Simple OpenSwathWorkflow to perform RT and m/z correction based on a set of known peptides. More...

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

Inheritance diagram for OpenSwathRetentionTimeNormalization:

Public Member Functions
	OpenSwathRetentionTimeNormalization ()

	OpenSwathRetentionTimeNormalization (bool use_ms1_traces)

TransformationDescription	performRTNormalization (const OpenSwath::LightTargetedExperiment &irt_transitions, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const String &mz_correction_function, const String &irt_mzml_out, Size debug_level, bool sonar=false, bool load_into_memory=false)
	Perform RT and m/z correction of the input data using RT-normalization peptides. More...

TransformationDescription	RTNormalization (const OpenSwath::LightTargetedExperiment &transition_exp_, const std::vector< OpenMS::MSChromatogram > &chromatograms, double min_rsq, double min_coverage, const Param &default_ffparam, const Param &irt_detection_param, std::vector< OpenSwath::SwathMap > &swath_maps, const String &mz_correction_function, double mz_extraction_window, bool ppm)
	Perform RT and m/z correction using the MRMFeatureFinderScoring. More...

void	simpleExtractChromatograms (const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram > &chromatograms, const TransformationDescription &trafo, const ChromExtractParams &cp, bool sonar, bool load_into_memory)
	Simple method to extract chromatograms (for the RT-normalization peptides) 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...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Member Functions
static void	addChromatograms (MSChromatogram &base_chrom, const MSChromatogram &newchrom)

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

Protected Member Functions inherited from OpenSwathWorkflowBase
	OpenSwathWorkflowBase (bool use_ms1_traces)

void	MS1Extraction_ (const std::vector< OpenSwath::SwathMap > &swath_maps, std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool load_into_memory, bool ms1only=false)
	Perform MS1 extraction and store result in ms1_chromatograms. More...

void	prepareExtractionCoordinates_ (std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const bool ms1, const TransformationDescription trafo_inverse, const ChromExtractParams &cp) const
	Function to prepare extraction coordinates that also correctly handles RT transformations. 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 OpenSwathWorkflowBase
OpenSwath::SpectrumAccessPtr	ms1_map_
	Spectrum Access to the MS1 map (note that this is not threadsafe!) More...

bool	use_ms1_traces_
	Whether to use the MS1 traces. 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

Simple OpenSwathWorkflow to perform RT and m/z correction based on a set of known peptides.

Constructor & Destructor Documentation

◆ OpenSwathRetentionTimeNormalization() [1/2]

OpenSwathRetentionTimeNormalization ( )

inlineexplicit

◆ OpenSwathRetentionTimeNormalization() [2/2]

OpenSwathRetentionTimeNormalization ( bool use_ms1_traces )

inlineexplicit

Member Function Documentation

◆ addChromatograms()

static void addChromatograms	(	MSChromatogram &	base_chrom,
		const MSChromatogram &	newchrom
	)

static

◆ performRTNormalization()

TransformationDescription performRTNormalization	(	const OpenSwath::LightTargetedExperiment &	irt_transitions,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		double	min_rsq,
		double	min_coverage,
		const Param &	feature_finder_param,
		const ChromExtractParams &	cp_irt,
		const Param &	irt_detection_param,
		const String &	mz_correction_function,
		const String &	irt_mzml_out,
		Size	debug_level,
		bool	sonar = `false`,
		bool	load_into_memory = `false`
	)

Perform RT and m/z correction of the input data using RT-normalization peptides.

This function extracts the RT normalization chromatograms and then uses the chromatograms to find features (in RTNormalization). If desired, also m/z correction is performed using the lock masses of the given peptides. Therefore, swath_maps may be changed in this function.

Parameters

irt_transitions	A set of transitions used for the RT normalization peptides
swath_maps	The raw data (swath maps)
min_rsq	Minimal R^2 value that is expected for the RT regression
min_coverage	Minimal coverage of the chromatographic space that needs to be achieved
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
cp_irt	Parameter set for the chromatogram extraction
irt_detection_param	Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
mz_correction_function	If correction in m/z is desired, which function should be used
debug_level	Debug level (writes out the RT normalization chromatograms if larger than 1)
irt_mzml_out	Output Chromatogram mzML containing the iRT peptides (if not empty, iRT chromatograms will be stored in this file)

◆ RTNormalization()

TransformationDescription RTNormalization	(	const OpenSwath::LightTargetedExperiment &	transition_exp_,
		const std::vector< OpenMS::MSChromatogram > &	chromatograms,
		double	min_rsq,
		double	min_coverage,
		const Param &	default_ffparam,
		const Param &	irt_detection_param,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		const String &	mz_correction_function,
		double	mz_extraction_window,
		bool	ppm
	)

Perform RT and m/z correction using the MRMFeatureFinderScoring.

Parameters

transition_exp_	The transitions for the normalization peptides
chromatograms	The extracted chromatograms
min_rsq	Minimal R^2 value that is expected for the RT regression
min_coverage	Minimal coverage of the chromatographic space that needs to be achieved
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
irt_detection_param	Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
swath_maps	The raw data for the m/z correction
mz_correction_function	If correction in m/z is desired, which function should be used

Note: : feature_finder_param are copied because they are changed here.; : This function is based on the algorithm inside the OpenSwathRTNormalizer tool

◆ simpleExtractChromatograms()

void simpleExtractChromatograms	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenSwath::LightTargetedExperiment &	irt_transitions,
		std::vector< OpenMS::MSChromatogram > &	chromatograms,
		const TransformationDescription &	trafo,
		const ChromExtractParams &	cp,
		bool	sonar,
		bool	load_into_memory
	)

Simple method to extract chromatograms (for the RT-normalization peptides)

Public Member Functions

Static Public Member Functions

Additional Inherited Members