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

#include <OpenMS/FEATUREFINDER/MultiplexFilteringProfile.h>

Inheritance 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, std::string averagine_type="peptide")
	constructor

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

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

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, std::string averagine_type="peptide")
	constructor

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

MSExperiment	getBlacklist ()
	returns the blacklisted, centroided peaks

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.

virtual	~ProgressLogger ()
	Destructor.

	ProgressLogger (const ProgressLogger &other)
	Copy constructor.

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!

LogType	getLogType () const
	Returns the type of progress log being used.

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.

void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.

void	setProgress (SignedSize value) const
	Sets the current progress.

void	endProgress (UInt64 bytes_processed=0) const

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

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

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

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

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

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

Protected Types inherited from MultiplexFiltering
typedef std::function< std::optional< MultiplexFilteredPeak >(SignedSize, std::vector< BlacklistEntry > *)>	PeakFilter
	decides on one peak of a 'white' spectrum

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_

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

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, std::vector< BlacklistEntry > *blacklist_reads=nullptr) const
	check if there are enough peaks in the RT band to form the pattern

void	blacklistPeak_ (const MultiplexFilteredPeak &peak)
	blacklist this peak

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

void	blacklistEntries_ (const MultiplexFilteredPeak &peak, unsigned pattern_idx, std::vector< BlacklistEntry > &entries) const
	the entries of blacklist_ that blacklistPeak_() sets, with their new values, in the order it sets them

void	filterSpectrum_ (size_t idx_rt, unsigned pattern_idx, const PeakFilter &filter_peak, MultiplexFilteredMSExperiment &result)
	filter all peaks of one 'white' spectrum, add the ones that pass to `result` and blacklist them

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

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

Protected Attributes inherited from MultiplexFiltering
MSExperiment	exp_centroided_
	centroided experimental data

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

std::vector< std::vector< BlacklistEntry > >	blacklist_reads_
	for each peak of the spectrum being filtered, the entries of blacklist_ its decision read (see filterSpectrum_())

std::vector< std::vector< BlacklistEntry > >	blacklist_writes_
	for each peak of the spectrum being filtered that passes, the entries of blacklist_ it sets (see filterSpectrum_())

MSExperiment	exp_centroided_white_
	"white" centroided experimental data

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

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

size_t	isotopes_per_peptide_min_
	minimum number of isotopic peaks per peptide

size_t	isotopes_per_peptide_max_
	maximum number of isotopic peaks per peptide

double	intensity_cutoff_
	intensity cutoff

double	rt_band_
	RT range used for filtering.

double	mz_tolerance_
	m/z shift tolerance

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

double	peptide_similarity_
	peptide similarity

double	averagine_similarity_
	averagine similarity

double	averagine_similarity_scaling_
	averagine similarity scaling

std::string	averagine_type_
	type of averagine to use

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static std::atomic< 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,
		std::string	averagine_type = `"peptide"`
	)

constructor

Parameters

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

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

Returns: 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

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

Returns: 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_