A helper class that is used by several OpenSWATH tools. More...

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

Static Public Member Functions
static String	computePrecursorId (const String &transition_group_id, int isotope)
	Compute unique precursor identifier. More...

static String	computeTransitionGroupId (const String &precursor_id)
	Compute transition group id. More...

static void	selectSwathTransitions (const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper)
	Select transitions between lower and upper and write them into the new TargetedExperiment. More...

static void	selectSwathTransitions (const OpenSwath::LightTargetedExperiment &targeted_exp, OpenSwath::LightTargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper)
	Select transitions between lower and upper and write them into the new TargetedExperiment. More...

static void	selectSwathTransitionsPasef (const OpenSwath::LightTargetedExperiment &transition_exp, std::vector< int > &tr_win_map, double min_upper_edge_dist, const std::vector< OpenSwath::SwathMap > &swath_maps)
	Match transitions with their "best" window across m/z and ion mobility, save results in a vector. More...

static void	checkSwathMap (const OpenMS::PeakMap &swath_map, double &lower, double &upper, double &center)
	Get the lower / upper offset for this SWATH map and do some sanity checks. More...

template<class TargetedExperimentT >
static bool	checkSwathMapAndSelectTransitions (const OpenMS::PeakMap &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &selected_transitions, double min_upper_edge_dist)
	Check the map and select transition in one function. More...

static std::pair< double, double >	estimateRTRange (const OpenSwath::LightTargetedExperiment &exp)
	Computes the min and max retention time value. More...

static OpenSwath::LightTargetedExperiment	sampleExperiment (const OpenSwath::LightTargetedExperiment &exp, Size bins, Size peptides_per_bin, unsigned int seed=0, bool sort_by_intensity=false, double top_fraction=1.0, const std::unordered_set< std::string > &priority_peptides=std::unordered_set< std::string >())
	Sample a subset of peptides uniformly across the RT range. More...

static std::map< std::string, double >	simpleFindBestFeature (const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map, bool useQualCutoff=false, double qualCutoff=0.0)
	Returns the feature with the highest score for each transition group. More...

Detailed Description

A helper class that is used by several OpenSWATH tools.

Member Function Documentation

◆ checkSwathMap()

static void checkSwathMap	(	const OpenMS::PeakMap &	swath_map,
		double &	lower,
		double &	upper,
		double &	center
	)

static

Get the lower / upper offset for this SWATH map and do some sanity checks.

Sanity check for the whole map:

all scans need to have exactly one precursor
all scans need to have the same MS levels (otherwise extracting an XIC from them makes no sense)
all scans need to have the same precursor isolation window (otherwise extracting an XIC from them makes no sense)

Parameters

[in]	swath_map	Input SWATH map to check
[out]	lower	Lower edge of SWATH window (in Th)
[out]	upper	Upper edge of SWATH window (in Th)
[out]	center	Center of SWATH window (in Th)

Exceptions

IllegalArgument exception if the sanity checks fail.

Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions().

◆ checkSwathMapAndSelectTransitions()

static bool checkSwathMapAndSelectTransitions	(	const OpenMS::PeakMap &	exp,
		const TargetedExperimentT &	targeted_exp,
		TargetedExperimentT &	selected_transitions,
		double	min_upper_edge_dist
	)

inlinestatic

Check the map and select transition in one function.

Computes lower and upper offset for the SWATH map and performs some sanity checks (see checkSwathMap()). Then selects transitions.

Parameters

[in]	exp	Input SWATH map to check
[in]	targeted_exp	Transition list for selection
[out]	selected_transitions	Selected transitions for SWATH window
[in]	min_upper_edge_dist	Distance in Th to the upper edge

References OpenSwathHelper::checkSwathMap(), MSExperiment::empty(), DocumentIdentifier::getLoadedFilePath(), and OpenSwathHelper::selectSwathTransitions().

◆ computePrecursorId()

static String computePrecursorId	(	const String &	transition_group_id,
		int	isotope
	)

inlinestatic

Compute unique precursor identifier.

Uses transition_group_id and isotope number to compute a unique precursor id of the form "groupID_Precursor_ix" where x is the isotope number, e.g. the monoisotopic precursor would become "groupID_Precursor_i0".

Parameters

[in]	transition_group_id	Unique id of the transition group (peptide/compound)
[in]	isotope	Precursor isotope number

Returns: Unique precursor identifier

◆ computeTransitionGroupId()

static String computeTransitionGroupId ( const String & precursor_id )

inlinestatic

Compute transition group id.

Uses the unique precursor identifier to compute the transition group id (peptide/compound identifier), reversing the operation performed by computePrecursorId().

Parameters

[in] precursor_id Precursor identifier as computed by computePrecursorId()

Returns: Original transition group id

References OpenMS::Constants::k, String::prefix(), and String::split().

Referenced by ChromatogramExtractor::return_chromatogram().

◆ estimateRTRange()

static std::pair<double,double> estimateRTRange ( const OpenSwath::LightTargetedExperiment & exp )

static

Computes the min and max retention time value.

Estimate the retention time span of a targeted experiment by returning the min/max values in retention time as a pair.

