Orchestrates calibration workflows for OpenSWATH analysis. More...

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

Inheritance diagram for CalibrationWorkflow:

Collaboration diagram for CalibrationWorkflow:

Classes
struct	CalibrationResult
	Results from calibration workflow. More...

struct	IrtExperiments
	Prepared iRT experiments ready for calibration. More...

Public Member Functions
	CalibrationWorkflow ()
	Default constructor.

	~CalibrationWorkflow () override
	Destructor

IrtStrategy	determineIrtStrategy (const OpenSwath::LightTargetedExperiment &full_transition_exp, size_t num_runs=1) const
	Determine the appropriate IRT strategy based on available data.

IrtExperiments	prepareIrtExperiments (IrtStrategy strategy, const OpenSwath::LightTargetedExperiment &full_transition_exp, const std::vector< String > &priority_peptides, size_t run_index=0, const IrtExperiments *cached_irts=nullptr)
	Prepare iRT experiments based on the determined strategy.

CalibrationResult	performCalibration (std::vector< OpenSwath::SwathMap > &swath_maps, OpenSwath::LightTargetedExperiment &transition_exp, ChromExtractParams &cp, ChromExtractParams &cp_ms1, const IrtExperiments &irt_experiments, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, bool pasef=false, bool load_into_memory=false, const String &irt_trafo_out="", const String &irt_mzml_out="", Size debug_level=0)
	Perform calibration workflow with pre-prepared iRT experiments.

OpenSwath::LightTargetedExperiment	loadIrtExperimentFromFile_ (const String &irt_file_path, const String &label) const
	Load iRT transition experiment from file.

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 Param &mrm_mapping_param, const String &irt_mzml_out, Size debug_level, bool pasef=false, bool load_into_memory=false)
	Perform RT and m/z correction of the input data using RT-normalization peptides.

TransformationDescription	doDataNormalization_ (const OpenSwath::LightTargetedExperiment &targeted_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.

double	getEstimatedMzWindow () const
	Get estimated MS2 m/z extraction window.

double	getEstimatedImWindow () const
	Get estimated MS2 ion mobility extraction window.

double	getEstimatedMs1MzWindow () const
	Get estimated MS1 m/z extraction window.

double	getEstimatedMs1ImWindow () const
	Get estimated MS1 ion mobility extraction window.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const 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 String &	getName () const
	Non-mutable access to the name.

void	setName (const String &name)
	Mutable access to the name.

const std::vector< 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 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)

Private Member Functions
Private implementation methods
CalibrationResult	performLinearCalibration_ (std::vector< OpenSwath::SwathMap > &swath_maps, const IrtExperiments &irt_experiments, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, bool pasef, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out, Size debug_level)
	Perform linear-only calibration workflow.

CalibrationResult	performLinearThenNonlinearCalibration_ (std::vector< OpenSwath::SwathMap > &swath_maps, const IrtExperiments &irt_experiments, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, bool pasef, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out, Size debug_level)
	Perform linear + nonlinear calibration workflow.

void	applyEstimatedWindows_ (const CalibrationResult &result, ChromExtractParams &cp, ChromExtractParams &cp_ms1, bool pasef, bool use_ms1_im) const
	Apply estimated extraction windows to parameters.

void	applyWindow_ (const char *label, double estimate, double &dst_param, double user_value, bool applicable=true, bool commit=true) const
	Validate and log an auto-estimated extraction window.

bool	isValidWindow_ (double v, double min_positive=1e-9) const noexcept
	Check if an estimated extraction window value is valid.

Private Attributes
Private member variables for parameter caching <br>
String	linear_irt_file_

String	nonlinear_irt_file_

std::vector< String >	linear_irt_files_list_

std::vector< String >	nonlinear_irt_files_list_

bool	auto_irt_enabled_

int	auto_irt_irt_bins_

int	auto_irt_irt_peptides_per_bin_

int	auto_irt_irt_seed_

int	auto_irt_irt_bins_nonlinear_

int	auto_irt_irt_peptides_per_bin_nonlinear_

double	auto_irt_linear_top_fraction_

double	auto_irt_nonlinear_top_fraction_

String	linear_outlier_detection_

String	nonlinear_outlier_detection_

bool	windows_estimate_rt_

bool	windows_estimate_mz_

bool	windows_estimate_im_

double	windows_rt_percentile_

double	rt_estimation_padding_factor_

double	min_rsq_

double	min_coverage_

Parameter handling
double	estimated_mz_window_ {-1.0}

double	estimated_im_window_ {-1.0}

double	estimated_ms1_mz_window_ {-1.0}

double	estimated_ms1_im_window_ {-1.0}

void	updateMembers_ () override
	Update member variables from parameters.

