Execute all steps for retention time and m/z calibration of SWATH-MS data. More...

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

Inheritance diagram for OpenSwathCalibrationWorkflow:

Collaboration diagram for OpenSwathCalibrationWorkflow:

Public Member Functions
	OpenSwathCalibrationWorkflow ()

	OpenSwathCalibrationWorkflow (bool use_ms1_traces)

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

TransformationDescription	doDataNormalization_ (const OpenSwath::LightTargetedExperiment &transition_exp_, const std::vector< OpenMS::MSChromatogram > &chromatograms, TransformationDescription &im_trafo, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &default_ffparam, const Param &irt_detection_param, const Param &calibration_param, const bool pasef)
	Perform retention time and m/z calibration. 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 pasef, bool load_into_memory)
	Simple method to extract chromatograms (for the RT-normalization peptides) More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~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 (UInt64 bytes_processed=0) const

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)
	Add two chromatograms. More...

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

Protected Member Functions inherited from OpenSwathWorkflowBase
	OpenSwathWorkflowBase ()
	Default constructor. More...

	OpenSwathWorkflowBase (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)
	Constructor. More...

void	MS1Extraction_ (const OpenSwath::SpectrumAccessPtr &ms1_map, const std::vector< OpenSwath::SwathMap > &swath_maps, std::vector< MSChromatogram > &ms1_chromatograms, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1only=false, int ms1_isotopes=0)
	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 TransformationDescription &trafo_inverse, const ChromExtractParams &cp, const bool ms1=false, const int ms1_isotopes=-1) 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_ = nullptr
	Spectrum Access to the MS1 map (note that this is not threadsafe!) More...

bool	use_ms1_traces_
	Whether to use the MS1 traces. More...

bool	use_ms1_ion_mobility_
	Whether to use ion mobility extraction on MS1 traces. More...

bool	prm_
	Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows. More...

bool	pasef_
	Whether data is diaPASEF data. More...

int	threads_outer_loop_
	How many threads should be used for the outer loop. 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

Execute all steps for retention time and m/z calibration of SWATH-MS data.

Uses a set of robust calibrant peptides (e.g. iRT peptides, common calibrants) perform RT and m/z correction in SWATH-MS data. Currently supports (non-)linear correction of RT against library RT as well as (non-)linear correction of m/z error as a function of m/z.

Note: The relevant algorithms are implemented in MRMRTNormalizer for RT calibration and SwathMapMassCorrection for m/z calibration.

The overall execution flow in this class is as follows (see performRTNormalization() function):

Extract chromatograms across the whole RT range using simpleExtractChromatograms_()
Compute calibration functions for RT and m/z using doDataNormalization_()

Constructor & Destructor Documentation

◆ OpenSwathCalibrationWorkflow() [1/2]

OpenSwathCalibrationWorkflow ( )

inline

◆ OpenSwathCalibrationWorkflow() [2/2]

OpenSwathCalibrationWorkflow ( bool use_ms1_traces )

inlineexplicit

Member Function Documentation

◆ addChromatograms()

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

static

Add two chromatograms.

Parameters

base_chrom	The base chromatogram to which we will add intensity
newchrom	The chromatogram to be added

◆ doDataNormalization_()

TransformationDescription doDataNormalization_	(	const OpenSwath::LightTargetedExperiment &	transition_exp_,
		const std::vector< OpenMS::MSChromatogram > &	chromatograms,
		TransformationDescription &	im_trafo,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		double	min_rsq,
		double	min_coverage,
		const Param &	default_ffparam,
		const Param &	irt_detection_param,
		const Param &	calibration_param,
		const bool	pasef
	)

Perform retention time and m/z calibration.

Uses MRMRTNormalizer for RT calibration and SwathMapMassCorrection for m/z calibration.

The overall execution flow is as follows:

Estimate the retention time range of the iRT peptides over all assays (see OpenSwathHelper::estimateRTRange())
Store the peptide retention times in an intermediate map
Pick input chromatograms to identify RT pairs from the input data using MRMFeatureFinderScoring, which will be used without the RT scoring enabled
Find most likely correct feature for each compound (see OpenSwathHelper::simpleFindBestFeature())
Perform the outlier detection (see MRMRTNormalizer)
Check whether the found peptides fulfill the binned coverage criteria set by the user.
Select the "correct" peaks for m/z correction (e.g. remove those not part of the linear regression)
Perform m/z calibration (see SwathMapMassCorrection)
Store transformation, using the selected model

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
default_ffparam	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)
calibration_param	Parameter for the m/z and im calibration (see SwathMapMassCorrection)
pasef	whether this data is pasef data with potentially overlapping m/z windows (differing by IM)

Note: This function is based on the algorithm inside the OpenSwathRTNormalizer tool

◆ performRTNormalization()

TransformationDescription performRTNormalization	(	const OpenSwath::LightTargetedExperiment &	irt_transitions,
		std::vector< OpenSwath::SwathMap > &	swath_maps,
		TransformationDescription &	im_trafo,
		double	min_rsq,
		double	min_coverage,
		const Param &	feature_finder_param,
		const ChromExtractParams &	cp_irt,
		const Param &	irt_detection_param,
		const Param &	calibration_param,
		const String &	irt_mzml_out,
		Size	debug_level,
		bool	sonar = `false`,
		bool	pasef = `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 using simpleExtractChromatograms_() and then uses the chromatograms to find features (in doDataNormalization_()). If desired, also m/z correction is performed using the lock masses of the given peptides. The provided raw data (swath_maps) are therefore not constant but 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)
calibration_param	Parameter for the m/z and im calibration (see SwathMapMassCorrection)
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)
sonar	Whether the data is SONAR data
pasef	whether the data is PASEF data (should match transitions by their IM)
load_into_memory	Whether to cache the current SWATH map in memory

Referenced by TOPPOpenSwathBase::performCalibration().

◆ 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	pasef,
		bool	load_into_memory
	)

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

Parameters

swath_maps	The raw data (swath maps)
irt_transitions	A set of transitions used for the RT normalization peptides
chromatograms	The extracted chromatograms (output)
trafo	Transformation description for RT normalization
cp	Parameter set for the chromatogram extraction
load_into_memory	Whether to cache the current SWATH map in memory
sonar	Whether the data is SONAR data
pasef	whether the data is PASEF data with possible overlapping m/z windows (with different ion mobility)

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ OpenSwathCalibrationWorkflow() [1/2]

◆ OpenSwathCalibrationWorkflow() [2/2]

Member Function Documentation

◆ addChromatograms()

◆ doDataNormalization_()

◆ performRTNormalization()

◆ simpleExtractChromatograms_()