Identification-free quantitative feature finder for SILAC / Dimethyl / ICPL-style label-pair experiments. More...

#include <OpenMS/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.h>

Inheritance diagram for FeatureFinderMultiplexAlgorithm:

Collaboration diagram for FeatureFinderMultiplexAlgorithm:

Public Member Functions
	FeatureFinderMultiplexAlgorithm ()
	Construct with built-in defaults; parameter sections `"algorithm"` and `"labels"` are registered. Call `setParameters` to override before run.

void	run (MSExperiment &exp, bool progress)
	Run the full detection pipeline on `exp` and populate the internal feature / consensus / blacklist maps.

FeatureMap &	getFeatureMap ()
	Return the FeatureMap populated by the most recent run call (empty before run).

ConsensusMap &	getConsensusMap ()
	Return the ConsensusMap of detected multiplets populated by the most recent run call (empty before run).

MSExperiment &	getBlacklist ()
	Return the per-pattern blacklist MSExperiment produced during run (peak regions consumed by detected multiplets).

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

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)

Protected Member Functions
std::vector< MultiplexIsotopicPeakPattern >	generatePeakPatterns_ (int charge_min, int charge_max, int peaks_per_peptide_max, const std::vector< MultiplexDeltaMasses > &mass_pattern_list)
	generate list of m/z shifts

void	correctPeptideIntensities_ (const MultiplexIsotopicPeakPattern &pattern, std::map< size_t, SplinePackage > &spline_chromatograms, const std::vector< double > &rt_peptide, std::vector< double > &intensity_peptide) const
	determine ratios through linear regression and correct peptide intensities

std::vector< double >	determinePeptideIntensitiesCentroided_ (const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteCentroided > &satellites)
	calculate peptide intensities

std::vector< double >	determinePeptideIntensitiesProfile_ (const MultiplexIsotopicPeakPattern &pattern, const std::multimap< size_t, MultiplexSatelliteProfile > &satellites)
	calculate peptide intensities

void	generateMapsCentroided_ (const std::vector< MultiplexIsotopicPeakPattern > &patterns, const std::vector< MultiplexFilteredMSExperiment > &filter_results, std::vector< std::map< int, GridBasedCluster > > &cluster_results)
	generates consensus and feature maps containing all peptide multiplets

void	generateMapsProfile_ (const std::vector< MultiplexIsotopicPeakPattern > &patterns, const std::vector< MultiplexFilteredMSExperiment > &filter_results, const std::vector< std::map< int, GridBasedCluster > > &cluster_results)
	generates consensus and feature maps containing all peptide multiplets

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Protected Attributes
MSExperiment	exp_profile_

MSExperiment	exp_centroid_

bool	centroided_

ProgressLogger	prog_log_

bool	progress_

unsigned	charge_min_

unsigned	charge_max_

unsigned	isotopes_per_peptide_min_

unsigned	isotopes_per_peptide_max_

std::map< std::string, double >	label_mass_shift_

FeatureMap	feature_map_

ConsensusMap	consensus_map_

MSExperiment	exp_blacklist_

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

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 Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Identification-free quantitative feature finder for SILAC / Dimethyl / ICPL-style label-pair experiments.

Detects pairs (or larger multiplets) of isotopic envelopes separated by fixed label-induced m/z shifts. Works on both profile and centroided MS1 spectra; no prior sequence identification is needed. Configurable via DefaultParamHandler (parameter sections "algorithm:*" and "labels:*"; defaults are set by the constructor).

Algorithm Three stages — filtering, clustering, and linear fitting:

Filtering retains data points where all isotope-pattern peaks (e.g. at m/z, m/z+0.5, m/z+1, m/z+3, m/z+3.5, m/z+4 for a doubly charged pair) clear an intensity threshold, show good profile correlation across the m/z range, and whose within-peptide intensity ratios match an averagine model within a per-call tolerance.
Clustering uses hierarchical methods on the surviving points in the t-m/z plane. Each cluster corresponds to the monoisotopic mass trace of the lightest peptide of a label pattern. The number of clusters is chosen by maximising the silhouette width.
Linear fitting on the in-cluster intensity pairs (e.g. [m/z, m/z+3], [m/z+0.5, m/z+3.5], [m/z+1, m/z+4] for a doubly charged pair) yields the relative amounts of labelled and unlabelled peptide.