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

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.

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< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

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

Orchestrates calibration workflows for OpenSWATH analysis.

This class provides a unified interface for performing RT, m/z, and ion mobility calibration workflows. It supports both linear-only calibration and linear+nonlinear calibration strategies, making calibration logic reusable across different OpenSWATH tools (DIA/SWATH, SRM/MRM, PRM).

The orchestrator handles:

Parameter validation and setup
iRT peptide sampling (when auto_irt is enabled)
Linear calibration workflow
Nonlinear calibration workflow (optional)
Extraction window estimation and application
Result aggregation and reporting

Class Documentation

◆ OpenMS::CalibrationWorkflow::CalibrationResult

struct OpenMS::CalibrationWorkflow::CalibrationResult

Results from calibration workflow.

Collaboration diagram for CalibrationWorkflow::CalibrationResult:

[legend]

Class Members
double	estimated_rt_window {-1.0}	Estimated RT extraction window (full width, seconds)
TransformationDescription	im_trafo	Ion mobility transformation (fitted). May be empty if no IM calibration performed.
double	ms1_im_window {-1.0}	MS1 ion mobility extraction window (full width). -1 if not applicable.
double	ms1_mz_window_ppm {-1.0}	MS1 m/z extraction window (full width, ppm). -1 if not computed.
double	ms2_im_window {-1.0}	MS2 ion mobility extraction window (full width). -1 if not applicable.
double	ms2_mz_window_ppm {-1.0}	MS2 m/z extraction window (full width, ppm). -1 if not computed.
TransformationDescription	rt_trafo	RT normalization transformation (fitted)

◆ OpenMS::CalibrationWorkflow::IrtExperiments

struct OpenMS::CalibrationWorkflow::IrtExperiments

Prepared iRT experiments ready for calibration.

Collaboration diagram for CalibrationWorkflow::IrtExperiments:

[legend]

Class Members
bool	is_prepared {false}	Whether experiments are available and ready for calibration.
LightTargetedExperiment	linear_irt	Linear iRT experiment (always required for calibration)
LightTargetedExperiment	nonlinear_irt	Nonlinear iRT experiment (optional, empty if not used)
IrtStrategy	strategy {IrtStrategy::STATIC_FILES}	Strategy used to prepare these experiments.

Constructor & Destructor Documentation

◆ CalibrationWorkflow()

CalibrationWorkflow ( )

Default constructor.

◆ ~CalibrationWorkflow()

~CalibrationWorkflow ( )

override

Destructor

Member Function Documentation

◆ applyEstimatedWindows_()

void applyEstimatedWindows_	(	const CalibrationResult &	result,
		ChromExtractParams &	cp,
		ChromExtractParams &	cp_ms1,
		bool	pasef,
		bool	use_ms1_im
	)		const

private

Apply estimated extraction windows to parameters.

Updates the provided extraction parameters with auto-estimated windows based on calibration results and user preferences.

Parameters

[in]	result	Calibration results containing estimated windows
[in,out]	cp	MS2 extraction parameters to update
[in,out]	cp_ms1	MS1 extraction parameters to update
[in]	pasef	Whether this is PASEF data (for IM applicability)
[in]	use_ms1_im	Whether MS1 uses ion mobility

◆ applyWindow_()

void applyWindow_	(	const char *	label,
		double	estimate,
		double &	dst_param,
		double	user_value,
		bool	applicable = `true`,
		bool	commit = `true`
	)		const

private

Validate and log an auto-estimated extraction window.

Behavior:

If applicable is false (e.g., no IM data), logs an INFO and leaves dst_param unchanged.
If the estimate is invalid, logs a WARN and leaves dst_param unchanged.
If the estimate is valid and commit is true, logs an INFO and assigns dst_param = estimate.
If the estimate is valid and commit is false, logs an INFO that reports the estimate and that the user value is kept.

Typical usage:

RT window (seconds)
MS2 m/z window (ppm)
MS1 m/z window (ppm)
IM window (1/k0), only when applicable (e.g., PASEF/IM data)

Parameters

[in]	label	Human-readable label for logging
[in]	estimate	Estimated window value
[in,out]	dst_param	Parameter to update
[in]	user_value	Current user-specified value
[in]	applicable	Whether this window type is applicable
[in]	commit	Whether to actually apply the estimate

◆ determineIrtStrategy()

IrtStrategy determineIrtStrategy	(	const OpenSwath::LightTargetedExperiment &	full_transition_exp,
		size_t	num_runs = `1`
	)		const

Determine the appropriate IRT strategy based on available data.

Analyzes the available iRT data to determine which IRT strategy should be used for calibration. Priority order:

If static iRT files are configured → STATIC_FILES or RUN_SPECIFIC
If full transition library is provided and auto-iRT is enabled → SAMPLE_ONCE or SAMPLE_PER_RUN
Otherwise → NULL_TRANSFORMATION (no iRT data available)

Parameters

[in]	full_transition_exp	Full transition experiment for auto-sampling (empty if not available)
[in]	num_runs	Total number of runs to process (affects strategy choice)

Returns: The determined IRT strategy

Note: When NULL_TRANSFORMATION is returned, callers can decide whether to skip calibration or throw an exception based on their requirements

◆ doDataNormalization_()

TransformationDescription doDataNormalization_	(	const OpenSwath::LightTargetedExperiment &	targeted_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 and IM calibration (see SwathMapMassCorrection)
Store transformation, using the selected model

Parameters

[in]	targeted_exp	The transitions for the normalization peptides
[out]	chromatograms	The extracted chromatograms
[out]	im_trafo	Ion mobility trafo values on the RT-normalization peptides
[in]	swath_maps	The raw data (swath maps)
[in]	min_rsq	Minimal R^2 value that is expected for the RT regression
[in]	min_coverage	Minimal coverage of the chromatographic space that needs to be achieved
[in]	default_ffparam	Parameter set for the feature finding in chromatographic dimension
[in]	irt_detection_param	Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
[in]	calibration_param	Parameter for the m/z and im calibration (see SwathMapMassCorrection)
[in]	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

◆ getEstimatedImWindow()

double getEstimatedImWindow ( ) const

inline

Get estimated MS2 ion mobility extraction window.

Returns the MS2 ion mobility extraction window (full width) estimated during calibration. This value is only valid after performCalibration() has been called on PASEF/ion mobility data with window estimation enabled.

Returns: Estimated MS2 IM window, or -1.0 if not applicable/computed

◆ getEstimatedMs1ImWindow()

double getEstimatedMs1ImWindow ( ) const

inline

Get estimated MS1 ion mobility extraction window.

Returns the MS1 ion mobility extraction window (full width) estimated during calibration. This value is only valid after performCalibration() has been called on PASEF/ion mobility data with MS1 IM window estimation enabled.

Returns: Estimated MS1 IM window, or -1.0 if not applicable/computed

◆ getEstimatedMs1MzWindow()

double getEstimatedMs1MzWindow ( ) const

inline

Get estimated MS1 m/z extraction window.

Returns the MS1 m/z extraction window (full width, in ppm) estimated during calibration. This value is only valid after performCalibration() has been called and MS1 window estimation was enabled.

Returns: Estimated MS1 m/z window in ppm, or -1.0 if not computed

◆ getEstimatedMzWindow()

double getEstimatedMzWindow ( ) const

inline

Get estimated MS2 m/z extraction window.

Returns the MS2 m/z extraction window (full width, in ppm) estimated during calibration. This value is only valid after performCalibration() has been called and window estimation was enabled.

Returns: Estimated MS2 m/z window in ppm, or -1.0 if not computed

◆ isValidWindow_()

bool isValidWindow_	(	double	v,
		double	min_positive = `1e-9`
	)		const

inlineprivatenoexcept

Check if an estimated extraction window value is valid.

