filters centroided and profile data for peak patterns More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteringProfile.h>

Inheritance diagram for MultiplexFilteringProfile:

Collaboration diagram for MultiplexFilteringProfile:

Public Member Functions
	MultiplexFilteringProfile (MSExperiment &exp_profile, const MSExperiment &exp_centroided, const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &boundaries, const std::vector< MultiplexIsotopicPeakPattern > &patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide")
	constructor More...

std::vector< MultiplexFilteredMSExperiment >	filter ()
	filter for patterns (generates a filter result for each of the patterns) More...

std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &	getPeakBoundaries ()
	returns the intensity-filtered peak boundaries More...

Public Member Functions inherited from MultiplexFiltering
	MultiplexFiltering (const MSExperiment &exp_centroided, const std::vector< MultiplexIsotopicPeakPattern > &patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide")
	constructor More...

MSExperiment &	getCentroidedExperiment ()
	returns the intensity-filtered, centroided spectral data More...

MSExperiment	getBlacklist ()
	returns the blacklisted, centroided peaks More...

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

virtual	~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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Member Functions
bool	filterAveragineModel_ (const MultiplexIsotopicPeakPattern &pattern, const MultiplexFilteredPeak &peak, const std::multimap< size_t, MultiplexSatelliteProfile > &satellites_profile) const
	averagine filter for profile mode More...

bool	filterPeptideCorrelation_ (const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteProfile > &satellites_profile) const
	peptide correlation filter for profile mode More...

Private Attributes
std::vector< SplineInterpolatedPeaks >	exp_spline_profile_
	spline interpolated profile data and peak boundaries More...

std::vector< std::vector< PeakPickerHiRes::PeakBoundary > >	boundaries_

Additional Inherited Members
Public Types inherited from MultiplexFiltering
typedef std::vector< std::map< int, int > >	White2Original
	index mapping from a 'white' experiment to its original experiment More...

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

Protected Member Functions inherited from MultiplexFiltering
void	updateWhiteMSExperiment_ ()
	construct an MS experiment from exp_centroided_ containing peaks which have not been previously blacklisted in blacklist_ More...

int	checkForSignificantPeak_ (double mz, double mz_tolerance, MSExperiment::ConstIterator &it_rt, double intensity_first_peak) const
	check for significant peak More...

bool	filterPeakPositions_ (double mz, const MSExperiment::ConstIterator &it_rt_begin, const MSExperiment::ConstIterator &it_rt_band_begin, const MSExperiment::ConstIterator &it_rt_band_end, const MultiplexIsotopicPeakPattern &pattern, MultiplexFilteredPeak &peak) const
	check if there are enough peaks in the RT band to form the pattern More...

void	blacklistPeak_ (const MultiplexFilteredPeak &peak)
	blacklist this peak More...

void	blacklistPeak_ (const MultiplexFilteredPeak &peak, unsigned pattern_idx)
	blacklist this peak More...

bool	filterAveragineModel_ (const MultiplexIsotopicPeakPattern &pattern, const MultiplexFilteredPeak &peak) const
	check if the satellite peaks conform with the averagine model More...

bool	filterPeptideCorrelation_ (const MultiplexIsotopicPeakPattern &pattern, const MultiplexFilteredPeak &peak) const
	check if corresponding satellite peaks of different peptides show a good correlation More...

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 MultiplexFiltering
MSExperiment	exp_centroided_
	centroided experimental data More...

std::vector< std::vector< int > >	blacklist_
	auxiliary structs for blacklisting More...

MSExperiment	exp_centroided_white_
	"white" centroided experimental data More...

White2Original	exp_centroided_mapping_
	mapping of peak indices from a 'white' experiment exp_centroided_white_ to its original experiment exp_centroided_ More...

std::vector< MultiplexIsotopicPeakPattern >	patterns_
	list of peak patterns More...

size_t	isotopes_per_peptide_min_
	minimum number of isotopic peaks per peptide More...

size_t	isotopes_per_peptide_max_
	maximum number of isotopic peaks per peptide More...

double	intensity_cutoff_
	intensity cutoff More...

double	rt_band_
	RT range used for filtering. More...

double	mz_tolerance_
	m/z shift tolerance More...

bool	mz_tolerance_unit_in_ppm_
	unit for m/z shift tolerance (ppm - true, Da - false) More...

double	peptide_similarity_
	peptide similarity More...

double	averagine_similarity_
	averagine similarity More...

double	averagine_similarity_scaling_
	averagine similarity scaling More...

