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

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

Public Member Functions
void	reannotateTransitions (OpenMS::TargetedExperiment &exp, double mz_threshold, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_alternative_localizations, bool enable_reannotation, bool enable_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_losses, bool enable_uis_scoring, bool enable_site_scoring, double mz_threshold, std::vector< std::pair< double, double > > swathes)
	Annotate UIS / site-specific transitions. More...

void	insilicoTransitions (OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4)
	Generates in silico 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
bool	isUIS_ (const double fragment_ion, std::vector< double > ions, const double mz_threshold)
	Check whether fragment ion are unique ion signatures in vector within threshold. More...

void	isSiteUIS_ (const AASequence sequence, ReactionMonitoringTransition &tr)
	Annotate fragment ions with site-specific attributes. 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::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 >	combineModifications_ (OpenMS::AASequence sequence)
	Generate alternative modified peptide forms according to ModificationsDB. More...

std::vector< OpenMS::AASequence >	addModificationsSequences_ (std::vector< OpenMS::AASequence > sequences, std::vector< std::vector< size_t > > mods_combs, OpenMS::String modification)
	Generate alternative modified peptide forms according to ModificationsDB. More...

void	addModification_ (std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, ResidueModification &rmod, const String &name)
	Adds ResidueModification to vector of modifications. 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 ConvertTSVToTraML.

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)) or site-specific transitions can be generated based on empirically observed or in silico generated ion series.

Member Typedef Documentation

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

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

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

Constructor & Destructor Documentation

MRMAssay ( )

Constructor.

~MRMAssay ( )

Destructor.

Member Function Documentation

void addModification_	(	std::vector< TargetedExperiment::Peptide::Modification > &	mods,
		int	location,
		ResidueModification &	rmod,
		const String &	name
	)

protected

Adds ResidueModification to vector of modifications.

Parameters

mods	a vector of targeted experiment modifications
location	the residue location of the modification
rmod	the residue modification
name	the name of the residue modification

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

protected

Generate alternative modified peptide forms according to ModificationsDB.

Parameters

sequence template AASequence

a vector of all alternative modified peptides.

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

protected

Generate alternative modified peptide forms according to ModificationsDB.

Parameters

sequence template AASequence

a vector of all alternative modified peptides.

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

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

void insilicoTransitions	(	OpenMS::TargetedExperiment &	exp,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_losses,
		int	round_decPow = `-4`
	)

Generates in silico 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_losses	whether neutral losses for the fragment ion (according to SpectraST) should be enabled
round_decPow	round product m/z values to decimal power (default: -4)

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
precursor_mz	the query product m/z

void isSiteUIS_	(	const AASequence	sequence,
		ReactionMonitoringTransition &	tr
	)

protected

Annotate fragment ions with site-specific attributes.

Parameters

sequence	the corresponding AASequence including modifications
tr	a reference to the query transition

bool isUIS_	(	const double	fragment_ion,
		std::vector< double >	ions,
		const double	mz_threshold
	)

protected

Check whether fragment ion are unique ion signatures in vector within threshold.

Parameters

fragment_ion	the queried fragment ion
ions	a vector of fragment ions which could interfere with fragment_ion
mz_threshold	the threshold within which to search for interferences

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

void reannotateTransitions	(	OpenMS::TargetedExperiment &	exp,
		double	mz_threshold,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_alternative_localizations,
		bool	enable_reannotation,
		bool	enable_losses,
		int	round_decPow = `-4`
	)

Annotates and filters transitions in a TargetedExperiment.

Parameters

exp	the input, unfiltered transitions
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_alternative_localizations	whether to trust the site-localizations of the transitions or whether alternative options should be generated
enable_reannotation	whether the original annotation should be taken or reannotation should be conducted
enable_losses	whether neutral losses for the fragment ion (according to SpectraST) should be enabled
round_decPow	round product m/z values to decimal power (default: -4)

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)

void uisTransitions	(	OpenMS::TargetedExperiment &	exp,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_losses,
		bool	enable_uis_scoring,
		bool	enable_site_scoring,
		double	mz_threshold,
		std::vector< std::pair< double, double > >	swathes
	)

Annotate UIS / site-specific transitions.

Parameters

exp	the input, unfiltered transitions
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_losses	whether neutral losses for the fragment ion (according to SpectraST) should be enabled
enable_uis_scoring	whether UIS transitions should be annotated
enable_site_scoring	whether site-specific transitions should be annotated
mz_threshold	the product m/z threshold in Th for annotation
swathes	the swath window settings (to exclude fragment ions falling

Public Types

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation