This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More...

#include <OpenMS/PROCESSING/CENTROIDING/PeakPickerHiRes.h>

Inheritance diagram for PeakPickerHiRes:

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Collaboration diagram for PeakPickerHiRes:

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Classes
struct	PeakBoundary
	structure for peak boundaries More...

Public Member Functions
	PeakPickerHiRes ()
	Constructor. More...

	~PeakPickerHiRes () override
	Destructor. More...

void	pick (const MSSpectrum &input, MSSpectrum &output) const
	Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. More...

void	pick (const MSChromatogram &input, MSChromatogram &output) const
	Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram. More...

void	pick (const MSSpectrum &input, MSSpectrum &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=true) const
	Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. Peak boundaries are written to a separate structure. More...

void	pick (const MSChromatogram &input, MSChromatogram &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=false) const
	Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram. More...

void	pickExperiment (const PeakMap &input, PeakMap &output, const bool check_spectrum_type=true) const
	Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. More...

void	pickExperiment (const PeakMap &input, PeakMap &output, std::vector< std::vector< PeakBoundary > > &boundaries_spec, std::vector< std::vector< PeakBoundary > > &boundaries_chrom, const bool check_spectrum_type=true) const
	Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. More...

void	pickExperiment (OnDiscMSExperiment &input, PeakMap &output, const bool check_spectrum_type=true) const
	Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. More...

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
template<typename ContainerType >
void	pick_ (const ContainerType &input, ContainerType &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=true, int im_index=-1) const

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

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

Protected Attributes
double	signal_to_noise_

double	spacing_difference_gap_

double	spacing_difference_

unsigned	missing_

std::vector< Int >	ms_levels_

bool	report_FWHM_
	add floatDataArray 'FWHM'/'FWHM_ppm' to spectra with peak FWHM More...

bool	report_FWHM_as_ppm_
	unit of 'FWHM' float data array (can be absolute or ppm). 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_

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

This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width.

This peak-picking algorithm detects ion signals in profile data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline.

So far, this peak picker was mainly tested on high resolution data. With appropriate preprocessing steps (e.g. noise reduction and baseline subtraction), it might be also applied to low resolution data.

This implementation performs peak picking in a single dimension (m/z); two-dimensional data such as ion mobility separated data needs additional pre-processing. The current implementation treats these data as one-dimensional data, performs peak picking in the m/z dimension and reports the intensity weighted ion mobility of the picked peaks (which will produce correct results if the data has been binned previously but incorrect results if fully 2D data is provided as input).

Parameters of this class are:

Name	Type	Default	Restrictions	Description
signal_to_noise	float	0.0	min: 0.0	Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)
spacing_difference_gap	float	4.0	min: 0.0	The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.
spacing_difference	float	1.5	min: 0.0	Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.
missing	int	1	min: 0	Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.
ms_levels	int list	[]	min: 1	List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes.
report_FWHM	string	false	true, false	Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.
report_FWHM_unit	string	relative	relative, absolute	Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).
SignalToNoise:max_intensity	int	-1	min: -1	maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.
SignalToNoise:auto_max_stdev_factor	float	3.0	min: 0.0 max: 999.0	parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev
SignalToNoise:auto_max_percentile	int	95	min: 0 max: 100	parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile
SignalToNoise:auto_mode	int	0	min: -1 max: 1	method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method
SignalToNoise:win_len	float	200.0	min: 1.0	window length in Thomson
SignalToNoise:bin_count	int	30	min: 3	number of bins for intensity values
SignalToNoise:min_required_elements	int	10	min: 1	minimum number of elements required in a window (otherwise it is considered sparse)
SignalToNoise:noise_for_empty_window	float	1.0e20		noise value used for sparse windows
SignalToNoise:write_log_messages	string	true	true, false	Write out log messages in case of sparse windows or median in rightmost histogram bin

Note:

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

Note: The peaks must be sorted according to ascending m/z!

Class Documentation

◆ OpenMS::PeakPickerHiRes::PeakBoundary

struct OpenMS::PeakPickerHiRes::PeakBoundary

structure for peak boundaries

Collaboration diagram for PeakPickerHiRes::PeakBoundary:

[legend]

Class Members
double	mz_max
double	mz_min

Constructor & Destructor Documentation

◆ PeakPickerHiRes()

PeakPickerHiRes ( )

Constructor.

