The MRMFeatureFinder finds and scores peaks of transitions that co-elute. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>

Inheritance diagram for MRMFeatureFinderScoring:

Public Types

typedef OpenSwath::LightTransition	TransitionType
	Type definitions. More...

typedef OpenSwath::LightTargetedExperiment	TargetedExpType

typedef OpenSwath::LightCompound	PeptideType

typedef OpenSwath::LightProtein	ProteinType

typedef OpenSwath::LightModification	ModificationType

typedef MRMTransitionGroup< MSChromatogram, TransitionType >	MRMTransitionGroupType

typedef std::map< String, MRMTransitionGroupType >	TransitionGroupMapType

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

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

	~MRMFeatureFinderScoring ()
	Destructor. More...

void	scorePeakgroups (MRMTransitionGroupType &transition_group, TransformationDescription &trafo, std::vector< OpenSwath::SwathMap > swath_maps, FeatureMap &output, bool ms1only=false)
	Score all peak groups of a transition group. More...

void	setStrictFlag (bool f)
	Set the flag for strict mapping. More...

void	setMS1Map (OpenSwath::SpectrumAccessPtr ms1_map)
	Add an MS1 map containing spectra. More...

void	mapExperimentToTransitionList (OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window)
	Map the chromatograms to the transitions. More...


void	pickExperiment (PeakMap &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, PeakMap &swath_map)
	Picker and prepare functions. More...

void	pickExperiment (OpenSwath::SpectrumAccessPtr input, FeatureMap &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, std::vector< OpenSwath::SwathMap > swath_maps, TransitionGroupMapType &transition_group_map)
	Pick features in one experiment containing chromatogram. More...

void	prepareProteinPeptideMaps_ (const OpenSwath::LightTargetedExperiment &transition_exp)
	Prepares the internal mappings of peptides and proteins. 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...

virtual 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...

	~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	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 () const
	Ends the progress display. More...

Private Member Functions
void	splitTransitionGroupsDetection_ (MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_detection)
	Splits combined transition groups into detection transition groups. More...

void	splitTransitionGroupsIdentification_ (MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_identification, MRMTransitionGroupType &transition_group_identification_decoy)
	Splits combined transition groups into identification transition groups. More...

OpenSwath_Scores	scoreIdentification_ (MRMTransitionGroupType &transition_group_identification, OpenSwathScoring &scorer, const size_t feature_idx, const std::vector< std::string > native_ids_detection, const double sn_win_len_, const unsigned int sn_bin_count_, bool write_log_messages, std::vector< OpenSwath::SwathMap > swath_maps)
	Provides scoring for target and decoy identification against detecting transitions. More...

void	updateMembers_ ()
	Synchronize members with param class. More...

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

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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

The MRMFeatureFinder finds and scores peaks of transitions that co-elute.

It does so using an internal peakpicker for each chromatogram and then creating consensus / meta-peaks (MRMFeatures) that contain the information of all corresponding chromatograms at the peak-position. It then goes on to score those MRMFeatures using different criteria described in the MRMScoring class.