Constructor & Destructor Documentation

◆ FeatureFinderMultiplexAlgorithm()

FeatureFinderMultiplexAlgorithm ( )

Construct with built-in defaults; parameter sections "algorithm" and "labels" are registered. Call setParameters to override before run.

Member Function Documentation

◆ correctPeptideIntensities_()

void correctPeptideIntensities_	(	const MultiplexIsotopicPeakPattern &	pattern,
		std::map< size_t, SplinePackage > &	spline_chromatograms,
		const std::vector< double > &	rt_peptide,
		std::vector< double > &	intensity_peptide
	)		const

protected

determine ratios through linear regression and correct peptide intensities

In most labelled mass spectrometry experiments, the fold change i.e. ratio and not the individual peptide intensities are of primary interest. For that reason, we determine the ratios from interpolated chromatogram data points directly, and then correct the current ones.

Parameters

[in]	pattern	Isotopic peak pattern
[in,out]	spline_chromatograms	Spline chromatograms to be used/modified
[in]	rt_peptide	Retention times of peptides
[out]	intensity_peptide	Corrected peptide intensities

◆ determinePeptideIntensitiesCentroided_()

std::vector< double > determinePeptideIntensitiesCentroided_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::multimap< size_t, MultiplexSatelliteCentroided > &	satellites
	)

protected

calculate peptide intensities

Parameters

[in]	pattern	Isotopic peak pattern
[in]	satellites	Satellite peaks

Returns: vector with intensities for each of the peptides

◆ determinePeptideIntensitiesProfile_()

std::vector< double > determinePeptideIntensitiesProfile_	(	const MultiplexIsotopicPeakPattern &	pattern,
		const std::multimap< size_t, MultiplexSatelliteProfile > &	satellites
	)

protected

calculate peptide intensities

Parameters

[in]	pattern	Isotopic peak pattern
[in]	satellites	Satellite peaks

Returns: vector with intensities for each of the peptides

◆ generateMapsCentroided_()

void generateMapsCentroided_	(	const std::vector< MultiplexIsotopicPeakPattern > &	patterns,
		const std::vector< MultiplexFilteredMSExperiment > &	filter_results,
		std::vector< std::map< int, GridBasedCluster > > &	cluster_results
	)

protected

generates consensus and feature maps containing all peptide multiplets

Parameters

[in]	patterns	patterns of isotopic peaks we have been searching for
[in]	filter_results	filter results for each of the patterns
[in,out]	cluster_results	clusters of filter results

◆ generateMapsProfile_()

void generateMapsProfile_	(	const std::vector< MultiplexIsotopicPeakPattern > &	patterns,
		const std::vector< MultiplexFilteredMSExperiment > &	filter_results,
		const std::vector< std::map< int, GridBasedCluster > > &	cluster_results
	)

protected

generates consensus and feature maps containing all peptide multiplets

Parameters

[in]	patterns	patterns of isotopic peaks we have been searching for
[in]	filter_results	filter results for each of the patterns
[in]	cluster_results	clusters of filter results

◆ generatePeakPatterns_()

std::vector< MultiplexIsotopicPeakPattern > generatePeakPatterns_	(	int	charge_min,
		int	charge_max,
		int	peaks_per_peptide_max,
		const std::vector< MultiplexDeltaMasses > &	mass_pattern_list
	)

protected

generate list of m/z shifts

Parameters

[in]	charge_min	minimum charge
[in]	charge_max	maximum charge
[in]	peaks_per_peptide_max	maximum number of isotopes in peptide
[in]	mass_pattern_list	mass shifts due to labelling

Returns: list of m/z shifts

◆ getBlacklist()

MSExperiment & getBlacklist ( )

Return the per-pattern blacklist MSExperiment produced during run (peak regions consumed by detected multiplets).

◆ getConsensusMap()

ConsensusMap & getConsensusMap ( )

Return the ConsensusMap of detected multiplets populated by the most recent run call (empty before run).

◆ getFeatureMap()

FeatureMap & getFeatureMap ( )

Return the FeatureMap populated by the most recent run call (empty before run).

◆ run()

void run	(	MSExperiment &	exp,
		bool	progress
	)

Run the full detection pipeline on exp and populate the internal feature / consensus / blacklist maps.

The pipeline:

Parses the configured charge and isotopes-per-peptide ranges from the "algorithm:charge" and "algorithm:isotopes_per_peptide" Param values (formatted as "min:max"; swapped silently if the input is reversed).
Loads the label mass shifts from the "labels:*" Param section into the in-class label_mass_shift_ map.
Clears exp's chromatograms, calls updateRanges and sortSpectra on it, and then moves exp into either the internal centroided or profile working buffer via MSExperiment::swap — after this call returns, the caller's exp is left empty.
Determines the spectrum type from "algorithm:spectrum_type": "automatic" reads exp[0].getType(true) and treats UNKNOWN as profile; "centroid" / "profile" force the choice.
When the input is in profile mode, runs PeakPickerHiRes::pickExperiment on "MS1" only with signal_to_noise = 0 (S/N estimation disabled).
Builds the label delta-mass list with MultiplexDeltaMassesGenerator, optionally extending it with knock-out delta masses when "algorithm:knock_out" is "true".
Generates isotopic peak patterns, runs the filter / cluster / linear-fit stages described in the class brief, and populates feature_map_, consensus_map_, and exp_blacklist_ accessible through the get* methods.

Parameters

[in,out]	exp	MS1 experiment to analyse. Chromatograms are cleared, ranges are recomputed, spectra sorted, and the container is moved into the internal working buffer — the caller's `exp` is empty on return.
[in]	progress	When `true`, progress is reported through the inherited ProgressLogger.

Exceptions

OpenMS::Exception::FileEmpty when exp has no spectra.

Member Data Documentation

◆ centroided_

bool centroided_

protected

◆ charge_max_

unsigned charge_max_

protected

◆ charge_min_

unsigned charge_min_

protected

◆ consensus_map_

ConsensusMap consensus_map_

protected

◆ exp_blacklist_

MSExperiment exp_blacklist_

protected

◆ exp_centroid_

MSExperiment exp_centroid_

protected

◆ exp_profile_

MSExperiment exp_profile_

protected

◆ feature_map_

FeatureMap feature_map_

protected

◆ isotopes_per_peptide_max_

unsigned isotopes_per_peptide_max_

protected

◆ isotopes_per_peptide_min_

unsigned isotopes_per_peptide_min_

protected

◆ label_mass_shift_

std::map<std::string, double> label_mass_shift_

protected

◆ prog_log_

ProgressLogger prog_log_

protected

◆ progress_

bool progress_

protected

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FeatureFinderMultiplexAlgorithm()

Member Function Documentation

◆ correctPeptideIntensities_()

◆ determinePeptideIntensitiesCentroided_()

◆ determinePeptideIntensitiesProfile_()

◆ generateMapsCentroided_()

◆ generateMapsProfile_()

◆ generatePeakPatterns_()

◆ getBlacklist()

◆ getConsensusMap()

◆ getFeatureMap()

◆ run()

Member Data Documentation

◆ centroided_

◆ charge_max_

◆ charge_min_

◆ consensus_map_

◆ exp_blacklist_

◆ exp_centroid_

◆ exp_profile_

◆ feature_map_

◆ isotopes_per_peptide_max_

◆ isotopes_per_peptide_min_

◆ label_mass_shift_

◆ prog_log_

◆ progress_