◆ ~PeakPickerHiRes()

~PeakPickerHiRes ( )

override

Destructor.

Member Function Documentation

◆ pick() [1/4]

void pick	(	const MSChromatogram &	input,
		MSChromatogram &	output
	)		const

Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram.

Parameters

input	input chromatogram in profile mode
output	output chromatogram with picked peaks

◆ pick() [2/4]

void pick	(	const MSChromatogram &	input,
		MSChromatogram &	output,
		std::vector< PeakBoundary > &	boundaries,
		bool	check_spacings = `false`
	)		const

Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram.

Parameters

input	input chromatogram in profile mode
output	output chromatogram with picked peaks
boundaries	boundaries of the picked peaks
check_spacings	check spacing constraints? (yes for spectra, no for chromatograms)

◆ pick() [3/4]

void pick	(	const MSSpectrum &	input,
		MSSpectrum &	output
	)		const

Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum.

Parameters

input	input spectrum in profile mode
output	output spectrum with picked peaks

Referenced by PeakPickerIterative::pick().

◆ pick() [4/4]

void pick	(	const MSSpectrum &	input,
		MSSpectrum &	output,
		std::vector< PeakBoundary > &	boundaries,
		bool	check_spacings = `true`
	)		const

Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. Peak boundaries are written to a separate structure.

Parameters

input	input spectrum in profile mode
output	output spectrum with picked peaks
boundaries	boundaries of the picked peaks
check_spacings	check spacing constraints? (yes for spectra, no for chromatograms)

◆ pick_()

void pick_	(	const ContainerType &	input,
		ContainerType &	output,
		std::vector< PeakBoundary > &	boundaries,
		bool	check_spacings = `true`,
		int	im_index = `-1`
	)		const

protected

◆ pickExperiment() [1/3]

void pickExperiment	(	const PeakMap &	input,
		PeakMap &	output,
		const bool	check_spectrum_type = `true`
	)		const

Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.

Parameters

input	input map in profile mode
output	output map with picked peaks
check_spectrum_type	if set, checks spectrum type and throws an exception if a centroided spectrum is passed

◆ pickExperiment() [2/3]

void pickExperiment	(	const PeakMap &	input,
		PeakMap &	output,
		std::vector< std::vector< PeakBoundary > > &	boundaries_spec,
		std::vector< std::vector< PeakBoundary > > &	boundaries_chrom,
		const bool	check_spectrum_type = `true`
	)		const

Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.

Parameters

input	input map in profile mode
output	output map with picked peaks
boundaries_spec	boundaries of the picked peaks in spectra
boundaries_chrom	boundaries of the picked peaks in chromatograms
check_spectrum_type	if set, checks spectrum type and throws an exception if a centroided spectrum is passed

◆ pickExperiment() [3/3]

void pickExperiment	(	OnDiscMSExperiment &	input,
		PeakMap &	output,
		const bool	check_spectrum_type = `true`
	)		const

Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.

Currently we have to give up const-correctness but we know that everything on disc is constant

◆ 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

◆ missing_

unsigned missing_

protected

◆ ms_levels_

std::vector<Int> ms_levels_

protected

◆ report_FWHM_

bool report_FWHM_

protected

add floatDataArray 'FWHM'/'FWHM_ppm' to spectra with peak FWHM

◆ report_FWHM_as_ppm_

bool report_FWHM_as_ppm_

protected

unit of 'FWHM' float data array (can be absolute or ppm).

◆ signal_to_noise_

double signal_to_noise_

protected

◆ spacing_difference_

double spacing_difference_

protected

◆ spacing_difference_gap_

double spacing_difference_gap_

protected

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::PeakPickerHiRes::PeakBoundary

Constructor & Destructor Documentation

◆ PeakPickerHiRes()

◆ ~PeakPickerHiRes()

Member Function Documentation

◆ pick() [1/4]

◆ pick() [2/4]

◆ pick() [3/4]

◆ pick() [4/4]

◆ pick_()

◆ pickExperiment() [1/3]

◆ pickExperiment() [2/3]

◆ pickExperiment() [3/3]

◆ updateMembers_()

Member Data Documentation

◆ missing_

◆ ms_levels_

◆ report_FWHM_

◆ report_FWHM_as_ppm_

◆ signal_to_noise_

◆ spacing_difference_

◆ spacing_difference_gap_