Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More...

#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.h>

Inheritance diagram for IsobaricChannelExtractor:

Collaboration diagram for IsobaricChannelExtractor:

Classes
struct	PuritySate_
	Small struct to capture the current state of the purity computation. More...

Public Member Functions
	IsobaricChannelExtractor (const IsobaricQuantitationMethod *const quant_method)
	C'tor to create a new channel extractor for the given quantitation method. More...

	IsobaricChannelExtractor (const IsobaricChannelExtractor &other)
	Copy c'tor. More...

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

void	extractChannels (const PeakMap &ms_exp_data, ConsensusMap &consensus_map)
	Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus 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...

Protected Member Functions
void	setDefaultParams_ ()
	implemented for DefaultParamHandler More...

void	updateMembers_ () override
	implemented for DefaultParamHandler 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
void	registerChannelsInOutputMap_ (ConsensusMap &consensus_map)
	add channel information to the map after it has been filled More...

bool	isValidPrecursor_ (const Precursor &precursor) const
	Checks if the given precursor fulfills all constraints for extractions. More...

bool	hasLowIntensityReporter_ (const ConsensusFeature &cf) const
	Checks whether the given ConsensusFeature contains a channel that is below the given intensity threshold. More...

double	computePrecursorPurity_ (const PeakMap::ConstIterator &ms2_spec, const PuritySate_ &precursor) const
	Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum. More...

double	computeSingleScanPrecursorPurity_ (const PeakMap::ConstIterator &ms2_spec, const PeakMap::SpectrumType &precursor_spec) const
	Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference to the potential precursor spectrum. More...

String	getActivationMethod_ (const PeakMap::SpectrumType &s) const
	Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum. More...

Private Attributes
const IsobaricQuantitationMethod *	quant_method_
	The used quantitation method (itraq4plex, tmt6plex,..). More...

String	selected_activation_
	Used to select only specific types of spectra for the channel extraction. More...

Peak2D::CoordinateType	reporter_mass_shift_
	Allowed deviation between the expected and observed reporter ion m/z. More...

Peak2D::IntensityType	min_precursor_intensity_
	Minimum intensity of the precursor to be considered for quantitation. More...

bool	keep_unannotated_precursor_
	Flag if precursor with missing intensity value or missing precursor spectrum should be included or not. More...

Peak2D::IntensityType	min_reporter_intensity_
	Minimum reporter ion intensity to be considered for quantitation. More...

bool	remove_low_intensity_quantifications_
	Flag if complete quantification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ . More...

double	min_precursor_purity_
	Minimum precursor purity to accept the spectrum for quantitation. More...

double	max_precursor_isotope_deviation_
	Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor. More...

bool	interpolate_precursor_purity_
	Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan. 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 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

Extracts individual channels from MS/MS spectra for isobaric labeling experiments.

In addition to extracting the channel information this class can also filter the extracted channel information according to several parameters, i.e., discard channel information if certain criteria are not met.

Precursor activation method (e.g., select only HCD scans).
Minimum precursor intensity.
Minimum reporter intensity (i.e., remove reporter channels below a certain intensity)
Precursor purity (i.e., fraction of TIC in the precursor window that can be assigned to the precursor)

The precursor purity computation uses the interpolation approach described in: Savitski MM, Sweetman G, Askenazi M, et al. (2011). Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers. Analytical chemistry 83: 8959-67. http://www.ncbi.nlm.nih.gov/pubmed/22017476

Note: Centroided MS and MS/MS data is required.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
select_activation	string	auto	auto, Collision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, Electron transfer and collision-induced dissociation, Electron transfer and higher-energy collision dissociation, Pulsed q dissociation, trap-type collision-induced dissociation, beam-type collision-induced dissociation, in-source collision-induced dissociation, any	Operate only on MSn scans where any of its precursors features a certain activation method. Setting to "auto" uses HCD and HCID spectra. Set to empty string if you want to disable filtering.
reporter_mass_shift	float	2.0e-03	min: 1.0e-04 max: 0.5	Allowed shift (left to right) in Th from the expected position.
min_precursor_intensity	float	1.0	min: 0.0	Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation.
keep_unannotated_precursor	string	true	true, false	Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.
min_reporter_intensity	float	0.0	min: 0.0	Minimum intensity of the individual reporter ions to be extracted.
discard_low_intensity_quantifications	string	false	true, false	Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'.
min_precursor_purity	float	0.0	min: 0.0 max: 1.0	Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor.
precursor_isotope_deviation	float	10.0	min: 0.0	Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.
purity_interpolation	string	true	true, false	If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan. If set to false, only the precursor scan will be used.

Note:

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

Constructor & Destructor Documentation

◆ IsobaricChannelExtractor() [1/2]

IsobaricChannelExtractor ( const IsobaricQuantitationMethod *const quant_method )

explicit

C'tor to create a new channel extractor for the given quantitation method.

Parameters

quant_method IsobaricQuantitationMethod providing the necessary information which channels should be extracted.