Internally, all peak group detection is performed in MRMTransitionGroupPicker which segments the data and determines consensus peaks across traces (MRMFeatures). All scoring is delegated to the OpenSwathScoring class which implements i) chromatographic scores, ii) library based scores and iii) full spectrum (DIA) scores. These scores are retrieved from the OpenSwathScoring class and added to the MRMFeatures found in this algorithm. Note that the OpenSwathScoring is a facade that can be used to communicate with the underlying actual scoring engines and assembles the scores inside a scoring object called OpenSwath_Scores where they are easy to retrieve.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
stop_report_after_feature	int	-1		Stop reporting after feature (ordered by quality; -1 means do not stop).
rt_extraction_window	float	-1		Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution). For this to work, the TraML input file needs to contain normalized RT values.
rt_normalization_factor	float	1		The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)
quantification_cutoff	float	0	min: 0	Cutoff in m/z below which peaks should not be used for quantification any more
write_convex_hull	string	false	true, false	Whether to write out all points of all features into the featureXML
add_up_spectra	int	1	min: 1	Add up spectra around the peak apex (needs to be a non-even integer)
spacing_for_spectra_resampling	float	0.005	min: 0	If spectra are to be added, use this spacing to add them up
uis_threshold_sn	int	-1		S/N threshold to consider identification transition (set to -1 to consider all)
uis_threshold_peak_area	int	0		Peak area threshold to consider identification transition (set to -1 to consider all)
TransitionGroupPicker:stop_after_feature	int	-1		Stop finding after feature (ordered by intensity; -1 means do not stop).
TransitionGroupPicker:stop_after_intensity_ratio	float	0.0001		Stop after reaching intensity ratio
TransitionGroupPicker:min_peak_width	float	-1		Minimal peak width (s), discard all peaks below this value (-1 means no action).
TransitionGroupPicker:background_subtraction	string	none	none, smoothed, original	Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that.
TransitionGroupPicker:recalculate_peaks	string	false	true, false	Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large.
TransitionGroupPicker:use_precursors	string	false	true, false	Use precursor chromatogram for peak picking
TransitionGroupPicker:recalculate_peaks_max_z	float	1		Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0).
TransitionGroupPicker:minimal_quality	float	-10000		Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold
TransitionGroupPicker:resample_boundary	float	15		For computing peak quality, how many extra seconds should be sample left and right of the actual peak
TransitionGroupPicker:compute_peak_quality	string	false	true, false	Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad.
TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length	int	15		The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order	int	3		Order of the polynomial that is fitted.
TransitionGroupPicker:PeakPickerMRM:gauss_width	float	50		Gaussian width in seconds, estimated peak size.
TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true	false, true	Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
TransitionGroupPicker:PeakPickerMRM:peak_width	float	-1		Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
TransitionGroupPicker:PeakPickerMRM:signal_to_noise	float	1	min: 0	Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
TransitionGroupPicker:PeakPickerMRM:sn_win_len	float	1000		Signal to noise window length.
TransitionGroupPicker:PeakPickerMRM:sn_bin_count	int	30		Signal to noise bin count.
TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages	string	true	true, false	Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks	string	false	false, true	Try to remove overlapping peaks during peak picking
TransitionGroupPicker:PeakPickerMRM:method	string	corrected	legacy, corrected, crawdad	Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).
DIAScoring:dia_extraction_window	float	0.05	min: 0	DIA extraction window in Th.
DIAScoring:dia_centroided	string	false	true, false	Use centroded DIA data.
DIAScoring:dia_byseries_intensity_min	float	300	min: 0	DIA b/y series minimum intensity to consider.
DIAScoring:dia_byseries_ppm_diff	float	10	min: 0	DIA b/y series minimal difference in ppm to consider.
DIAScoring:dia_nr_isotopes	int	4	min: 0	DIA nr of isotopes to consider.
DIAScoring:dia_nr_charges	int	4	min: 0	DIA nr of charges to consider.
DIAScoring:peak_before_mono_max_ppm_diff	float	20	min: 0	DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic.
EMGScoring:interpolation_step	float	0.2		Sampling rate for the interpolation of the model function.
EMGScoring:tolerance_stdev_bounding_box	float	3		Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
EMGScoring:max_iteration	int	500		Maximum number of iterations using by Levenberg-Marquardt algorithm.
EMGScoring:statistics:mean	float	1		Centroid position of the model.
EMGScoring:statistics:variance	float	1		Variance of the model.
Scores:use_shape_score	string	true	true, false	Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)
Scores:use_coelution_score	string	true	true, false	Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)
Scores:use_rt_score	string	true	true, false	Use the retention time score (this score measure the difference in retention time)
Scores:use_library_score	string	true	true, false	Use the library score
Scores:use_elution_model_score	string	true	true, false	Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)
Scores:use_intensity_score	string	true	true, false	Use the intensity score
Scores:use_nr_peaks_score	string	true	true, false	Use the number of peaks score
Scores:use_total_xic_score	string	true	true, false	Use the total XIC score
Scores:use_sn_score	string	true	true, false	Use the SN (signal to noise) score
Scores:use_dia_scores	string	true	true, false	Use the DIA (SWATH) scores. If turned off, will not use fragment ion spectra for scoring.
Scores:use_ms1_correlation	string	false	true, false	Use the correlation scores with the MS1 elution profiles
Scores:use_sonar_scores	string	false	true, false	Use the scores for SONAR scans (scanning swath)
Scores:use_ms1_fullscan	string	false	true, false	Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)
Scores:use_uis_scores	string	false	true, false	Use UIS scores for peptidoform identification

Note:

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

Member Typedef Documentation

◆ ModificationType

typedef OpenSwath::LightModification ModificationType

◆ MRMTransitionGroupType

typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType

◆ PeptideType

typedef OpenSwath::LightCompound PeptideType

◆ ProteinType

typedef OpenSwath::LightProtein ProteinType

◆ TargetedExpType

typedef OpenSwath::LightTargetedExperiment TargetedExpType

◆ TransitionGroupMapType

typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

Type definitions.

Constructor & Destructor Documentation

◆ MRMFeatureFinderScoring()

MRMFeatureFinderScoring ( )

Constructor.

