OpenSwathHelper Class Reference

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 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	checkSwathMap (const OpenMS::PeakMap &swath_map, double &lower, double &upper)
	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)
	Estimate the retention time span of a targeted experiment (returns min/max values as a pair) More...
static std::map< std::string, double >	simpleFindBestFeature (const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map, bool useQualCutoff=false, double qualCutoff=0.0)
	Simple method to extract the best Feature for each transition group (e.g. for RT alignment) 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  )

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
[in]	lower	Lower edge of SWATH window (in Th)
[in]	upper	Upper edge of SWATH window (in Th)

Exceptions

throws

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.

Performs sanity check for input experiment and selects appropriate transitions for the provided SWATH MS2 map.

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(), DocumentIdentifier::getLoadedFilePath(), OpenSwathHelper::selectSwathTransitions(), and MSExperiment::size().

computePrecursorId()

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

inlinestatic

Compute unique precursor identifier.

estimateRTRange()

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

static

Estimate the retention time span of a targeted experiment (returns min/max values as a pair)

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)

simpleFindBestFeature()

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

static

Simple method to extract the best Feature for each transition group (e.g. for RT alignment)

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)