A mass trace extraction method that gathers peaks similar in m/z and moving along retention time. More...

#include <OpenMS/FEATUREFINDER/MassTraceDetection.h>

Inheritance diagram for MassTraceDetection:

Collaboration diagram for MassTraceDetection:

Classes
struct	Apex

struct	PeakCandidate
	Encapsulates peak finding logic for both up and down directions. More...

struct	TraceExtensionState
	Encapsulates trace extension state. More...

Public Types
enum	TraceTerminationCriterion { OUTLIER , SAMPLE_RATE }
	Trace termination criteria enum for performance optimization. More...

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

Public Member Functions
	MassTraceDetection ()
	Default constructor. More...

	~MassTraceDetection () override
	Default destructor. More...

Main computation methods
void	run (const PeakMap &, std::vector< MassTrace > &, const Size max_traces=0)
	Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container. More...

void	run (PeakMap::ConstAreaIterator &begin, PeakMap::ConstAreaIterator &end, std::vector< MassTrace > &found_masstraces)
	Invokes the run method (see above) on merely a subregion of a MSExperiment map. More...

bool	hasFwhmMz () const
	determine if meta array is available More...

bool	hasFwhmIm () const

bool	hasCentroidIm () const

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...

Private methods and members
bool	has_fwhm_mz_ = false

bool	has_fwhm_im_ = false

bool	has_centroid_im_ = false

double	mass_error_ppm_

double	mass_error_da_

double	noise_threshold_int_

double	chrom_peak_snr_

double	ion_mobility_tolerance_

MassTrace::MT_QUANTMETHOD	quant_method_

TraceTerminationCriterion	trace_termination_criterion_

Size	trace_termination_outliers_

double	min_sample_rate_

double	min_trace_length_

double	max_trace_length_

bool	reestimate_mt_sd_

int	fwhm_meta_idx_ = -1

int	ion_mobility_idx_ = -1

int	im_fwhm_idx_ = -1

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

static void	updateIterativeWeightedMean_ (const double &added_value, const double &added_intensity, double &centroid_value, double &prev_counter, double &prev_denom)
	allows for the iterative computation of intensity weighted of a mass trace's centroid m/z or ion mobility More...

void	run_ (const std::vector< Apex > &chrom_apices, const Size peak_count, const PeakMap &work_exp, const std::vector< Size > &spec_offsets, std::vector< MassTrace > &found_masstraces, const Size max_traces=0)
	The internal run method. More...

void	getIMIndices_ (const PeakMap &spectra, int &fwhm_meta_idx, bool &has_fwhm_mz, int &im_idx, bool &has_centroid_im, int &im_fwhm_idx, bool &has_fwhm_im) const
	Internal helper to extract and validate metadata float array indices. More...

PeakCandidate	findBestPeak_ (const MSSpectrum &spectrum, double centroid_mz, double ftl_sd, double centroid_im=-1.0) const
	Find the best matching peak in a spectrum considering m/z and optionally ion mobility. More...

bool	isPeakAcceptable_ (const PeakCandidate &candidate, double centroid_mz, double ftl_sd, double centroid_im, Size spectrum_idx, const std::vector< Size > &spec_offsets, const boost::dynamic_bitset<> &peak_visited) const
	Check if peak candidate meets acceptance criteria. More...

void	processPeak_ (const PeakCandidate &candidate, const MSSpectrum &spectrum, std::list< PeakType > &current_trace, std::vector< std::pair< Size, Size >> &gathered_idx, std::vector< double > &fwhms_mz, std::vector< double > &fwhms_im, double &centroid_mz, double &centroid_im, double &prev_counter, double &prev_denom, double &prev_counter_im, double &prev_denom_im, double &ftl_sd, double &intensity_so_far, Size spectrum_idx, bool is_upward_extension)
	Process a single peak during trace extension. More...

bool	isTraceValid_ (const std::list< PeakType > &trace, Size total_scans_visited, Size consecutive_missed_down, Size consecutive_missed_up) const
	Check if a mass trace meets quality criteria. More...

Additional Inherited Members
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...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

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_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.

