Peak picking algorithm for ion mobility data. More...

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

Inheritance diagram for PeakPickerIM:

Collaboration diagram for PeakPickerIM:

Public Member Functions
	PeakPickerIM ()
	Default constructor initializing parameters with default values. More...

	~PeakPickerIM () override=default
	Destructor. More...

void	pickIMTraces (MSSpectrum &spectrum)
	Centroids ion mobility data by iteratively extracting mobilograms for each m/z peak centroid. More...

void	pickIMCluster (MSSpectrum &spec) const
	Converts an ion mobility frame to a single spectrum with averaged IM values. More...

void	pickIMElutionProfiles (MSSpectrum &input) const
	Picks ion mobility elution profiles from the given spectrum using eluting profiles. More...

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

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

Protected Member Functions
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...

Private Member Functions
double	computeOptimalSamplingRate (const std::vector< MSSpectrum > &spectra)
	determine sampling rate for linear resampler More...

void	sumFrame_ (const MSSpectrum &input_spectrum, MSSpectrum &output_spectrum, double tolerance=0.01, bool use_ppm=true)
	Sum up the intensity of data points with nearly identical float values. More...

std::pair< double, double >	ppmBounds (double mz, double ppm)
	Compute lower and upper m/z bounds based on ppm. More...

std::vector< MSSpectrum >	extractIonMobilityTraces (const MSSpectrum &picked_spectrum, const MSSpectrum &raw_spectrum)

MSSpectrum	computeCentroids_ (const std::vector< MSSpectrum > &mobilogram_traces, const std::vector< MSSpectrum > &picked_traces)
	compute m/z and ion mobility centers for picked traces. Returns centroided spectrum. More...

Private Attributes
double	sum_tolerance_mz_ {1.0}

double	gauss_ppm_tolerance_ {5.0}

double	sum_tolerance_im_ {0.0006}

int	sgolay_frame_length_ {5}

int	sgolay_polynomial_order_ {3}

double	ppm_tolerance_cluster_ {50.0}

double	im_tolerance_cluster_ {0.1}

double	ppm_tolerance_elution_ {50.0}

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 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...

Detailed Description

Peak picking algorithm for ion mobility data.

This class provides three specialized methods for peak picking in ion mobility (IM) data:

pickIMTraces: Mobilogram-based peak picking that extracts ion mobility traces from raw IM data and performs centroiding on the extracted mobilograms. This method processes IM data by analyzing intensity profiles along the ion mobility dimension.
pickIMCluster: Clustering-based peak picking that groups peaks close in both m/z and ion mobility space. Peaks within specified m/z (ppm) and IM tolerances are averaged together using intensity-weighted averaging, reducing an IM frame to a single spectrum with representative peak positions.
pickIMElutionProfiles: Elution profile-based peak picking that extracts peaks based on their elution characteristics across the ion mobility dimension. This method uses m/z tolerance (ppm) to identify and pick peaks from IM elution profiles.

Constructor & Destructor Documentation

◆ PeakPickerIM()

PeakPickerIM ( )

Default constructor initializing parameters with default values.

◆ ~PeakPickerIM()

~PeakPickerIM ( )

overridedefault

Destructor.

Member Function Documentation

◆ computeCentroids_()

MSSpectrum computeCentroids_	(	const std::vector< MSSpectrum > &	mobilogram_traces,
		const std::vector< MSSpectrum > &	picked_traces
	)

private

compute m/z and ion mobility centers for picked traces. Returns centroided spectrum.

◆ computeOptimalSamplingRate()

double computeOptimalSamplingRate ( const std::vector< MSSpectrum > & spectra )

private

determine sampling rate for linear resampler

◆ extractIonMobilityTraces()

std::vector<MSSpectrum> extractIonMobilityTraces	(	const MSSpectrum &	picked_spectrum,
		const MSSpectrum &	raw_spectrum
	)

private

Extract ion mobility traces as MSSpectra from the raw TimsTOF frame Ion mobility is temporarily written in place of m/z inside Peak1D object. raw m/z values are allocated to float data arrays with the label 'raw_mz'

◆ getParameters()

const Param& getParameters

Non-mutable access to the parameters.

◆ pickIMCluster()

void pickIMCluster ( MSSpectrum & spec ) const

Converts an ion mobility frame to a single spectrum with averaged IM values.

