TransitionListEvidenceFilter Class Reference

Prefilter transition-library precursors by quick raw-data evidence. More...

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

Inheritance diagram for TransitionListEvidenceFilter:

Collaboration diagram for TransitionListEvidenceFilter:

Classes
struct	PrecursorEvidence
	Compact evidence summary for one target precursor candidate. More...
struct	Result
	Result of filtering one run against one transition experiment. More...

Constructors and Destructors
bool	enabled_ {false}
std::string	evidence_sources_ {"hybrid"}
Size	ms1_top_peaks_per_spectrum_ {1000}
Size	ms2_top_peaks_per_spectrum_ {1000}
Size	ms2_top_transitions_per_precursor_ {6}
Size	ms2_min_fragment_hits_ {4}
Size	min_supported_precursors_ {3}
bool	peak_picking_enabled_ {false}
bool	peak_picking_use_gauss_ {true}
	TransitionListEvidenceFilter ()
	Default constructor.
	~TransitionListEvidenceFilter () override=default
	Destructor.
void	updateMembers_ () override
	Synchronize members with the parameter object.
Result	filter (const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &transition_exp, const ChromExtractParams &ms1_params, const ChromExtractParams &ms2_params, bool pasef, int threads=1) const
	Filter target precursors by MS1/MS2 evidence observed in the current run.

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.
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

Prefilter transition-library precursors by quick raw-data evidence.

This module scans MS1 and/or SWATH MS2 spectra directly through the OpenSWATH spectrum access layer. It keeps a target precursor when the run contains precursor m/z evidence in MS1 or enough distinct library fragment hits in MS2. The output experiment is target-only and can be used as a data-supported auto-iRT sampling pool or as the target selection step for a caller that adds matching decoys before downstream scoring.

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Class Documentation

OpenMS::TransitionListEvidenceFilter::PrecursorEvidence

struct OpenMS::TransitionListEvidenceFilter::PrecursorEvidence

Compact evidence summary for one target precursor candidate.

Collaboration diagram for TransitionListEvidenceFilter::PrecursorEvidence:

Class Members
string	compound_id	Compound/peptide identifier in the transition experiment.
double	ms1_best_rt {-1.0}	RT of the strongest matched MS1 peak, or -1 if unsupported.
Size	ms1_hit_count {0}	Number of MS1 peak matches.
double	ms1_max_intensity {0.0}	Maximum matched MS1 peak intensity.
double	ms1_sum_intensity {0.0}	Sum of matched MS1 peak intensities.
Size	ms2_best_fragment_hits {0}	Best number of distinct MS2 fragment hits in a single spectrum.
double	ms2_best_rt {-1.0}	RT of the strongest supporting MS2 spectrum, or -1 if unsupported.
Size	ms2_hit_count {0}	Total number of distinct MS2 fragment matches across supporting spectra.
double	ms2_max_intensity {0.0}	Maximum matched MS2 peak intensity.
double	ms2_sum_intensity {0.0}	Sum of matched MS2 peak intensities from supporting spectra.
double	precursor_im {-1.0}	Library precursor ion mobility, or -1 if unavailable.
double	precursor_mz {0.0}	Precursor m/z used for matching.
string	sequence	Peptide sequence, if present in the transition experiment.
bool	supported_ms1 {false}	Whether MS1 precursor evidence was observed.
bool	supported_ms2 {false}	Whether MS2 fragment evidence was observed.

OpenMS::TransitionListEvidenceFilter::Result

struct OpenMS::TransitionListEvidenceFilter::Result

Result of filtering one run against one transition experiment.

Collaboration diagram for TransitionListEvidenceFilter::Result:

Class Members
vector< PrecursorEvidence >	evidence	Per-candidate evidence, in the same order as the internal target candidates.
LightTargetedExperiment	filtered_targets	Target-only filtered transition experiment for auto-iRT sampling.
Size	hybrid_supported {0}	Number of candidates with both MS1 and MS2 evidence.
Size	ms1_supported {0}	Number of candidates with MS1 evidence.
Size	ms2_supported {0}	Number of candidates with MS2 evidence.
double	precursor_im_scale {1.0}	Scale factor applied to precursor ion mobility values for matching and filtered output.
bool	precursor_im_scaled_by_charge {false}	Whether precursor ion mobility values were also multiplied by precursor charge.
string	summary	Human-readable summary for logging.
Size	supported_precursors {0}	Number of candidates supported by the configured evidence source(s).
Size	total_target_precursors {0}	Total number of non-decoy precursor candidates considered.

Constructor & Destructor Documentation

TransitionListEvidenceFilter()

TransitionListEvidenceFilter

(

)

Default constructor.

~TransitionListEvidenceFilter()

~TransitionListEvidenceFilter ( )

overridedefault

Destructor.

Member Function Documentation

filter()

Result filter	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		const ChromExtractParams &	ms1_params,
		const ChromExtractParams &	ms2_params,
		bool	pasef,
		int	threads = 1
	)		const

Filter target precursors by MS1/MS2 evidence observed in the current run.

Parameters

[in]	swath_maps	Raw SWATH maps for the current run
[in]	transition_exp	Input transition experiment
[in]	ms1_params	MS1 extraction parameters used as precursor m/z/IM tolerances
[in]	ms2_params	MS2/iRT extraction parameters used as fragment m/z/IM tolerances
[in]	pasef	Whether the run uses PASEF windows with ion mobility boundaries
[in]	threads	Number of OpenMP worker threads to use (1 = serial, -1 = OpenMP maximum)

Returns

Filtered target experiment and compact evidence summaries

Exceptions

Exception::IllegalArgument

if the configured evidence source cannot be used or too few precursors remain

updateMembers_()

void updateMembers_ ( )

overridevirtual

Synchronize members with the parameter object.

Reimplemented from DefaultParamHandler.

Member Data Documentation

enabled_

bool enabled_ {false}

private

evidence_sources_

std::string evidence_sources_ {"hybrid"}

private

min_supported_precursors_

Size min_supported_precursors_ {3}

private

ms1_top_peaks_per_spectrum_

Size ms1_top_peaks_per_spectrum_ {1000}

private

ms2_min_fragment_hits_

Size ms2_min_fragment_hits_ {4}

private

ms2_top_peaks_per_spectrum_

Size ms2_top_peaks_per_spectrum_ {1000}

private

ms2_top_transitions_per_precursor_

Size ms2_top_transitions_per_precursor_ {6}

private

peak_picking_enabled_

bool peak_picking_enabled_ {false}

private

peak_picking_use_gauss_

bool peak_picking_use_gauss_ {true}

private