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

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

Inheritance diagram for MultiplexFiltering:

Classes
struct	BlackListEntry
	structure for peak blacklisting More...

struct	PeakReference
	structure for peak position in neighbouring spectra More...

Public Member Functions
	MultiplexFiltering (const PeakMap &exp_picked, const std::vector< MultiplexIsotopicPeakPattern > patterns, int peaks_per_peptide_min, int peaks_per_peptide_max, bool missing_peaks, double intensity_cutoff, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide")
	constructor 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
int	positionsAndBlacklistFilter_ (const MultiplexIsotopicPeakPattern &pattern, int spectrum, const std::vector< double > &peak_position, int peak, std::vector< double > &mz_shifts_actual, std::vector< int > &mz_shifts_actual_indices) const
	position and blacklist filter More...

bool	monoIsotopicPeakIntensityFilter_ (const MultiplexIsotopicPeakPattern &pattern, int spectrum_index, const std::vector< int > &mz_shifts_actual_indices) const
	mono-isotopic peak intensity filter More...

bool	zerothPeakFilter_ (const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &intensities_actual) const
	zeroth peak filter More...

bool	peptideSimilarityFilter_ (const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &intensities_actual, int peaks_found_in_all_peptides_spline) const
	peptide similarity filter More...

bool	averagineSimilarityFilter_ (const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &intensities_actual, int peaks_found_in_all_peptides_spline, double mz) const
	averagine similarity filter More...

void	blacklistPeaks_ (const MultiplexIsotopicPeakPattern &pattern, int spectrum, const std::vector< int > &mz_shifts_actual_indices, int peaks_found_in_all_peptides_spline)
	blacklist peaks More...

int	getPeakIndex_ (const std::vector< double > &peak_position, int start, double mz, double scaling) const
	returns the index of a peak at m/z (finds not only a valid peak, i.e. within certain m/z deviation, but the best of the valid peaks) More...

double	getPatternSimilarity_ (const std::vector< double > &pattern1, const std::vector< double > &pattern2) const
	returns similarity of two isotope patterns (simple Pearson correlation coefficient) More...

double	getAveragineSimilarity_ (const std::vector< double > &pattern, double m) const
	returns similarity of an isotope pattern and an averagine pattern at mass m More...

Protected Attributes
PeakMap	exp_picked_
	centroided experimental data More...

std::vector< std::vector< PeakReference > >	registry_
	auxiliary structs for navigation and blacklisting More...

std::vector< std::vector< BlackListEntry > >	blacklist_

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

int	peaks_per_peptide_min_
	minimum number of isotopic peaks per peptide More...

int	peaks_per_peptide_max_
	maximum number of isotopic peaks per peptide More...

bool	missing_peaks_
	flag for missing peaks More...

double	intensity_cutoff_
	intensity cutoff More...

double	mz_tolerance_
	m/z shift tolerance More...

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

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; MultiplexFilterResult; MultiplexFilteringCentroided; MultiplexFilteringProfile

Constructor & Destructor Documentation

◆ MultiplexFiltering()

MultiplexFiltering	(	const PeakMap &	exp_picked,
		const std::vector< MultiplexIsotopicPeakPattern >	patterns,
		int	peaks_per_peptide_min,
		int	peaks_per_peptide_max,
		bool	missing_peaks,
		double	intensity_cutoff,
		double	mz_tolerance,
		bool	mz_tolerance_unit,
		double	peptide_similarity,
		double	averagine_similarity,
		double	averagine_similarity_scaling,
		String	averagine_type = `"peptide"`
	)

constructor

Parameters

exp_picked	experimental data in centroid mode
patterns	patterns of isotopic peaks to be searched for
peaks_per_peptide_min	minimum number of isotopic peaks in peptides
peaks_per_peptide_max	maximum number of isotopic peaks in peptides
missing_peaks	flag for missing peaks
intensity_cutoff	intensity cutoff
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).

Member Function Documentation

◆ averagineSimilarityFilter_()

bool averagineSimilarityFilter_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::vector< double > &	intensities_actual,
		int	peaks_found_in_all_peptides_spline,
		double	mz
	)		const

protected

averagine similarity filter

Checks similarity of the isotopic distribution with the expected averagine distribution. Does the isotope distribution look like a peptide?

Parameters

pattern	pattern of isotopic peaks to be searched for
intensities_actual	spline-interpolated intensities at the actual m/z shift positions
peaks_found_in_all_peptides_spline	number of isotopic peaks seen for each peptide (profile)
mz	m/z at which the averagine distribution is calculated

Returns: true if isotope distribution looks like an average peptide

◆ blacklistPeaks_()

void blacklistPeaks_	(	const MultiplexIsotopicPeakPattern &	pattern,
		int	spectrum,
		const std::vector< int > &	mz_shifts_actual_indices,
		int	peaks_found_in_all_peptides_spline
	)

protected

blacklist peaks

If a datapoint passes all filters, the corresponding peak in this and the two neighbouring spectra is blacklisted.

Parameters

pattern	pattern of isotopic peaks to be searched for
spectrum	index of the spectrum in exp_picked_ and boundaries_
peaks_found_in_all_peptides_spline	number of isotopic peaks seen for each peptide (profile)

◆ getAveragineSimilarity_()

double getAveragineSimilarity_	(	const std::vector< double > &	pattern,
		double	m
	)		const

protected

returns similarity of an isotope pattern and an averagine pattern at mass m

Parameters

pattern	isotope pattern
m	mass at which the averagine distribution is calculated

Returns: similarity (+1 best, -1 worst)

◆ getPatternSimilarity_()

double getPatternSimilarity_	(	const std::vector< double > &	pattern1,
		const std::vector< double > &	pattern2
	)		const

protected

returns similarity of two isotope patterns (simple Pearson correlation coefficient)

Parameters

pattern1	isotope pattern 1
pattern2	isotope pattern 2

Returns: similarity (+1 best, -1 worst)

◆ getPeakIndex_()

int getPeakIndex_	(	const std::vector< double > &	peak_position,
		int	start,
		double	mz,
		double	scaling
	)		const

protected

returns the index of a peak at m/z (finds not only a valid peak, i.e. within certain m/z deviation, but the best of the valid peaks)

Parameters

peak_position	m/z position of the peaks
start	index in peak_position for starting the search
mz	m/z position of the peak
scaling	rescaling of limits

Returns: index of the peak in spectrum

◆ monoIsotopicPeakIntensityFilter_()

bool monoIsotopicPeakIntensityFilter_	(	const MultiplexIsotopicPeakPattern &	pattern,
		int	spectrum_index,
		const std::vector< int > &	mz_shifts_actual_indices
	)		const

protected

mono-isotopic peak intensity filter

Quick check if the intensities of the mono-isotopic peaks are above the intensity cutoff.

Parameters

pattern	pattern of isotopic peaks to be searched for
spectrum_index	index of the spectrum in exp_picked_ and boundaries_
mz_shifts_actual_indices	indices of peaks corresponding to the pattern

Returns: true if all intensities above threshold

◆ peptideSimilarityFilter_()

bool peptideSimilarityFilter_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::vector< double > &	intensities_actual,
		int	peaks_found_in_all_peptides_spline
	)		const

protected

peptide similarity filter

The algorithm takes only MS1 spectra into account i.e. we have no knowledge of the peptide sequences. But we do know that peptides in a pair should have the same sequence and hence the same isotopic distributions. The filter checks the similarity of the lightest peptide with all of the other peptides of the pattern. (In high-complexity samples two peptides can have the correct mass shift by chance. Such accidental pairs show different isotopic distributions and are therefore filtered out.)

Parameters

pattern	pattern of isotopic peaks to be searched for
intensities_actual	spline-interpolated intensities at the actual m/z shift positions
peaks_found_in_all_peptides_spline	number of isotopic peaks seen for each peptide (profile)

Returns: true if peptide isotope patterns are similar

◆ positionsAndBlacklistFilter_()

int positionsAndBlacklistFilter_	(	const MultiplexIsotopicPeakPattern &	pattern,
		int	spectrum,
		const std::vector< double > &	peak_position,
		int	peak,
		std::vector< double > &	mz_shifts_actual,
		std::vector< int > &	mz_shifts_actual_indices
	)		const

protected

position and blacklist filter

Checks if there are peaks at positions corresponding to the pattern and that these peaks are not blacklisted.

Parameters

pattern	pattern of isotopic peaks to be searched for
spectrum	index of the spectrum in exp_picked_ and boundaries_
peak_position	m/z positions of the peaks in spectrum
peak	index of the peak in peak_position
mz_shifts_actual	output for actual m/z shifts seen in the spectrum (will differ slightly from expected m/z shifts in pattern)
mz_shifts_actual_indices	output for indices of peaks corresponding to the pattern

Returns: number of isotopic peaks seen for each peptide

◆ zerothPeakFilter_()

bool zerothPeakFilter_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::vector< double > &	intensities_actual
	)		const

protected

zeroth peak filter

The mono-isotopic peak is the first peak of each peptide. A peak one m/z shift to the left (e.g. 0.5Th for 2+) is called zeroth peak. High-intensity zeroth peaks indicate incorrect pattern matches. A different pattern is likely to be a better fit.

Parameters

pattern	pattern of isotopic peaks to be searched for
intensities_actual	spline-interpolated intensities at the actual m/z shift positions

Returns: true if there are high-intensity zeroth peaks

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<BlackListEntry> > blacklist_

protected

◆ exp_picked_

PeakMap exp_picked_

protected

centroided experimental data

◆ intensity_cutoff_

double intensity_cutoff_

protected

intensity cutoff

◆ missing_peaks_

bool missing_peaks_

protected

flag for missing peaks

◆ mz_tolerance_

double mz_tolerance_

protected

m/z shift tolerance

◆ mz_tolerance_unit_

bool mz_tolerance_unit_

protected

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

◆ patterns_

std::vector<MultiplexIsotopicPeakPattern> patterns_

protected

list of peak patterns

◆ peaks_per_peptide_max_

int peaks_per_peptide_max_

protected

maximum number of isotopic peaks per peptide

◆ peaks_per_peptide_min_

int peaks_per_peptide_min_

protected

minimum number of isotopic peaks per peptide

◆ peptide_similarity_

double peptide_similarity_

protected

peptide similarity

◆ registry_

std::vector<std::vector<PeakReference> > registry_

protected

auxiliary structs for navigation and blacklisting

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MultiplexFiltering()

Member Function Documentation

◆ averagineSimilarityFilter_()

◆ blacklistPeaks_()

◆ getAveragineSimilarity_()

◆ getPatternSimilarity_()

◆ getPeakIndex_()

◆ monoIsotopicPeakIntensityFilter_()

◆ peptideSimilarityFilter_()

◆ positionsAndBlacklistFilter_()

◆ zerothPeakFilter_()

Member Data Documentation

◆ averagine_similarity_

◆ averagine_similarity_scaling_

◆ averagine_type_

◆ blacklist_

◆ exp_picked_

◆ intensity_cutoff_

◆ missing_peaks_

◆ mz_tolerance_

◆ mz_tolerance_unit_

◆ patterns_

◆ peaks_per_peptide_max_

◆ peaks_per_peptide_min_

◆ peptide_similarity_

◆ registry_