◆ ~MRMFeatureFinderScoring()

~MRMFeatureFinderScoring ( )

Destructor.

Member Function Documentation

◆ mapExperimentToTransitionList()

void mapExperimentToTransitionList	(	OpenSwath::SpectrumAccessPtr	input,
		OpenSwath::LightTargetedExperiment &	transition_exp,
		TransitionGroupMapType &	transition_group_map,
		TransformationDescription	trafo,
		double	rt_extraction_window
	)

Map the chromatograms to the transitions.

Map an input chromatogram experiment (mzML) and transition list (TraML) onto each other when they share identifiers, e.g. if the transition id is the same as the chromatogram native id.

Parameters

input	The input chromatograms
transition_exp	The transition list describing the experiment
transition_group_map	Mapping of transition groups
trafo	Optional transformation of the experimental retention time to the normalized retention time space used in the transition list.
rt_extraction_window	The used retention time extraction window

◆ pickExperiment() [1/2]

void pickExperiment	(	PeakMap &	chromatograms,
		FeatureMap &	output,
		TargetedExperiment &	transition_exp,
		TransformationDescription	trafo,
		PeakMap &	swath_map
	)

Picker and prepare functions.

Pick features in one experiment containing chromatogram

Function for for wrapping in Python, only uses OpenMS datastructures and does not return the map.

Parameters

chromatograms	The input chromatograms
output	The output features with corresponding scores
transition_exp	The transition list describing the experiment
trafo	Optional transformation of the experimental retention time to the normalized retention time space used in the transition list
swath_map	Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted

◆ pickExperiment() [2/2]

void pickExperiment	(	OpenSwath::SpectrumAccessPtr	input,
		FeatureMap &	output,
		OpenSwath::LightTargetedExperiment &	transition_exp,
		TransformationDescription	trafo,
		std::vector< OpenSwath::SwathMap >	swath_maps,
		TransitionGroupMapType &	transition_group_map
	)

Pick features in one experiment containing chromatogram.

Parameters

input	The input chromatograms
output	The output features with corresponding scores
transition_exp	The transition list describing the experiment
trafo	Optional transformation of the experimental retention time to the normalized retention time space used in the transition list.
swath_map	Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available.
transition_group_map	Output mapping of transition groups

◆ prepareProteinPeptideMaps_()

void prepareProteinPeptideMaps_ ( const OpenSwath::LightTargetedExperiment & transition_exp )

Prepares the internal mappings of peptides and proteins.

Calling this method _is_ required before calling scorePeakgroups.

Parameters

transition_exp The transition list describing the experiment

◆ scoreIdentification_()

OpenSwath_Scores scoreIdentification_	(	MRMTransitionGroupType &	transition_group_identification,
		OpenSwathScoring &	scorer,
		const size_t	feature_idx,
		const std::vector< std::string >	native_ids_detection,
		const double	sn_win_len_,
		const unsigned int	sn_bin_count_,
		bool	write_log_messages,
		std::vector< OpenSwath::SwathMap >	swath_maps
	)

private

Provides scoring for target and decoy identification against detecting transitions.

The function is used twice, for target and decoy identification transitions. The results are reported analogously to the ones for detecting transitions but must be stored separately.

Parameters

transition_group	Containing all detecting, identifying transitions
transition_group_identification	Containing all detecting and identifying transitions
scorer	An instance of OpenSwathScoring
feature_idx	The index of the current feature
native_ids_detection	The native IDs of the detecting transitions
sn_win_len_	The signal to noise window length
sn_bin_count_	The signal to noise bin count
write_log_messages	Whether to write signal to noise log messages a struct of type OpenSwath_Scores containing either target or decoy values

◆ scorePeakgroups()

void scorePeakgroups	(	MRMTransitionGroupType &	transition_group,
		TransformationDescription &	trafo,
		std::vector< OpenSwath::SwathMap >	swath_maps,
		FeatureMap &	output,
		bool	ms1only = `false`
	)

Score all peak groups of a transition group.

Iterate through all features found along the chromatograms of the transition group and score each one individually.

Parameters

transition_group	The MRMTransitionGroup to be scored (input)
trafo	Optional transformation of the experimental retention time to the normalized retention time space used in the transition list.
swath_map	Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available.
output	The output features with corresponding scores (the found features will be added to this FeatureMap).
ms1only	Whether to only do MS1 scoring and skip all MS2 scoring

◆ setMS1Map()

void setMS1Map ( OpenSwath::SpectrumAccessPtr ms1_map )

inline

Add an MS1 map containing spectra.

