMap
std::map< std::string, std::set< std::string > > ModifiedSequenceMap
Maps an unmodified sequence to all its modified sequences.
Definition MRMAssay.h:59
OpenMS::MRMAssay::~MRMAssay
~MRMAssay() override
Destructor.
OpenMS::MRMAssay::addModificationsSequences_
std::vector< OpenMS::AASequence > addModificationsSequences_(const std::vector< OpenMS::AASequence > &sequences, const std::vector< std::vector< size_t > > &mods_combs, const std::string &modification)
Generate modified peptide forms based on all possible combinations.
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition ProgressLogger.h:28
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition TargetedExperiment.h:40
OpenMS
Main OpenMS namespace.
Definition openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
OpenSwath::LightTargetedExperiment
Definition TransitionExperiment.h:369