base class for filtering centroided and profile data for peak patterns More...

#include <OpenMS/FEATUREFINDER/MultiplexFiltering.h>

Inheritance diagram for MultiplexFiltering:

Collaboration diagram for MultiplexFiltering:

Public Types
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...

Public Member Functions
	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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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...

Protected Member Functions
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...

Protected Attributes
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_

Additional Inherited Members
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

base class for filtering 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.

The algorithm differs slightly for centroided and profile input data. This base class comprises code common to both. The two child classes MultiplexFilteringCentroided and MultiplexFilteringProfile contain specific functions and the primary filter() method.

See also: MultiplexIsotopicPeakPattern; MultiplexFilteredMSExperiment; MultiplexFilteringCentroided; MultiplexFilteringProfile

Member Typedef Documentation

◆ White2Original

typedef std::vector<std::map<int, int> > White2Original

index mapping from a 'white' experiment to its original experiment

An MSExperiment contains a set of spectra each containing a number of peaks. In the course of the filtering, some peaks are blacklisted since they are identified to belong to a certain pattern i.e. peptide. An experiment in which blacklisted peaks are removed is called 'white'. White spectra contain fewer peaks than their corresponding primary spectra. Consequently, their indices are shifted. The type maps a peak index in a 'white' spectrum back to its original spectrum.

Constructor & Destructor Documentation

◆ 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

Parameters

exp_centroided	experimental data in centroid mode
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	Averagine model to use: 'peptide', 'RNA', 'DNA'

Member Function Documentation

◆ blacklistPeak_() [1/2]

void blacklistPeak_ ( const MultiplexFilteredPeak & peak )

protected

blacklist this peak

Blacklist all satellites associated with this peak.

Parameters

peak	peak to be blacklisted

◆ blacklistPeak_() [2/2]

void blacklistPeak_	(	const MultiplexFilteredPeak &	peak,
		unsigned	pattern_idx
	)

protected

blacklist this peak

Each of the satellites is associated with a specific mass trace. We blacklist all peaks in these mass traces (even if they are not a satellite) extending them by a margin rt_band_.

Parameters

peak	peak to be blacklisted
pattern_idx	index of the pattern in patterns_

◆ checkForSignificantPeak_()

int checkForSignificantPeak_	(	double	mz,
		double	mz_tolerance,
		MSExperiment::ConstIterator &	it_rt,
		double	intensity_first_peak
	)		const

protected

check for significant peak

Parameters

mz	position where the peak is expected
mz_tolerance	m/z tolerance within the peak may lie
it_rt	pointer to the spectrum
intensity_first_peak	intensity to compare to

Returns: -1 (if there is no significant peak), or peak index mz_idx (if there is a significant peak)

◆ filterAveragineModel_()

bool filterAveragineModel_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const MultiplexFilteredPeak &	peak
	)		const

protected

check if the satellite peaks conform with the averagine model

Check if the intensities of the satellite peaks correlate with the peak intensities of the averagine model. We check both Pearson and Spearman rank correlation.

Parameters

pattern	m/z pattern to search for
peak	peak with set of satellite peaks

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

◆ filterPeakPositions_()

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

protected

check if there are enough peaks in the RT band to form the pattern

Checks if there are peaks at m/z positions corresponding to the pattern and that the primary peak position is not blacklisted.

Parameters

mz	m/z of the primary peak
it_rt_begin	RT iterator of the very first spectrum of the experiment (needed to determine indices)
it_rt_band_begin	RT iterator of the first spectrum in the RT band
it_rt_band_end	RT iterator of the spectrum after the last spectrum in the RT band
pattern	m/z pattern to search for
peak	filter result output

Returns: boolean if this filter was passed i.e. there are isotopes_per_peptide_min_ or more mass traces which form the pattern.

◆ filterPeptideCorrelation_()

bool filterPeptideCorrelation_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const MultiplexFilteredPeak &	peak
	)		const

protected

check if corresponding satellite peaks of different peptides show a good correlation

Different peptides in the same multiplet have the same amino acid sequence and should therefore exhibit very similar isotope distributions. The filter checks if satellite peaks corresponding to different isotopes in different peptide features show a strong correlation. The filter is of course ignored for singlet feature detection.

Parameters

pattern	m/z pattern to search for
peak	peak with set of satellite peaks

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

◆ getBlacklist()

MSExperiment getBlacklist ( )

returns the blacklisted, centroided peaks

◆ getCentroidedExperiment()

MSExperiment& getCentroidedExperiment ( )

returns the intensity-filtered, centroided spectral data

◆ updateWhiteMSExperiment_()

void updateWhiteMSExperiment_ ( )

protected

construct an MS experiment from exp_centroided_ containing peaks which have not been previously blacklisted in blacklist_

In addition, construct an index mapping of 'white' peak positions to their position in the corresponding, original spectrum.

Member Data Documentation

◆ averagine_similarity_

double averagine_similarity_

protected

averagine similarity

◆ averagine_similarity_scaling_

double averagine_similarity_scaling_

protected

averagine similarity scaling

◆ averagine_type_

String averagine_type_

protected

type of averagine to use

◆ blacklist_

std::vector<std::vector<int> > blacklist_

protected

auxiliary structs for blacklisting

◆ exp_centroided_

MSExperiment exp_centroided_

protected

centroided experimental data

◆ exp_centroided_mapping_

White2Original exp_centroided_mapping_

protected

mapping of peak indices from a 'white' experiment exp_centroided_white_ to its original experiment exp_centroided_

◆ exp_centroided_white_

MSExperiment exp_centroided_white_

protected

"white" centroided experimental data

subset of all peaks of exp_centroided_ which are not blacklisted in blacklist_

◆ intensity_cutoff_

double intensity_cutoff_

protected

intensity cutoff

◆ isotopes_per_peptide_max_

size_t isotopes_per_peptide_max_

protected

maximum number of isotopic peaks per peptide

◆ isotopes_per_peptide_min_

size_t isotopes_per_peptide_min_

protected

minimum number of isotopic peaks per peptide

◆ mz_tolerance_

double mz_tolerance_

protected

m/z shift tolerance

◆ mz_tolerance_unit_in_ppm_

bool mz_tolerance_unit_in_ppm_

protected

unit for m/z shift tolerance (ppm - true, Da - false)

◆ patterns_

std::vector<MultiplexIsotopicPeakPattern> patterns_

protected

list of peak patterns

◆ peptide_similarity_

double peptide_similarity_

protected

peptide similarity

◆ rt_band_

double rt_band_

protected

RT range used for filtering.

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ White2Original

Constructor & Destructor Documentation

◆ MultiplexFiltering()

Member Function Documentation

◆ blacklistPeak_() [1/2]

◆ blacklistPeak_() [2/2]

◆ checkForSignificantPeak_()

◆ filterAveragineModel_()

◆ filterPeakPositions_()

◆ filterPeptideCorrelation_()

◆ getBlacklist()

◆ getCentroidedExperiment()

◆ updateWhiteMSExperiment_()

Member Data Documentation

◆ averagine_similarity_

◆ averagine_similarity_scaling_

◆ averagine_type_

◆ blacklist_

◆ exp_centroided_

◆ exp_centroided_mapping_

◆ exp_centroided_white_

◆ intensity_cutoff_

◆ isotopes_per_peptide_max_

◆ isotopes_per_peptide_min_

◆ mz_tolerance_

◆ mz_tolerance_unit_in_ppm_

◆ patterns_

◆ peptide_similarity_

◆ rt_band_