Generate assays from a TargetedExperiment. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMAssay.h>

Inheritance diagram for MRMAssay:

Public Types
typedef std::vector< OpenMS::TargetedExperiment::Protein >	ProteinVectorType

typedef std::vector< OpenMS::TargetedExperiment::Peptide >	PeptideVectorType

typedef std::vector< OpenMS::ReactionMonitoringTransition >	TransitionVectorType

typedef boost::unordered_map< size_t, boost::unordered_map< String, std::set< std::string > > >	SequenceMapT

typedef boost::unordered_map< size_t, boost::unordered_map< String, std::vector< std::pair< double, std::string > > > >	IonMapT

typedef std::map< String, std::vector< std::pair< std::string, double > > >	PeptideMapT

typedef boost::unordered_map< String, String >	SequenceMap_T

typedef boost::unordered_map< String, TargetedExperiment::Peptide >	TargetDecoyMapT

Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

Public Member Functions
void	reannotateTransitions (OpenMS::TargetedExperiment &exp, double precursor_mz_threshold, double product_mz_threshold, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_reannotation, bool enable_specific_losses, bool enable_unspecific_losses, int round_decPow=-4)
	Annotates and filters transitions in a TargetedExperiment. More...

void	restrictTransitions (OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, std::vector< std::pair< double, double > > swathes)
	Restrict and filter transitions in a TargetedExperiment. More...

void	detectingTransitions (OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)
	Select detecting fragment ions. More...

void	uisTransitions (OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, double mz_threshold, std::vector< std::pair< double, double > > swathes, int round_decPow=-4, size_t max_num_alternative_localizations=20, int shuffle_seed=-1)
	Annotate UIS / site-specific transitions. More...


	MRMAssay ()
	Constructor. More...

	~MRMAssay ()
	Destructor. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

Protected Member Functions
std::vector< std::string >	getMatchingPeptidoforms_ (const double fragment_ion, const std::vector< std::pair< double, std::string > > &ions, const double mz_threshold)
	Check whether fragment ion are unique ion signatures in vector within threshold and return matching peptidoforms. More...

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. More...

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. More...

std::string	getRandomSequence_ (size_t sequence_size, boost::variate_generator< boost::mt19937 &, boost::uniform_int<> > pseudoRNG)
	Generates random peptide sequence. More...

std::vector< std::vector< size_t > >	nchoosekcombinations_ (std::vector< size_t > n, size_t k)
	Computes all N choose K combinations. More...

std::vector< OpenMS::AASequence >	addModificationsSequences_ (std::vector< OpenMS::AASequence > sequences, std::vector< std::vector< size_t > > mods_combs, OpenMS::String modification)
	Generate modified peptide forms based on all possible combinations. More...

std::vector< OpenMS::AASequence >	combineModifications_ (OpenMS::AASequence sequence)
	Generate alternative modified peptide forms according to ModificationsDB. More...

std::vector< OpenMS::AASequence >	combineDecoyModifications_ (OpenMS::AASequence sequence, OpenMS::AASequence decoy_sequence)
	Generate alternative modified peptide forms according to ModificationsDB. More...

void	generateTargetInSilicoMap_ (OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, 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. More...

void	generateDecoySequences_ (boost::unordered_map< size_t, boost::unordered_map< String, std::set< std::string > > > &TargetSequenceMap, boost::unordered_map< String, String > &DecoySequenceMap, int shuffle_seed)
	Generate decoy sequences. More...

void	generateDecoyInSilicoMap_ (OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool enable_ms2_precursors, std::vector< std::pair< double, double > > swathes, int round_decPow, TargetDecoyMapT &TargetDecoyMap, PeptideMapT &TargetPeptideMap, boost::unordered_map< String, String > &DecoySequenceMap, IonMapT &DecoyIonMap, PeptideMapT &DecoyPeptideMap)
	Generate decoy in silico map. More...

void	generateTargetAssays_ (OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, std::vector< std::pair< double, double > > swathes, int round_decPow, PeptideMapT &TargetPeptideMap, IonMapT &TargetIonMap)
	Generate target assays. More...

void	generateDecoyAssays_ (OpenMS::TargetedExperiment &exp, TransitionVectorType &transitions, double mz_threshold, std::vector< std::pair< double, double > > swathes, int round_decPow, PeptideMapT &DecoyPeptideMap, TargetDecoyMapT &TargetDecoyMap, IonMapT DecoyIonMap, IonMapT TargetIonMap)
	Generate decoy assays. More...