A window is considered valid if it is finite and strictly greater than a small positive threshold. This guards against denormals (e.g., ~1e-310), zeros, negative values, and NaNs/Inf.

Parameters

[in]	v	Window value to check
[in]	min_positive	Minimum positive threshold

Returns: True if window is valid for use

◆ loadIrtExperimentFromFile_()

OpenSwath::LightTargetedExperiment loadIrtExperimentFromFile_	(	const String &	irt_file_path,
		const String &	label
	)		const

Load iRT transition experiment from file.

Helper method to load iRT experiments from configured file paths. Supports TraML, TSV, and PQP formats.

Parameters

[in]	irt_file_path	Path to iRT file (empty = skip loading)
[in]	label	Label for logging (e.g., "linear", "nonlinear")

Returns: Loaded iRT experiment (empty if file path was empty)

Exceptions

Exception::FileNotFound	if file doesn't exist
Exception::ParseError	if file format is invalid

◆ performCalibration()

CalibrationResult performCalibration	(	std::vector< OpenSwath::SwathMap > &	swath_maps,
		OpenSwath::LightTargetedExperiment &	transition_exp,
		ChromExtractParams &	cp,
		ChromExtractParams &	cp_ms1,
		const IrtExperiments &	irt_experiments,
		const Param &	feature_finder_param,
		const ChromExtractParams &	cp_irt,
		const Param &	irt_detection_param,
		const Param &	calibration_param,
		const Param &	mrm_mapping_param,
		bool	pasef = `false`,
		bool	load_into_memory = `false`,
		const String &	irt_trafo_out = `""`,
		const String &	irt_mzml_out = `""`,
		Size	debug_level = `0`
	)

Perform calibration workflow with pre-prepared iRT experiments.

This is the main calibration entry point that accepts pre-prepared iRT experiments and performs RT, m/z, and ion mobility calibration. It automatically chooses between linear-only or linear+nonlinear calibration based on whether nonlinear iRT experiments are provided.

Parameters

[in,out]	swath_maps	Raw SWATH/SRM data maps (modified in-place by calibration)
[in,out]	transition_exp	Target transition experiment (IM values may be corrected)
[in,out]	cp	Extraction parameters (windows may be updated with estimates)
[in,out]	cp_ms1	MS1 extraction parameters (windows may be updated)
[in]	irt_experiments	Pre-prepared iRT experiments for calibration
[in]	feature_finder_param	Parameters for MRMFeatureFinderScoring
[in]	cp_irt	Extraction parameters for iRT peptides
[in]	irt_detection_param	Parameters for iRT detection and outlier removal
[in]	calibration_param	Parameters for m/z and IM calibration
[in]	mrm_mapping_param	Parameters for MRM chromatogram mapping
[in]	pasef	Whether data is PASEF (ion mobility) data
[in]	load_into_memory	Whether to load data into memory for processing
[in]	irt_trafo_out	Output file for RT transformation (empty = no output)
[in]	irt_mzml_out	Output file for iRT chromatograms (empty = no output)
[in]	debug_level	Debug level (0 = no debug output, >1 = verbose)

Returns: Calibration results including transformations and estimated windows

Exceptions

Exception::IllegalArgument	If configuration is invalid
Exception::MissingInformation	If iRT experiments are not ready

◆ performLinearCalibration_()

CalibrationResult performLinearCalibration_	(	std::vector< OpenSwath::SwathMap > &	swath_maps,
		const IrtExperiments &	irt_experiments,
		const Param &	feature_finder_param,
		const ChromExtractParams &	cp_irt,
		const Param &	irt_detection_param,
		const Param &	calibration_param,
		const Param &	mrm_mapping_param,
		bool	pasef,
		bool	load_into_memory,
		const String &	irt_trafo_out,
		const String &	irt_mzml_out,
		Size	debug_level
	)

private

Perform linear-only calibration workflow.

