Implements different algorithms for precursor ion selection. More...

#include <OpenMS/ANALYSIS/TARGETED/OfflinePrecursorIonSelection.h>

Inheritance diagram for OfflinePrecursorIonSelection:

Public Types
typedef PSLPFormulation::IndexTriple	IndexTriple

Public Member Functions
	OfflinePrecursorIonSelection ()

virtual	~OfflinePrecursorIonSelection ()

void	makePrecursorSelectionForKnownLCMSMap (const FeatureMap &features, const PeakMap &experiment, PeakMap &ms2, std::set< Int > &charges_set, bool feature_based)
	Makes the precursor selection for a given feature map, either feature or scan based. More...

void	getMassRanges (const FeatureMap &features, const PeakMap &experiment, std::vector< std::vector< std::pair< Size, Size > > > &indices)
	Calculates the mass ranges for each feature and stores them as indices of the raw data. More...

void	createProteinSequenceBasedLPInclusionList (String include, String rt_model_file, String pt_model_file, FeatureMap &precursors)

void	setLPSolver (LPWrapper::SOLVER solver)

LPWrapper::SOLVER	getLPSolver ()

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Private Types
typedef std::map< std::pair< double, double >, int, PairComparatorSecondElement< std::pair< double, double > > >	ExclusionListType_

Private Member Functions
void	calculateXICs_ (const FeatureMap &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, double > > > &xics)
	Calculate the sum of intensities of relevant features for each scan separately. More...

void	checkMassRanges_ (std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment)
	Eliminates overlapping peaks. More...

void	updateExclusionList_ (ExclusionListType_ &exclusion_list) const
	reduce scan count for each entry, and remove every entry which has reached 0 counts More...

Private Attributes
LPWrapper::SOLVER	solver_

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Implements different algorithms for precursor ion selection.

Implements different algorithms for precursor ion selection, either based on a whole FeatureMap (e.g. like with LC-MALDI MS data) or based on single scans (e.g. with LC-ESI MS data).

Parameters of this class are:

Name	Type	Default	Restrictions	Description
ms2_spectra_per_rt_bin	int	5	min: 1	Number of allowed MS/MS spectra in a retention time bin.
min_mz_peak_distance	float	2	min: 0.0001	The minimal distance (in Th) between two peaks for concurrent selection for fragmentation. Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor.
mz_isolation_window	float	2	min: 0	All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.
exclude_overlapping_peaks	string	false	true, false	If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.
Exclusion:use_dynamic_exclusion	string	false	true, false	If true dynamic exclusion is applied.
Exclusion:exclusion_time	float	100	min: 0	The time (in seconds) a feature is excluded.
ProteinBasedInclusion:max_list_size	int	1000	min: 1	The maximal number of precursors in the inclusion list.
ProteinBasedInclusion:rt:min_rt	float	960	min: 0	Minimal rt in seconds.
ProteinBasedInclusion:rt:max_rt	float	3840	min: 0	Maximal rt in seconds.
ProteinBasedInclusion:rt:rt_step_size	float	30	min: 1	rt step size in seconds.
ProteinBasedInclusion:rt:rt_window_size	int	100	min: 1	rt window size in seconds.
ProteinBasedInclusion:thresholds:min_protein_id_probability	float	0.95	min: 0 max: 1	Minimal protein probability for a protein to be considered identified.
ProteinBasedInclusion:thresholds:min_pt_weight	float	0.5	min: 0 max: 1	Minimal pt weight of a precursor
ProteinBasedInclusion:thresholds:min_mz	float	500	min: 0	Minimal mz to be considered in protein based LP formulation.
ProteinBasedInclusion:thresholds:max_mz	float	5000	min: 0	Minimal mz to be considered in protein based LP formulation.
ProteinBasedInclusion:thresholds:use_peptide_rule	string	false	true, false	Use peptide rule instead of minimal protein id probability
ProteinBasedInclusion:thresholds:min_peptide_ids	int	2	min: 1	If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
ProteinBasedInclusion:thresholds:min_peptide_probability	float	0.95	min: 0 max: 1	If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

◆ ExclusionListType_

typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_

private

◆ IndexTriple

typedef PSLPFormulation::IndexTriple IndexTriple

Constructor & Destructor Documentation

◆ OfflinePrecursorIonSelection()

OfflinePrecursorIonSelection ( )

◆ ~OfflinePrecursorIonSelection()

virtual ~OfflinePrecursorIonSelection ( )

virtual

Member Function Documentation

◆ calculateXICs_()

void calculateXICs_	(	const FeatureMap &	features,
		const std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const PeakMap &	experiment,
		const std::set< Int > &	charges_set,
		std::vector< std::vector< std::pair< Size, double > > > &	xics
	)

private

Calculate the sum of intensities of relevant features for each scan separately.

◆ checkMassRanges_()

void checkMassRanges_	(	std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const PeakMap &	experiment
	)

private

Eliminates overlapping peaks.

◆ createProteinSequenceBasedLPInclusionList()

void createProteinSequenceBasedLPInclusionList	(	String	include,
		String	rt_model_file,
		String	pt_model_file,
		FeatureMap &	precursors
	)

◆ getLPSolver()

LPWrapper::SOLVER getLPSolver ( )

inline

◆ getMassRanges()

void getMassRanges	(	const FeatureMap &	features,
		const PeakMap &	experiment,
		std::vector< std::vector< std::pair< Size, Size > > > &	indices
	)

Calculates the mass ranges for each feature and stores them as indices of the raw data.

Parameters

features	Input feature map
experiment	Input raw data
indices	The boundaries of the features as indices in the raw data

◆ makePrecursorSelectionForKnownLCMSMap()

void makePrecursorSelectionForKnownLCMSMap	(	const FeatureMap &	features,
		const PeakMap &	experiment,
		PeakMap &	ms2,
		std::set< Int > &	charges_set,
		bool	feature_based
	)

Makes the precursor selection for a given feature map, either feature or scan based.

Parameters

features	Input feature map
experiment	Input raw data
ms2	Precursors are added as empty MS2 spectra to this MSExperiment
charges_set	Allowed charge states
feature_based	If true the selection is feature based, if false it is scan based and the highest signals in each spectrum are chosen

◆ setLPSolver()

void setLPSolver ( LPWrapper::SOLVER solver )

inline

◆ updateExclusionList_()

void updateExclusionList_ ( ExclusionListType_ & exclusion_list ) const

private

reduce scan count for each entry, and remove every entry which has reached 0 counts

Member Data Documentation

◆ solver_

LPWrapper::SOLVER solver_

private

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ExclusionListType_

◆ IndexTriple

Constructor & Destructor Documentation

◆ OfflinePrecursorIonSelection()

◆ ~OfflinePrecursorIonSelection()

Member Function Documentation

◆ calculateXICs_()

◆ checkMassRanges_()

◆ createProteinSequenceBasedLPInclusionList()

◆ getLPSolver()

◆ getMassRanges()

◆ makePrecursorSelectionForKnownLCMSMap()

◆ setLPSolver()

◆ updateExclusionList_()

Member Data Documentation

◆ solver_