#include <OpenMS/FEATUREFINDER/FeatureFinderMultiplexAlgorithm.h>

Inheritance diagram for FeatureFinderMultiplexAlgorithm:

Collaboration diagram for FeatureFinderMultiplexAlgorithm:

Public Member Functions
	FeatureFinderMultiplexAlgorithm ()
	default constructor More...

void	run (MSExperiment &exp, bool progress)
	main method for feature detection More...

FeatureMap &	getFeatureMap ()
	get methods More...

ConsensusMap &	getConsensusMap ()

MSExperiment &	getBlacklist ()

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

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

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

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

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

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

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

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

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

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

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

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 More...

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 More...

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

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

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 More...

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 More...

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. More...

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

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< 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. More...

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

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

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

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

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. 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 Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

FeatureFinderMultiplexAlgorithm is a tool for the fully automated analysis of quantitative proteomics data. It detects pairs of isotopic envelopes with fixed m/z separation. It requires no prior sequence identification of the peptides and works on both profile or centroided spectra. In what follows we outline the algorithm.

Algorithm The algorithm is divided into three parts: filtering, clustering and linear fitting, see Fig. (d), (e) and (f). In the following discussion let us consider a particular mass spectrum at retention time 1350 s, see Fig. (a). It contains a peptide of mass 1492 Da and its 6 Da heavier labelled counterpart. Both are doubly charged in this instance. Their isotopic envelopes therefore appear at 746 and 749 in the spectrum. The isotopic peaks within each envelope are separated by 0.5. The spectrum was recorded at finite intervals. In order to read accurate intensities at arbitrary m/z we spline-fit over the data, see Fig. (b). We would like to search for such peptide pairs in our LC-MS data set. As a warm-up let us consider a standard intensity cut-off filter, see Fig. (c).

Scanning through the entire m/z range (red dot) only data points with intensities above a certain threshold pass the filter. Unlike such a local filter, the filter used in our algorithm takes intensities at a range of m/z positions into account, see Fig. (d). A data point (red dot) passes if

all six intensities at m/z, m/z+0.5, m/z+1, m/z+3, m/z+3.5 and m/z+4 lie above a certain threshold,
the intensity profiles in neighbourhoods around all six m/z positions show a good correlation and
the relative intensity ratios within a peptide agree up to a factor with the ratios of a theoretic averagine model.

Let us now filter not only a single spectrum but all spectra in our data set. Data points that pass the filter form clusters in the t-m/z plane, see Fig. (e). Each cluster corresponds to the mono-isotopic mass trace of the lightest peptide of a SILAC pattern. We now use hierarchical clustering methods to assign each data point to a specific cluster. The optimum number of clusters is determined by maximizing the silhouette width of the partitioning. Each data point in a cluster corresponds to three pairs of intensities (at [m/z, m/z+3], [m/z+0.5, m/z+3.5] and [m/z+1, m/z+4]). A plot of all intensity pairs in a cluster shows a clear linear correlation, see Fig. (f). Using linear regression we can determine the relative amounts of labelled and unlabelled peptides in the sample.

Constructor & Destructor Documentation

◆ FeatureFinderMultiplexAlgorithm()

FeatureFinderMultiplexAlgorithm ( )

default constructor

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.

◆ determinePeptideIntensitiesCentroided_()

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

protected

calculate peptide intensities

Parameters

pattern
satellites

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

pattern
satellites

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

patterns	patterns of isotopic peaks we have been searching for
filter_results	filter results for each of the patterns
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

patterns	patterns of isotopic peaks we have been searching for
filter_results	filter results for each of the patterns
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

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

Returns: list of m/z shifts

◆ getBlacklist()

MSExperiment& getBlacklist ( )

◆ getConsensusMap()

ConsensusMap& getConsensusMap ( )

◆ getFeatureMap()

FeatureMap& getFeatureMap ( )

get methods

◆ run()

void run	(	MSExperiment &	exp,
		bool	progress
	)

main method for feature detection

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<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_