For DIA (SWATH-MS), an optional MS1 map can be supplied which can be used to extract precursor ion signal and provides additional scores. If no MS1 map is provided, the respective scores are not calculated.

Parameters

ms1_map The raw mass spectrometric MS1 data

◆ setStrictFlag()

void setStrictFlag ( bool f )

inline

Set the flag for strict mapping.

◆ splitTransitionGroupsDetection_()

void splitTransitionGroupsDetection_	(	MRMTransitionGroupType &	transition_group,
		MRMTransitionGroupType &	transition_group_detection
	)

private

Splits combined transition groups into detection transition groups.

For standard assays, transition_group_detection is identical to transition_group and the others are empty.

Parameters

transition_group	Containing all detecting, identifying transitions
transition_group_detection	To be filled with detecting transitions

◆ splitTransitionGroupsIdentification_()

void splitTransitionGroupsIdentification_	(	MRMTransitionGroupType &	transition_group,
		MRMTransitionGroupType &	transition_group_identification,
		MRMTransitionGroupType &	transition_group_identification_decoy
	)

private

Splits combined transition groups into identification transition groups.

For standard assays, transition_group_identification is empty. When UIS scoring is enabled, it contains the corresponding identification transitions.

Parameters

transition_group	Containing all detecting, identifying transitions
transition_group_identification	To be filled with identifying transitions
transition_group_identification_decoy	To be filled with identifying decoy transitions

◆ updateMembers_()

void updateMembers_ ( )

privatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ add_up_spectra_

int add_up_spectra_

private

◆ diascoring_

OpenMS::DIAScoring diascoring_

private

◆ emgscoring_

OpenMS::EmgScoring emgscoring_

private

◆ ms1_map_

OpenSwath::SpectrumAccessPtr ms1_map_

private

◆ PeptideRefMap_

std::map<OpenMS::String, const PeptideType*> PeptideRefMap_

private

◆ quantification_cutoff_

double quantification_cutoff_

private

◆ rt_extraction_window_

double rt_extraction_window_

private

◆ rt_normalization_factor_

double rt_normalization_factor_

private

◆ sonarscoring_

OpenMS::SONARScoring sonarscoring_

private

◆ spacing_for_spectra_resampling_

double spacing_for_spectra_resampling_

private

◆ stop_report_after_feature_

int stop_report_after_feature_

private

◆ strict_

bool strict_

private

◆ su_

OpenSwath_Scores_Usage su_

private

◆ uis_threshold_peak_area_

double uis_threshold_peak_area_

private

◆ uis_threshold_sn_

double uis_threshold_sn_

private

◆ write_convex_hull_

bool write_convex_hull_

private

Private Attributes
double	rt_extraction_window_

double	quantification_cutoff_

int	stop_report_after_feature_

bool	write_convex_hull_

bool	strict_

double	rt_normalization_factor_

int	add_up_spectra_

double	spacing_for_spectra_resampling_

double	uis_threshold_sn_

double	uis_threshold_peak_area_

std::map< OpenMS::String, const PeptideType * >	PeptideRefMap_

OpenSwath_Scores_Usage	su_

OpenMS::DIAScoring	diascoring_

OpenMS::SONARScoring	sonarscoring_

OpenMS::EmgScoring	emgscoring_

OpenSwath::SpectrumAccessPtr	ms1_map_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ModificationType

◆ MRMTransitionGroupType

◆ PeptideType

◆ ProteinType

◆ TargetedExpType

◆ TransitionGroupMapType

◆ TransitionType

Constructor & Destructor Documentation

◆ MRMFeatureFinderScoring()

◆ ~MRMFeatureFinderScoring()

Member Function Documentation

◆ mapExperimentToTransitionList()

◆ pickExperiment() [1/2]

◆ pickExperiment() [2/2]

◆ prepareProteinPeptideMaps_()

◆ scoreIdentification_()

◆ scorePeakgroups()

◆ setMS1Map()

◆ setStrictFlag()

◆ splitTransitionGroupsDetection_()

◆ splitTransitionGroupsIdentification_()

◆ updateMembers_()

Member Data Documentation

◆ add_up_spectra_

◆ diascoring_

◆ emgscoring_

◆ ms1_map_

◆ PeptideRefMap_

◆ quantification_cutoff_

◆ rt_extraction_window_

◆ rt_normalization_factor_

◆ sonarscoring_

◆ spacing_for_spectra_resampling_

◆ stop_report_after_feature_

◆ strict_

◆ su_

◆ uis_threshold_peak_area_

◆ uis_threshold_sn_

◆ write_convex_hull_