Peaks of a MSExperiment are sorted by their intensity and stored in a list of potential chromatographic apex positions. Only peaks that are above the noise threshold (user-defined) are analyzed and only peaks that are n times above this minimal threshold are considered as apices. This saves computational resources and decreases the noise in the resulting output.

Starting with these, mass traces are extended in- and decreasingly in retention time. During this extension phase, the centroid m/z is computed on-line as an intensity-weighted mean of peaks.

The extension phase ends when either the frequency of gathered peaks drops below a threshold (min_sample_rate, see MassTraceDetection parameters) or when the number of missed scans exceeds a threshold (trace_termination_outliers, see MassTraceDetection parameters).

Finally, only mass traces that pass a filter (a certain minimal and maximal length as well as having the minimal sample rate criterion fulfilled) get added to the result.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
mass_error_ppm	float	20.0		Allowed mass deviation (in ppm).
noise_threshold_int	float	10.0		Intensity threshold below which peaks are removed as noise.
chrom_peak_snr	float	3.0		Minimum intensity above noise_threshold_int (signal-to-noise) a peak should have to be considered an apex.
ion_mobility_tolerance	float	0.01		Allowed ion mobility deviation (in 1/k0).
reestimate_mt_sd	string	true	true, false	Enables dynamic re-estimation of m/z variance during mass trace collection stage.
quant_method	string	area	area, median, max_height	Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace.
trace_termination_criterion	string	outlier	outlier, sample_rate	Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold.
trace_termination_outliers	int	5		Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.
min_sample_rate	float	0.5		Minimum fraction of scans along the mass trace that must contain a peak.
min_trace_length	float	5.0		Minimum expected length of a mass trace (in seconds).
max_trace_length	float	-1.0		Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Enumeration Documentation

◆ TraceTerminationCriterion

enum TraceTerminationCriterion

Trace termination criteria enum for performance optimization.

Enumerator
OUTLIER	Terminate when consecutive outliers exceed threshold.
SAMPLE_RATE	Terminate when sample rate falls below threshold.

Constructor & Destructor Documentation

◆ MassTraceDetection()

MassTraceDetection ( )

Default constructor.

◆ ~MassTraceDetection()

~MassTraceDetection ( )

override

Default destructor.

Member Function Documentation

◆ findBestPeak_()

PeakCandidate findBestPeak_	(	const MSSpectrum &	spectrum,
		double	centroid_mz,
		double	ftl_sd,
		double	centroid_im = `-1.0`
	)		const

private

Find the best matching peak in a spectrum considering m/z and optionally ion mobility.

◆ getIMIndices_()

void getIMIndices_	(	const PeakMap &	spectra,
		int &	fwhm_meta_idx,
		bool &	has_fwhm_mz,
		int &	im_idx,
		bool &	has_centroid_im,
		int &	im_fwhm_idx,
		bool &	has_fwhm_im
	)		const

private

Internal helper to extract and validate metadata float array indices.

◆ hasCentroidIm()

bool hasCentroidIm ( ) const

inline

◆ hasFwhmIm()

bool hasFwhmIm ( ) const

inline

◆ hasFwhmMz()

bool hasFwhmMz ( ) const

inline

determine if meta array is available

◆ isPeakAcceptable_()

bool isPeakAcceptable_	(	const PeakCandidate &	candidate,
		double	centroid_mz,
		double	ftl_sd,
		double	centroid_im,
		Size	spectrum_idx,
		const std::vector< Size > &	spec_offsets,
		const boost::dynamic_bitset<> &	peak_visited
	)		const

private

Check if peak candidate meets acceptance criteria.

◆ isTraceValid_()

bool isTraceValid_	(	const std::list< PeakType > &	trace,
		Size	total_scans_visited,
		Size	consecutive_missed_down,
		Size	consecutive_missed_up
	)		const

private

Check if a mass trace meets quality criteria.