◆ IsobaricChannelExtractor() [2/2]

IsobaricChannelExtractor ( const IsobaricChannelExtractor & other )

Copy c'tor.

Member Function Documentation

◆ computePrecursorPurity_()

double computePrecursorPurity_	(	const PeakMap::ConstIterator &	ms2_spec,
		const PuritySate_ &	precursor
	)		const

private

Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum.

Parameters

ms2_spec	Iterator pointing to the MS2 spectrum.
precursor	Iterator pointing to the precursor spectrum of ms2_spec.

Returns: Fraction of the total intensity in the isolation window of the precursor spectrum that was assigned to the precursor.

◆ computeSingleScanPrecursorPurity_()

double computeSingleScanPrecursorPurity_	(	const PeakMap::ConstIterator &	ms2_spec,
		const PeakMap::SpectrumType &	precursor_spec
	)		const

private

Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference to the potential precursor spectrum.

Parameters

ms2_spec	Iterator pointing to the MS2 spectrum.
precursor_spec	Precursor spectrum of ms2_spec.

Returns: Fraction of the total intensity in the isolation window of the precursor spectrum that was assigned to the precursor.

◆ extractChannels()

void extractChannels	(	const PeakMap &	ms_exp_data,
		ConsensusMap &	consensus_map
	)

Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map.

Parameters

ms_exp_data	Raw data to search for isobaric quantitation channels.
consensus_map	Output map containing the identified channels and the corresponding intensities.

◆ getActivationMethod_()

String getActivationMethod_ ( const PeakMap::SpectrumType & s ) const

inlineprivate

Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.

Parameters

s	The spectrum

Returns: Entry from Precursor::NamesOfActivationMethod or empty string.

References SpectrumSettings::getPrecursors(), and Precursor::NamesOfActivationMethod.

◆ hasLowIntensityReporter_()

bool hasLowIntensityReporter_ ( const ConsensusFeature & cf ) const

private

Checks whether the given ConsensusFeature contains a channel that is below the given intensity threshold.

Parameters

cf	The ConsensusFeature to check.

Returns: $true$ if a low intensity reporter is contained, $false$ otherwise.

◆ isValidPrecursor_()

bool isValidPrecursor_ ( const Precursor & precursor ) const

private

Checks if the given precursor fulfills all constraints for extractions.

Parameters

precursor The precursor to test.

Returns: $true$ if the precursor can be used for extraction, $false$ otherwise.

◆ operator=()

IsobaricChannelExtractor& operator= ( const IsobaricChannelExtractor & rhs )

Assignment operator.

◆ registerChannelsInOutputMap_()

void registerChannelsInOutputMap_ ( ConsensusMap & consensus_map )

private

add channel information to the map after it has been filled

◆ setDefaultParams_()

void setDefaultParams_ ( )

protected

implemented for DefaultParamHandler

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ interpolate_precursor_purity_

bool interpolate_precursor_purity_

private

Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan.

◆ keep_unannotated_precursor_

bool keep_unannotated_precursor_

private

Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.

◆ max_precursor_isotope_deviation_

double max_precursor_isotope_deviation_

private

Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.

◆ min_precursor_intensity_

Peak2D::IntensityType min_precursor_intensity_

private

Minimum intensity of the precursor to be considered for quantitation.

◆ min_precursor_purity_

double min_precursor_purity_

private

Minimum precursor purity to accept the spectrum for quantitation.

◆ min_reporter_intensity_

Peak2D::IntensityType min_reporter_intensity_

private

Minimum reporter ion intensity to be considered for quantitation.

◆ quant_method_

const IsobaricQuantitationMethod* quant_method_

private

The used quantitation method (itraq4plex, tmt6plex,..).

◆ remove_low_intensity_quantifications_

bool remove_low_intensity_quantifications_

private

Flag if complete quantification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ .

◆ reporter_mass_shift_

Peak2D::CoordinateType reporter_mass_shift_

private

Allowed deviation between the expected and observed reporter ion m/z.

◆ selected_activation_

String selected_activation_

private

Used to select only specific types of spectra for the channel extraction.

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IsobaricChannelExtractor() [1/2]

◆ IsobaricChannelExtractor() [2/2]

Member Function Documentation

◆ computePrecursorPurity_()

◆ computeSingleScanPrecursorPurity_()

◆ extractChannels()

◆ getActivationMethod_()

◆ hasLowIntensityReporter_()

◆ isValidPrecursor_()

◆ operator=()

◆ registerChannelsInOutputMap_()

◆ setDefaultParams_()

◆ updateMembers_()

Member Data Documentation

◆ interpolate_precursor_purity_

◆ keep_unannotated_precursor_

◆ max_precursor_isotope_deviation_

◆ min_precursor_intensity_

◆ min_precursor_purity_

◆ min_reporter_intensity_

◆ quant_method_

◆ remove_low_intensity_quantifications_

◆ reporter_mass_shift_

◆ selected_activation_