filters centroided data for peak patterns More...

#include <OpenMS/FEATUREFINDER/MultiplexFilteringCentroided.h>

Inheritance diagram for MultiplexFilteringCentroided:

Public Member Functions
	MultiplexFilteringCentroided (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

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

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

std::vector< std::vector< BlacklistOwner > >	getBlacklistOwners () const
	the owners of the blacklisted peaks, aligned with getBlacklist(): one list per spectrum, one entry per peak

std::vector< BlacklistOwner >	getBlacklistOwners (Size spectrum_index) const
	the owners of the blacklisted peaks of one spectrum, aligned with that spectrum of getBlacklist()

void	setDeuteriumLabels (const std::map< std::string, DeuteriumLabel > &labels)
	take the lower isotopologue of deuterium labels into account where a peak one isotope below a peptide is checked

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)

Additional Inherited Members
Public Types inherited from MultiplexFiltering
typedef std::vector< std::vector< 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...

Static Public Member Functions inherited from MultiplexFiltering
static double	deuteriumLowerFraction (unsigned deuterium, double enrichment, const IsotopeDistribution &isotopes)
	the peak one isotope below a deuterium-labelled peptide that its own label isotopologues produce, relative to its monoisotopic peak

static double	deuteriumAllowance (unsigned deuterium, double enrichment, const IsotopeDistribution &isotopes)
	the part of the peak one isotope below a deuterium-labelled peptide that the check for another envelope allows, relative to its monoisotopic peak

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, double fraction=0.3) const
	check for significant peak

double	deuteriumAllowance_ (const MultiplexIsotopicPeakPattern &pattern, size_t peptide, double mz) const
	deuteriumAllowance() for peptide `peptide` of `pattern` (monoisotopic m/z `mz`), with its deuterium labels (setDeuteriumLabels()); 0 without 2H

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, unsigned pattern_idx, size_t peak_idx)
	blacklist this peak

void	applyBlacklistEntries_ (const std::vector< BlacklistEntry > &entries, unsigned pattern_idx, size_t peak_idx)
	write `entries` to blacklist_, with the filtered peak (`pattern_idx`, `peak_idx`) as their owner

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

const IsotopeDistribution &	averagineDistribution_ (double mass) const
	averagine isotope distribution (of the type averagine_type_, with isotopes_per_peptide_max_ isotopes) of a molecule of `mass`

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< int > >	blacklist_owner_
	for every peak of blacklist_, who reserved it

std::vector< BlacklistOwnerRecord >	blacklist_owner_records_
	the first and the last owner of every peak reserved by more than one filtered peak (see blacklist_owner_)

std::vector< std::pair< unsigned, unsigned > >	filtered_peaks_
	every filtered peak that passed, in the order they passed: index of its pattern and its index in the pattern's filter result

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_())

std::vector< std::optional< MultiplexFilteredPeak > >	passed_
	the decision of filterSpectrum_() on each peak of the spectrum (reused, as blacklist_reads_)

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

std::vector< std::vector< DeuteriumLabel > >	deuterium_
	the deuterium labels of each peptide of each mass shift pattern (index: MultiplexIsotopicPeakPattern::getMassShiftIndex()), empty for a pattern without 2H (setDeuteriumLabels())

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 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 search the centroided data for such patterns. For each peak pattern the algorithm generates a filter result.

See also: MultiplexIsotopicPeakPattern; MultiplexFilterResult; MultiplexFiltering

Constructor & Destructor Documentation

◆ MultiplexFilteringCentroided()

MultiplexFilteringCentroided	(	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

Parameters

[in]	exp_centroided	experimental data in centroid mode
[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 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.

Member Function Documentation

◆ filter()

std::vector< MultiplexFilteredMSExperiment > filter ( )

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

See also: MultiplexIsotopicPeakPattern, MultiplexFilterResult

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MultiplexFilteringCentroided()

Member Function Documentation

◆ filter()