Returns: A std::pair that contains (min,max)

◆ sampleExperiment()

static OpenSwath::LightTargetedExperiment sampleExperiment	(	const OpenSwath::LightTargetedExperiment &	exp,
		Size	bins,
		Size	peptides_per_bin,
		unsigned int	seed = `0`,
		bool	sort_by_intensity = `false`,
		double	top_fraction = `1.0`,
		const std::unordered_set< std::string > &	priority_peptides = `std::unordered_set< std::string >()`
	)

static

Sample a subset of peptides uniformly across the RT range.

Splits the RT span (min→max) into bins and randomly picks up to peptides_per_bin compounds from each bin. Useful for on-the-fly iRT calibration without external .irt files.

Parameters

[in]	exp	Full LightTargetedExperiment (the input peptide query parameter assay list for targeted extraction)
[in]	bins	Number of retention‐time bins (i.e. 10 bins across the RT range for linear iRT, 500-1000 bins across the RT for nonlinear iRT)
[in]	peptides_per_bin	How many peptides to draw per bin (i.e. 5 peptides for linear iRT, 25 - 50 for non-linear iRT)
[in]	seed	If non‐zero, used to seed the RNG (deterministic). If zero, will use std::random_device for non-deterministic.
[in]	sort_by_intensity	Whether to sort the assays by the highest cumulative intense transitions. This is useful for sampling the most intense peptides for iRTs.
[in]	top_fraction	Only sample from the top N fraction of sorted assays to narrow down on only really intense peptides. This is useful for selecting a few "high quality" peptides to use for linear iRTs.
[in]	priority_peptides	Optional set of peptide sequences to prioritize during sampling. If provided, these peptides will be sampled first if found in `exp`, before the remaining quota is filled with regular sampling. Useful for ensuring common iRT peptides (e.g., from irtkit or cirtkit) are included when present.

Returns: A new LightTargetedExperiment containing only the sampled compounds, their transitions, and associated proteins.

◆ selectSwathTransitions() [1/2]

static void selectSwathTransitions	(	const OpenMS::TargetedExperiment &	targeted_exp,
		OpenMS::TargetedExperiment &	selected_transitions,
		double	min_upper_edge_dist,
		double	lower,
		double	upper
	)

static

Select transitions between lower and upper and write them into the new TargetedExperiment.

Version for the OpenMS TargetedExperiment

Parameters

[in]	targeted_exp	Transition list for selection
[out]	selected_transitions	Selected transitions for SWATH window
[in]	min_upper_edge_dist	Distance in Th to the upper edge
[in]	lower	Lower edge of SWATH window (in Th)
[in]	upper	Upper edge of SWATH window (in Th)

Referenced by OpenSwathHelper::checkSwathMapAndSelectTransitions().

◆ selectSwathTransitions() [2/2]

static void selectSwathTransitions	(	const OpenSwath::LightTargetedExperiment &	targeted_exp,
		OpenSwath::LightTargetedExperiment &	selected_transitions,
		double	min_upper_edge_dist,
		double	lower,
		double	upper
	)

static

Select transitions between lower and upper and write them into the new TargetedExperiment.

Version for the LightTargetedExperiment

Parameters

[in]	targeted_exp	Transition list for selection
[out]	selected_transitions	Selected transitions for SWATH window
[in]	min_upper_edge_dist	Distance in Th to the upper edge
[in]	lower	Lower edge of SWATH window (in Th)
[in]	upper	Upper edge of SWATH window (in Th)

◆ selectSwathTransitionsPasef()

static void selectSwathTransitionsPasef	(	const OpenSwath::LightTargetedExperiment &	transition_exp,
		std::vector< int > &	tr_win_map,
		double	min_upper_edge_dist,
		const std::vector< OpenSwath::SwathMap > &	swath_maps
	)

static

Match transitions with their "best" window across m/z and ion mobility, save results in a vector.

Parameters

[in]	transition_exp	Transition list for selection
[out]	tr_win_map	Mapping from transition (index) to the best matching entry in `swath_maps`
[in]	min_upper_edge_dist	Distance in Th to the upper edge
[in]	swath_maps	vector of SwathMap objects defining mz and im bounds

◆ simpleFindBestFeature()

static std::map<std::string, double> simpleFindBestFeature	(	const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &	transition_group_map,
		bool	useQualCutoff = `false`,
		double	qualCutoff = `0.0`
	)

static

Returns the feature with the highest score for each transition group.

Simple method to extract the best feature for each transition group (e.g. for RT alignment). A quality cutoff can be used to skip some low-quality features altogether.

Parameters

[in]	transition_group_map	Input data containing the picked and scored map
	useQualCutoff	Whether to apply a quality cutoff to the data
	qualCutoff	What quality cutoff should be applied (all data above the cutoff will be kept)

Returns: Result of the best scoring peaks (stored as map of peptide id and RT)

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ checkSwathMap()

◆ checkSwathMapAndSelectTransitions()

◆ computePrecursorId()

◆ computeTransitionGroupId()

◆ estimateRTRange()

◆ sampleExperiment()

◆ selectSwathTransitions() [1/2]

◆ selectSwathTransitions() [2/2]

◆ selectSwathTransitionsPasef()

◆ simpleFindBestFeature()