This function takes an MS spectrum containing ion mobility data and reduces it to a single spectrum where peaks that are close in both m/z and ion mobility space are averaged together. The averaging is intensity-weighted for both m/z and ion mobility values.

The algorithm processes peaks sequentially and groups them based on two criteria:

m/z tolerance: peaks must be within the configured ppm tolerance of each other
ion mobility tolerance: the range of IM values must not exceed the configured tolerance

Uses parameters pickIMCluster:ppm_tolerance_cluster and pickIMCluster:im_tolerance_cluster.

Parameters

spec	Spectrum containing ion mobility data in its FloatDataArrays

Exceptions

Exception::MissingInformation if input spectrum lacks ion mobility data

Note: The input spectrum should contain ion mobility data in its FloatDataArrays. The output spectrum will contain averaged peaks with their corresponding intensity-weighted average ion mobility values.

Example:

MSSpectrum spectrum;  // spectrum with IM FloatDataArrays
PeakPickerIM picker;
picker.pickIMCluster(spectrum);

◆ pickIMElutionProfiles()

void pickIMElutionProfiles ( MSSpectrum & input ) const

Picks ion mobility elution profiles from the given spectrum using eluting profiles.

This function processes an MS spectrum containing ion mobility data and extracts IM elution profiles based on the configured ppm tolerance.

Parameters

input Spectrum containing ion mobility data in its FloatDataArrays

◆ pickIMTraces()

void pickIMTraces ( MSSpectrum & spectrum )

Centroids ion mobility data by iteratively extracting mobilograms for each m/z peak centroid.

This function processes an MS spectrum containing ion mobility data (geared towards TimsTOF data) Peaks in a given MS spectrum are projected to the m/z axis and centroided. Then, the mobilogram of each m/z peak centroid is retrieved using the m/z peak FWHM. Peak picking algorithm is applied to the mobilogram to resolve isobaric species with different ion mobility measurement.

Parameters

spectrum Spectrum containing ion mobility data in its FloatDataArrays

◆ ppmBounds()

std::pair<double, double> ppmBounds	(	double	mz,
		double	ppm
	)

private

Compute lower and upper m/z bounds based on ppm.

◆ setParameters()

void setParameters

Sets the parameters for peak picking.

◆ sumFrame_()

void sumFrame_	(	const MSSpectrum &	input_spectrum,
		MSSpectrum &	output_spectrum,
		double	tolerance = `0.01`,
		bool	use_ppm = `true`
	)

private

Sum up the intensity of data points with nearly identical float values.

By default, this function assumes the tolerance provided is in parts per million. But it can be adjusted to use absolute value tolerance.

Parameters

input_spectrum	Sorted raw spectrum with duplicate peaks due to scan merging or presence of ion mobility data.
output_spectrum	Output spectrum containing the summed peaks.
tolerance	Mass tolerance between peaks
use_ppm	Whether to use parts per million tolerance. If set to False, absolute tolerance will be used.

◆ 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

◆ gauss_ppm_tolerance_

double gauss_ppm_tolerance_ {5.0}

private

◆ im_tolerance_cluster_

double im_tolerance_cluster_ {0.1}

private

◆ ppm_tolerance_cluster_

double ppm_tolerance_cluster_ {50.0}

private

◆ ppm_tolerance_elution_

double ppm_tolerance_elution_ {50.0}

private

◆ sgolay_frame_length_

int sgolay_frame_length_ {5}

private

◆ sgolay_polynomial_order_

int sgolay_polynomial_order_ {3}

private

◆ sum_tolerance_im_

double sum_tolerance_im_ {0.0006}

private

◆ sum_tolerance_mz_

double sum_tolerance_mz_ {1.0}

private

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PeakPickerIM()

◆ ~PeakPickerIM()

Member Function Documentation

◆ computeCentroids_()

◆ computeOptimalSamplingRate()

◆ extractIonMobilityTraces()

◆ getParameters()

◆ pickIMCluster()

◆ pickIMElutionProfiles()

◆ pickIMTraces()

◆ ppmBounds()

◆ setParameters()

◆ sumFrame_()

◆ updateMembers_()

Member Data Documentation

◆ gauss_ppm_tolerance_

◆ im_tolerance_cluster_

◆ ppm_tolerance_cluster_

◆ ppm_tolerance_elution_

◆ sgolay_frame_length_

◆ sgolay_polynomial_order_

◆ sum_tolerance_im_

◆ sum_tolerance_mz_