Parameters

[in,out]	swath_maps	SWATH data maps
[in]	irt_experiments	Prepared iRT experiments
[in]	feature_finder_param	Parameters for MRMFeatureFinderScoring
[in]	cp_irt	Extraction parameters for iRT peptides
[in]	irt_detection_param	Parameters for iRT detection
[in]	calibration_param	Parameters for calibration
[in]	mrm_mapping_param	Parameters for MRM mapping
[in]	pasef	Whether this is PASEF data
[in]	load_into_memory	Whether to load data into memory
[in]	irt_trafo_out	Output transformation file
[in]	irt_mzml_out	Output iRT chromatograms file
[in]	debug_level	Debug level (0 = no debug output, >1 = verbose)

Returns: Linear calibration results

◆ performLinearThenNonlinearCalibration_()

CalibrationResult performLinearThenNonlinearCalibration_	(	std::vector< OpenSwath::SwathMap > &	swath_maps,
		const IrtExperiments &	irt_experiments,
		const Param &	feature_finder_param,
		const ChromExtractParams &	cp_irt,
		const Param &	irt_detection_param,
		const Param &	calibration_param,
		const Param &	mrm_mapping_param,
		bool	pasef,
		bool	load_into_memory,
		const String &	irt_trafo_out,
		const String &	irt_mzml_out,
		Size	debug_level
	)

private

Perform linear + nonlinear calibration workflow.

First performs a linear calibration, then applies nonlinear refinement using a separate set of iRT transitions.

Parameters

[in,out]	swath_maps	SWATH data maps
[in]	irt_experiments	Prepared iRT experiments
[in]	feature_finder_param	Parameters for MRMFeatureFinderScoring
[in]	cp_irt	Extraction parameters for iRT peptides
[in]	irt_detection_param	Parameters for iRT detection
[in]	calibration_param	Parameters for calibration
[in]	mrm_mapping_param	Parameters for MRM mapping
[in]	pasef	Whether this is PASEF data
[in]	load_into_memory	Whether to load data into memory
[in]	irt_trafo_out	Output transformation file
[in]	irt_mzml_out	Output iRT chromatograms file
[in]	debug_level	Debug level (0 = no debug output, >1 = verbose)

Returns: Combined calibration results

◆ 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 Param &	mrm_mapping_param,
		const String &	irt_mzml_out,
		Size	debug_level,
		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

[in]	irt_transitions	A set of transitions used for the RT normalization peptides
[in]	swath_maps	The raw data (swath maps)
[out]	im_trafo	Ion mobility trafo values on the RT-normalization peptides
[in]	min_rsq	Minimal R^2 value that is expected for the RT regression
[in]	min_coverage	Minimal coverage of the chromatographic space that needs to be achieved
[in]	feature_finder_param	Parameter set for the feature finding in chromatographic dimension
[in]	cp_irt	Parameter set for the chromatogram extraction
[in]	irt_detection_param	Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
[in]	calibration_param	Parameter for the m/z and im calibration (see SwathMapMassCorrection)
[in]	mrm_mapping_param	Parameter for mapping chromatograms to transitions (MRMMapping)
[in]	debug_level	Debug level (writes out the RT normalization chromatograms if larger than 1)
[out]	irt_mzml_out	Output Chromatogram mzML containing the iRT peptides (if not empty, iRT chromatograms will be stored in this file)
[in]	pasef	whether the data is PASEF data (should match transitions by their IM)
[in]	load_into_memory	Whether to cache the current SWATH map in memory

◆ prepareIrtExperiments()

IrtExperiments prepareIrtExperiments	(	IrtStrategy	strategy,
		const OpenSwath::LightTargetedExperiment &	full_transition_exp,
		const std::vector< String > &	priority_peptides,
		size_t	run_index = `0`,
		const IrtExperiments *	cached_irts = `nullptr`
	)

Prepare iRT experiments based on the determined strategy.

This function handles all aspects of iRT experiment preparation:

Loading static iRT files
Auto-sampling from transition libraries with priority peptides
Validation and quality checks
Multi-run consistency management

The prepared experiments are ready for use with performCalibration().

Parameters

[in]	strategy	The IRT strategy to use
[in]	full_transition_exp	Full transition experiment for auto-sampling (required for sampling strategies)
[in]	priority_peptides	Priority peptide sequences for sampling (empty = no priorities)
[in]	run_index	Current run index (0-based, for run-specific strategies)
[in]	cached_irts	Previously prepared iRT experiments (for reusing sampled iRTs across runs)

Returns: Prepared iRT experiments ready for calibration

Exceptions

Exception::MissingInformation	if required data is not available
Exception::InvalidParameter	if configuration is invalid

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Update member variables from parameters.