◆ processPeak_()

void processPeak_	(	const PeakCandidate &	candidate,
		const MSSpectrum &	spectrum,
		std::list< PeakType > &	current_trace,
		std::vector< std::pair< Size, Size >> &	gathered_idx,
		std::vector< double > &	fwhms_mz,
		std::vector< double > &	fwhms_im,
		double &	centroid_mz,
		double &	centroid_im,
		double &	prev_counter,
		double &	prev_denom,
		double &	prev_counter_im,
		double &	prev_denom_im,
		double &	ftl_sd,
		double &	intensity_so_far,
		Size	spectrum_idx,
		bool	is_upward_extension
	)

private

Process a single peak during trace extension.

◆ run() [1/2]

void run	(	const PeakMap &	,
		std::vector< MassTrace > &	,
		const Size	max_traces = `0`
	)

Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container.

◆ run() [2/2]

void run	(	PeakMap::ConstAreaIterator &	begin,
		PeakMap::ConstAreaIterator &	end,
		std::vector< MassTrace > &	found_masstraces
	)

Invokes the run method (see above) on merely a subregion of a MSExperiment map.

◆ run_()

void run_	(	const std::vector< Apex > &	chrom_apices,
		const Size	peak_count,
		const PeakMap &	work_exp,
		const std::vector< Size > &	spec_offsets,
		std::vector< MassTrace > &	found_masstraces,
		const Size	max_traces = `0`
	)

private

The internal run method.

◆ updateIterativeWeightedMean_()

static void updateIterativeWeightedMean_	(	const double &	added_value,
		const double &	added_intensity,
		double &	centroid_value,
		double &	prev_counter,
		double &	prev_denom
	)

staticprotected

allows for the iterative computation of intensity weighted of a mass trace's centroid m/z or ion mobility

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ chrom_peak_snr_

double chrom_peak_snr_

private

◆ fwhm_meta_idx_

int fwhm_meta_idx_ = -1

mutableprivate

◆ has_centroid_im_

bool has_centroid_im_ = false

private

◆ has_fwhm_im_

bool has_fwhm_im_ = false

private

◆ has_fwhm_mz_

bool has_fwhm_mz_ = false

private

◆ im_fwhm_idx_

int im_fwhm_idx_ = -1

mutableprivate

◆ ion_mobility_idx_

int ion_mobility_idx_ = -1

mutableprivate

◆ ion_mobility_tolerance_

double ion_mobility_tolerance_

private

◆ mass_error_da_

double mass_error_da_

private

◆ mass_error_ppm_

double mass_error_ppm_

private

◆ max_trace_length_

double max_trace_length_

private

◆ min_sample_rate_

double min_sample_rate_

private

◆ min_trace_length_

double min_trace_length_

private

◆ noise_threshold_int_

double noise_threshold_int_

private

◆ quant_method_

MassTrace::MT_QUANTMETHOD quant_method_

private

◆ reestimate_mt_sd_

bool reestimate_mt_sd_

private

◆ trace_termination_criterion_

TraceTerminationCriterion trace_termination_criterion_

private

◆ trace_termination_outliers_

Size trace_termination_outliers_

private

Classes

Public Types

Public Member Functions

Private methods and members

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ TraceTerminationCriterion

Constructor & Destructor Documentation

◆ MassTraceDetection()

◆ ~MassTraceDetection()

Member Function Documentation

◆ findBestPeak_()

◆ getIMIndices_()

◆ hasCentroidIm()

◆ hasFwhmIm()

◆ hasFwhmMz()

◆ isPeakAcceptable_()

◆ isTraceValid_()

◆ processPeak_()

◆ run() [1/2]

◆ run() [2/2]

◆ run_()

◆ updateIterativeWeightedMean_()

◆ updateMembers_()

Member Data Documentation

◆ chrom_peak_snr_

◆ fwhm_meta_idx_

◆ has_centroid_im_

◆ has_fwhm_im_

◆ has_fwhm_mz_

◆ im_fwhm_idx_

◆ ion_mobility_idx_

◆ ion_mobility_tolerance_

◆ mass_error_da_

◆ mass_error_ppm_

◆ max_trace_length_

◆ min_sample_rate_

◆ min_trace_length_

◆ noise_threshold_int_

◆ quant_method_

◆ reestimate_mt_sd_

◆ trace_termination_criterion_

◆ trace_termination_outliers_