Additional Inherited Members
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Generate assays from a TargetedExperiment.

Will generate assays from a raw, unfiltered TargetedExperiment, as can be generated by TargetedFileConverter.

Transitions can be selected according to a set of rules, as described in Schubert et al., 2015 (PMID: 25675208).

In addition, unique ion signature (UIS) (Sherman et al., 2009 (PMID: 19556279)) transitions can be generated based on empirically observed or in silico generated ion series.

Member Typedef Documentation

◆ IonMapT

typedef boost::unordered_map<size_t, boost::unordered_map<String, std::vector<std::pair<double, std::string> > > > IonMapT

◆ PeptideMapT

typedef std::map<String, std::vector<std::pair<std::string, double> > > PeptideMapT

◆ PeptideVectorType

typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType

◆ ProteinVectorType

typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType

◆ SequenceMap_T

typedef boost::unordered_map<String, String> SequenceMap_T

◆ SequenceMapT

typedef boost::unordered_map<size_t, boost::unordered_map<String, std::set<std::string> > > SequenceMapT

◆ TargetDecoyMapT

typedef boost::unordered_map<String, TargetedExperiment::Peptide> TargetDecoyMapT

◆ TransitionVectorType

typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType

Constructor & Destructor Documentation

◆ MRMAssay()

MRMAssay ( )

Constructor.

◆ ~MRMAssay()

~MRMAssay ( )

Destructor.

Member Function Documentation

◆ addModificationsSequences_()

std::vector<OpenMS::AASequence> addModificationsSequences_	(	std::vector< OpenMS::AASequence >	sequences,
		std::vector< std::vector< size_t > >	mods_combs,
		OpenMS::String	modification
	)

protected

Generate modified peptide forms based on all possible combinations.

Parameters

sequences	template AASequences
mods_combs	all possible combinations (e.g. from nchoosekcombinations)
modification	String of the modification

a vector of all modified peptides.

◆ combineDecoyModifications_()

std::vector<OpenMS::AASequence> combineDecoyModifications_	(	OpenMS::AASequence	sequence,
		OpenMS::AASequence	decoy_sequence
	)

protected

Generate alternative modified peptide forms according to ModificationsDB.

An input peptide sequence containing modifications is used as template to generate all modification-carrying residue permutations (n choose k possibilities) that are physicochemically possible according to ModificationsDB. Instead of the target sequence, the permutations are transferred to the decoy sequence that might contain additional modifiable residues. E.g. target sequence SAS(Phospho)K could result in [SAS(Phospho)K, S(Phospho)ASK] but the responding set of the decoy sequence SSS(Phospho)K would be [SSS(Phospho)K, S(Phospho)SSK].

Parameters

sequence	template AASequence
decoy_sequence	template decoy AASequence

a vector of all alternative modified peptides.

◆ combineModifications_()

std::vector<OpenMS::AASequence> combineModifications_ ( OpenMS::AASequence sequence )

protected

Generate alternative modified peptide forms according to ModificationsDB.

An input peptide sequence containing modifications is used as template to generate all modification-carrying residue permutations (n choose k possibilities) that are physicochemically possible according to ModificationsDB.

Parameters

sequence template AASequence

a vector of all alternative modified peptides.

◆ detectingTransitions()

void detectingTransitions	(	OpenMS::TargetedExperiment &	exp,
		int	min_transitions,
		int	max_transitions
	)

Select detecting fragment ions.