This method is called automatically when parameters change. Updates internal member variables from current parameter values.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ auto_irt_enabled_

bool auto_irt_enabled_

private

◆ auto_irt_irt_bins_

int auto_irt_irt_bins_

private

◆ auto_irt_irt_bins_nonlinear_

int auto_irt_irt_bins_nonlinear_

private

◆ auto_irt_irt_peptides_per_bin_

int auto_irt_irt_peptides_per_bin_

private

◆ auto_irt_irt_peptides_per_bin_nonlinear_

int auto_irt_irt_peptides_per_bin_nonlinear_

private

◆ auto_irt_irt_seed_

int auto_irt_irt_seed_

private

◆ auto_irt_linear_top_fraction_

double auto_irt_linear_top_fraction_

private

◆ auto_irt_nonlinear_top_fraction_

double auto_irt_nonlinear_top_fraction_

private

◆ estimated_im_window_

double estimated_im_window_ {-1.0}

private

◆ estimated_ms1_im_window_

double estimated_ms1_im_window_ {-1.0}

private

◆ estimated_ms1_mz_window_

double estimated_ms1_mz_window_ {-1.0}

private

◆ estimated_mz_window_

double estimated_mz_window_ {-1.0}

private

◆ linear_irt_file_

String linear_irt_file_

private

◆ linear_irt_files_list_

std::vector<String> linear_irt_files_list_

private

◆ linear_outlier_detection_

String linear_outlier_detection_

private

◆ min_coverage_

double min_coverage_

private

◆ min_rsq_

double min_rsq_

private

◆ nonlinear_irt_file_

String nonlinear_irt_file_

private

◆ nonlinear_irt_files_list_

std::vector<String> nonlinear_irt_files_list_

private

◆ nonlinear_outlier_detection_

String nonlinear_outlier_detection_

private

◆ rt_estimation_padding_factor_

double rt_estimation_padding_factor_

private

◆ windows_estimate_im_

bool windows_estimate_im_

private

◆ windows_estimate_mz_

bool windows_estimate_mz_

private

◆ windows_estimate_rt_

bool windows_estimate_rt_

private

◆ windows_rt_percentile_

double windows_rt_percentile_

private

Classes

Public Member Functions

Private Member Functions

Private Attributes

Parameter handling

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::CalibrationWorkflow::CalibrationResult

◆ OpenMS::CalibrationWorkflow::IrtExperiments

Constructor & Destructor Documentation

◆ CalibrationWorkflow()

◆ ~CalibrationWorkflow()

Member Function Documentation

◆ applyEstimatedWindows_()

◆ applyWindow_()

◆ determineIrtStrategy()

◆ doDataNormalization_()

◆ getEstimatedImWindow()

◆ getEstimatedMs1ImWindow()

◆ getEstimatedMs1MzWindow()

◆ getEstimatedMzWindow()

◆ isValidWindow_()

◆ loadIrtExperimentFromFile_()

◆ performCalibration()

◆ performLinearCalibration_()

◆ performLinearThenNonlinearCalibration_()

◆ performRTNormalization()

◆ prepareIrtExperiments()

◆ updateMembers_()

Member Data Documentation

◆ auto_irt_enabled_

◆ auto_irt_irt_bins_

◆ auto_irt_irt_bins_nonlinear_

◆ auto_irt_irt_peptides_per_bin_

◆ auto_irt_irt_peptides_per_bin_nonlinear_

◆ auto_irt_irt_seed_

◆ auto_irt_linear_top_fraction_

◆ auto_irt_nonlinear_top_fraction_

◆ estimated_im_window_

◆ estimated_ms1_im_window_

◆ estimated_ms1_mz_window_

◆ estimated_mz_window_

◆ linear_irt_file_

◆ linear_irt_files_list_

◆ linear_outlier_detection_

◆ min_coverage_

◆ min_rsq_

◆ nonlinear_irt_file_

◆ nonlinear_irt_files_list_

◆ nonlinear_outlier_detection_

◆ rt_estimation_padding_factor_

◆ windows_estimate_im_

◆ windows_estimate_mz_

◆ windows_estimate_rt_

◆ windows_rt_percentile_