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 ()
template<typename InputPeakType >
void	makePrecursorSelectionForKnownLCMSMap (const FeatureMap<> &features, const MSExperiment< InputPeakType > &experiment, MSExperiment< InputPeakType > &ms2, std::set< Int > &charges_set, bool feature_based)
	Makes the precursor selection for a given feature map, either feature or scan based.
template<typename InputPeakType >
void	getMassRanges (const FeatureMap<> &features, const MSExperiment< InputPeakType > &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.
void	createProteinSequenceBasedLPInclusionList (String include, String rt_model_file, String pt_model_file, FeatureMap<> &precursors)
void	setLPSolver (LPWrapper::SOLVER solver)
LPWrapper::SOLVER	getLPSolver ()
Private Member Functions
template<typename InputPeakType >
void	calculateXICs_ (const FeatureMap<> &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, DoubleReal > > > &xics)
	Calculate the sum of intensities of relevant features for each scan separately.
template<typename InputPeakType >
void	checkMassRanges_ (std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const MSExperiment< InputPeakType > &experiment)
	Eliminates overlapping peaks.
template<typename T >
void	updateExclusionList_ (std::vector< std::pair< T, Size > > &exclusion_list)
void	updateExclusionList_ (std::map< std::pair< DoubleReal, DoubleReal >, Size, PairComparatorSecondElement< std::pair< DoubleReal, DoubleReal > > > &exclusion_list)
Private Attributes
LPWrapper::SOLVER	solver_

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_peak_distance	float	3	min: 0	The minimal distance (in Da) of two peaks in one spectrum so that they can be selected.
selection_window	float	2	min: 0	All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation.
exclude_overlapping_peaks	string	false	true, false	If true overlapping or nearby peaks (within min_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

typedef PSLPFormulation::IndexTriple IndexTriple

Constructor & Destructor Documentation

OfflinePrecursorIonSelection ( )

virtual ~OfflinePrecursorIonSelection ( ) [virtual]

Member Function Documentation

void calculateXICs_	(	const FeatureMap<> &	features,
		const std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const MSExperiment< InputPeakType > &	experiment,
		const std::set< Int > &	charges_set,
		std::vector< std::vector< std::pair< Size, DoubleReal > > > &	xics
	)			`[private]`

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

void checkMassRanges_	(	std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const MSExperiment< InputPeakType > &	experiment
	)			`[private]`

Eliminates overlapping peaks.

References Param::getValue(), and DefaultParamHandler::param_.

Referenced by OfflinePrecursorIonSelection::getMassRanges().

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

LPWrapper::SOLVER getLPSolver ( ) [inline]

void getMassRanges	(	const FeatureMap<> &	features,
		const MSExperiment< InputPeakType > &	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

References OfflinePrecursorIonSelection::checkMassRanges_(), Param::getValue(), DefaultParamHandler::param_, and MSExperiment< PeakT, ChromatogramPeakT >::RTBegin().

Referenced by OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().

void makePrecursorSelectionForKnownLCMSMap	(	const FeatureMap<> &	features,
		const MSExperiment< InputPeakType > &	experiment,
		MSExperiment< InputPeakType > &	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

References IntList::create(), PSLPFormulation::createAndSolveILPForKnownLCMSMapFeatureBased(), OfflinePrecursorIonSelection::getMassRanges(), Peak1D::getMZ(), MSSpectrum< PeakT >::getRT(), Param::getValue(), DIntervalBase< D >::maxY(), DIntervalBase< D >::minY(), OPENMS_PRECONDITION, DefaultParamHandler::param_, MSExperiment< PeakT, ChromatogramPeakT >::RTBegin(), MSExperiment< PeakT, ChromatogramPeakT >::RTEnd(), Precursor::setCharge(), Peak1D::setIntensity(), DIntervalBase< D >::setMaxY(), MetaInfoInterface::setMetaValue(), DIntervalBase< D >::setMinY(), MSSpectrum< PeakT >::setMSLevel(), Peak1D::setMZ(), SpectrumSettings::setPrecursors(), MSSpectrum< PeakT >::setRT(), MSSpectrum< PeakT >::sortByIntensity(), and OfflinePrecursorIonSelection::updateExclusionList_().

void setLPSolver ( LPWrapper::SOLVER solver ) [inline]

void updateExclusionList_ ( std::vector< std::pair< T, Size > > & exclusion_list ) [private]

Referenced by OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap().

void updateExclusionList_ ( std::map< std::pair< DoubleReal, DoubleReal >, Size, PairComparatorSecondElement< std::pair< DoubleReal, DoubleReal > > > & exclusion_list ) [inline, private]

Member Data Documentation

LPWrapper::SOLVER solver_ [private]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1

OfflinePrecursorIonSelection Class Reference

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation