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

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

Inheritance diagram for MultiplexFilteringProfile:

Public Member Functions
	MultiplexFilteringProfile (const PeakMap &exp_profile, const PeakMap &exp_picked, const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &boundaries, 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...

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

Public Member Functions inherited from 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 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...

Private Member Functions
int	nonLocalIntensityFilter_ (const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &mz_shifts_actual, const std::vector< int > &mz_shifts_actual_indices, SplineSpectrum::Navigator nav, std::vector< double > &intensities_actual, int peaks_found_in_all_peptides, double mz) const
	non-local intensity filter More...

int	findNearest_ (int spectrum_index, double mz, double scaling) const
	returns the index of a peak which is nearest m/z (for initialisation of peak registry) More...

Private Attributes
PeakMap	exp_profile_
	profile experimental data and peak boundaries More...

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

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

Protected Member Functions inherited from MultiplexFiltering
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...

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
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_

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	(	const PeakMap &	exp_profile,
		const PeakMap &	exp_picked,
		const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &	boundaries,
		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_profile	experimental data in profile mode
exp_picked	experimental data in centroid mode
boundaries	peak boundaries for exp_picked
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).
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<MultiplexFilterResult> 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; MultiplexFilterResult

◆ findNearest_()

int findNearest_	(	int	spectrum_index,
		double	mz,
		double	scaling
	)		const

private

returns the index of a peak which is nearest m/z (for initialisation of peak registry)

Parameters

spectrum_index	index of the spectrum in exp_picked_ and boundaries_
mz	m/z position of the peak
scaling	rescaling of the peak boundaries

Returns: index of the peak in spectrum or -1 if no peak is present within this tolerance

◆ nonLocalIntensityFilter_()

int nonLocalIntensityFilter_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::vector< double > &	mz_shifts_actual,
		const std::vector< int > &	mz_shifts_actual_indices,
		SplineSpectrum::Navigator	nav,
		std::vector< double > &	intensities_actual,
		int	peaks_found_in_all_peptides,
		double	mz
	)		const

private

non-local intensity filter

Checks if the intensities at the pattern positions are above the intensity cutoff. We check not only at m/z but at all pattern positions i.e. non-locally.

Parameters

pattern	pattern of isotopic peaks to be searched for
mz_shifts_actual	actual m/z shifts seen in the spectrum (will differ slightly from expected m/z shifts in pattern)
mz_shifts_actual_indices	indices of peaks corresponding to the pattern
nav	navigator for moving on the spline-interpolated spectrum
intensities_actual	output for the spline-interpolated intensities at the actual m/z shift positions
peaks_found_in_all_peptides	number of isotopic peaks seen for each peptide (peaks)
mz	reference m/z position of the pattern (mono-isotopic peak of the lightest peptide)

Returns: number of isotopic peaks seen for each peptide (profile)

Member Data Documentation

◆ boundaries_

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

private

◆ exp_profile_

PeakMap exp_profile_

private

profile experimental 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()

◆ findNearest_()

◆ nonLocalIntensityFilter_()

Member Data Documentation

◆ boundaries_

◆ exp_profile_