Parameters

exp	the input, unfiltered transitions
min_transitions	the minimum number of transitions required per assay
max_transitions	the maximum number of transitions required per assay

◆ generateDecoyAssays_()

void generateDecoyAssays_	(	OpenMS::TargetedExperiment &	exp,
		TransitionVectorType &	transitions,
		double	mz_threshold,
		std::vector< std::pair< double, double > >	swathes,
		int	round_decPow,
		PeptideMapT &	DecoyPeptideMap,
		TargetDecoyMapT &	TargetDecoyMap,
		IonMapT	DecoyIonMap,
		IonMapT	TargetIonMap
	)

protected

Generate decoy assays.

Used internally by MRMAssay::uisTransitions

TODO: why make copy of IonMapT ?

◆ generateDecoyInSilicoMap_()

void generateDecoyInSilicoMap_	(	OpenMS::TargetedExperiment &	exp,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_specific_losses,
		bool	enable_unspecific_losses,
		bool	enable_ms2_precursors,
		std::vector< std::pair< double, double > >	swathes,
		int	round_decPow,
		TargetDecoyMapT &	TargetDecoyMap,
		PeptideMapT &	TargetPeptideMap,
		boost::unordered_map< String, String > &	DecoySequenceMap,
		IonMapT &	DecoyIonMap,
		PeptideMapT &	DecoyPeptideMap
	)

protected

Generate decoy in silico map.

Used internally by MRMAssay::uisTransitions

◆ generateDecoySequences_()

void generateDecoySequences_	(	boost::unordered_map< size_t, boost::unordered_map< String, std::set< std::string > > > &	TargetSequenceMap,
		boost::unordered_map< String, String > &	DecoySequenceMap,
		int	shuffle_seed
	)

protected

Generate decoy sequences.

Used internally by MRMAssay::uisTransitions

◆ generateTargetAssays_()

void generateTargetAssays_	(	OpenMS::TargetedExperiment &	exp,
		TransitionVectorType &	transitions,
		double	mz_threshold,
		std::vector< std::pair< double, double > >	swathes,
		int	round_decPow,
		PeptideMapT &	TargetPeptideMap,
		IonMapT &	TargetIonMap
	)

protected

Generate target assays.

Used internally by MRMAssay::uisTransitions

◆ generateTargetInSilicoMap_()

void generateTargetInSilicoMap_	(	OpenMS::TargetedExperiment &	exp,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_specific_losses,
		bool	enable_unspecific_losses,
		bool	enable_ms2_precursors,
		std::vector< std::pair< double, double > >	swathes,
		int	round_decPow,
		size_t	max_num_alternative_localizations,
		SequenceMapT &	TargetSequenceMap,
		IonMapT &	TargetIonMap,
		PeptideMapT &	TargetPeptideMap
	)

protected

Generate target in silico map.

Used internally by MRMAssay::uisTransitions

◆ getMatchingPeptidoforms_()

std::vector<std::string> getMatchingPeptidoforms_	(	const double	fragment_ion,
		const std::vector< std::pair< double, std::string > > &	ions,
		const double	mz_threshold
	)

protected

Check whether fragment ion are unique ion signatures in vector within threshold and return matching peptidoforms.

Parameters

fragment_ion	the queried fragment ion
ions	a vector of pairs of fragment ion m/z and peptide sequences which could interfere with fragment_ion
mz_threshold	the threshold within which to search for interferences

a vector of strings containing all peptidoforms with which fragment_ion overlaps

◆ getRandomSequence_()

std::string getRandomSequence_	(	size_t	sequence_size,
		boost::variate_generator< boost::mt19937 &, boost::uniform_int<> >	pseudoRNG
	)

protected

Generates random peptide sequence.

Parameters

sequence_size	length of peptide sequence
pseudoRNG	a Boost pseudo RNG

random peptide sequence

◆ getSwath_()

int getSwath_	(	const std::vector< std::pair< double, double > >	swathes,
		const double	precursor_mz
	)

protected

Get swath index (precursor isolation window ordinal) for a particular precursor.

Parameters

swathes	the swath window settings
precursor_mz	the query precursor m/z

index of swath where precursor_mz falls into

◆ isInSwath_()

bool isInSwath_	(	const std::vector< std::pair< double, double > >	swathes,
		const double	precursor_mz,
		const double	product_mz
	)

protected

Check whether the product m/z of a transition falls into the precursor isolation window.