String	averagine_type_
	type of averagine to use 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

filters centroided and profile data for peak patterns

The algorithm searches for patterns of multiple peptides in the data. The peptides appear as characteristic patterns of isotopic peaks in MS1 spectra. We first search the centroided data, and optionally in a second step the spline interpolated profile data. For each peak pattern the algorithm generates a filter result.

See also: MultiplexIsotopicPeakPattern; MultiplexFilterResult; MultiplexFiltering

Constructor & Destructor Documentation

◆ MultiplexFilteringProfile()

MultiplexFilteringProfile	(	MSExperiment &	exp_profile,
		const MSExperiment &	exp_centroided,
		const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &	boundaries,
		const std::vector< MultiplexIsotopicPeakPattern > &	patterns,
		int	isotopes_per_peptide_min,
		int	isotopes_per_peptide_max,
		double	intensity_cutoff,
		double	rt_band,
		double	mz_tolerance,
		bool	mz_tolerance_unit,
		double	peptide_similarity,
		double	averagine_similarity,
		double	averagine_similarity_scaling,
		String	averagine_type = `"peptide"`
	)

constructor

Parameters

exp_profile	experimental data in profile mode
exp_centroided	experimental data in centroid mode
boundaries	peak boundaries for exp_centroided
patterns	patterns of isotopic peaks to be searched for
isotopes_per_peptide_min	minimum number of isotopic peaks in peptides
isotopes_per_peptide_max	maximum number of isotopic peaks in peptides
intensity_cutoff	intensity cutoff
rt_band	RT range used for filtering
mz_tolerance	error margin in m/z for matching expected patterns to experimental data
mz_tolerance_unit	unit for mz_tolerance, ppm (true), Da (false)
peptide_similarity	similarity score for two peptides in the same multiplet
averagine_similarity	similarity score for peptide isotope pattern and averagine model
averagine_similarity_scaling	scaling factor x for the averagine similarity parameter p when detecting peptide singlets. With p' = p + x(1-p).
averagine_type	The averagine model to use, current options are RNA DNA or peptide.

Exceptions

Exception::IllegalArgument	if profile and centroided data do not contain same number of spectra
Exception::IllegalArgument	if centroided data and the corresponding list of peak boundaries do not contain same number of spectra

Member Function Documentation

◆ filter()

std::vector<MultiplexFilteredMSExperiment> filter ( )

filter for patterns (generates a filter result for each of the patterns)

Exceptions

Exception::IllegalArgument if number of peaks and number of peak boundaries differ

See also: MultiplexIsotopicPeakPattern; MultiplexFilteredMSExperiment

◆ filterAveragineModel_()

bool filterAveragineModel_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const MultiplexFilteredPeak &	peak,
		const std::multimap< size_t, MultiplexSatelliteProfile > &	satellites_profile
	)		const

private

averagine filter for profile mode

Parameters

pattern	m/z pattern to search for
peak	peak to be filtered
satellites	spline-interpolated satellites of the peak. If they pass, they will be added to the peak.

Returns: boolean if this filter was passed i.e. the correlation coefficient is greater than <averagine_similarity_>

◆ filterPeptideCorrelation_()

bool filterPeptideCorrelation_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::multimap< size_t, MultiplexSatelliteProfile > &	satellites_profile
	)		const

private

peptide correlation filter for profile mode

Parameters

pattern	m/z pattern to search for
satellites	spline-interpolated satellites of the peak. If they pass, they will be added to the peak.

Returns: boolean if this filter was passed i.e. the correlation coefficient is greater than <averagine_similarity_>

◆ getPeakBoundaries()

std::vector<std::vector<PeakPickerHiRes::PeakBoundary> >& getPeakBoundaries ( )

returns the intensity-filtered peak boundaries

Member Data Documentation

◆ boundaries_

std::vector<std::vector<PeakPickerHiRes::PeakBoundary> > boundaries_

private

◆ exp_spline_profile_

std::vector<SplineInterpolatedPeaks> exp_spline_profile_

private

spline interpolated profile data and peak boundaries

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MultiplexFilteringProfile()

Member Function Documentation

◆ filter()

◆ filterAveragineModel_()

◆ filterPeptideCorrelation_()

◆ getPeakBoundaries()

Member Data Documentation

◆ boundaries_

◆ exp_spline_profile_