Parameters

swathes	the swath window settings
precursor_mz	the query precursor m/z
product_mz	the query product m/z

whether product m/z falls into precursor isolation window

◆ nchoosekcombinations_()

std::vector<std::vector<size_t> > nchoosekcombinations_	(	std::vector< size_t >	n,
		size_t	k
	)

protected

Computes all N choose K combinations.

Parameters

n	vector of N indices
k	number of K

a vector of all N index combinations

◆ reannotateTransitions()

void reannotateTransitions	(	OpenMS::TargetedExperiment &	exp,
		double	precursor_mz_threshold,
		double	product_mz_threshold,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_reannotation,
		bool	enable_specific_losses,
		bool	enable_unspecific_losses,
		int	round_decPow = `-4`
	)

Annotates and filters transitions in a TargetedExperiment.

Parameters

exp	the input, unfiltered transitions
precursor_mz_threshold	the precursor m/z threshold in Th for annotation
product_mz_threshold	the product m/z threshold in Th for annotation
fragment_types	the fragment types to consider for annotation
fragment_charges	the fragment charges to consider for annotation
enable_reannotation	whether the original annotation should be taken
enable_specific_losses	whether specific neutral losses should be considered
enable_unspecific_losses	whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
round_decPow	round product m/z values to decimal power (default: -4)

◆ restrictTransitions()

void restrictTransitions	(	OpenMS::TargetedExperiment &	exp,
		double	lower_mz_limit,
		double	upper_mz_limit,
		std::vector< std::pair< double, double > >	swathes
	)

Restrict and filter transitions in a TargetedExperiment.

Parameters

exp	the input, unfiltered transitions
lower_mz_limit	the lower product m/z limit in Th
upper_mz_limit	the upper product m/z limit in Th
swathes	the swath window settings (to exclude fragment ions falling into the precursor isolation window)

◆ uisTransitions()

void uisTransitions	(	OpenMS::TargetedExperiment &	exp,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_specific_losses,
		bool	enable_unspecific_losses,
		bool	enable_ms2_precursors,
		double	mz_threshold,
		std::vector< std::pair< double, double > >	swathes,
		int	round_decPow = `-4`,
		size_t	max_num_alternative_localizations = `20`,
		int	shuffle_seed = `-1`
	)

Annotate UIS / site-specific transitions.

Parameters

exp	the input, unfiltered transitions
fragment_types	the fragment types to consider for annotation
fragment_charges	the fragment charges to consider for annotation
enable_specific_losses	whether specific neutral losses should be considered
enable_unspecific_losses	whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
enable_ms2_precursors	whether MS2 precursors should be considered
mz_threshold	the product m/z threshold in Th for annotation
swathes	the swath window settings (to exclude fragment ions falling
round_decPow	round product m/z values to decimal power (default: -4)
max_num_alternative_localizations	maximum number of allowed peptide sequence permutations
shuffle_seed	set seed for shuffle (-1: select seed based on time)

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IonMapT

◆ PeptideMapT

◆ PeptideVectorType

◆ ProteinVectorType

◆ SequenceMap_T

◆ SequenceMapT

◆ TargetDecoyMapT

◆ TransitionVectorType

Constructor & Destructor Documentation

◆ MRMAssay()

◆ ~MRMAssay()

Member Function Documentation

◆ addModificationsSequences_()

◆ combineDecoyModifications_()

◆ combineModifications_()

◆ detectingTransitions()

◆ generateDecoyAssays_()

◆ generateDecoyInSilicoMap_()

◆ generateDecoySequences_()

◆ generateTargetAssays_()

◆ generateTargetInSilicoMap_()

◆ getMatchingPeptidoforms_()

◆ getRandomSequence_()

◆ getSwath_()

◆ isInSwath_()

◆ nchoosekcombinations_()

◆ reannotateTransitions()

◆ restrictTransitions()

◆ uisTransitions()