ChromatogramExtractor Class Reference

The ChromatogramExtractor extracts chromatograms (intensity vs retention time) from mass spectrometry data. More...

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

Inheritance diagram for ChromatogramExtractor:

Collaboration diagram for ChromatogramExtractor:

Public Types
typedef ChromatogramExtractorAlgorithm::ExtractionCoordinates	ExtractionCoordinates
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
void	extractChromatograms (const OpenSwath::SpectrumAccessPtr input, std::vector< OpenSwath::ChromatogramPtr > &output, const std::vector< ExtractionCoordinates > &extraction_coordinates, double mz_extraction_window, bool ppm, const std::string &filter)
	Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.
void	extractChromatograms (const OpenSwath::SpectrumAccessPtr input, std::vector< OpenSwath::ChromatogramPtr > &output, const std::vector< ExtractionCoordinates > &extraction_coordinates, double mz_extraction_window, bool ppm, double im_extraction_window, const std::string &filter)
	Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.
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 std::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)

Static Public Member Functions
static void	prepare_coordinates (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const double rt_extraction_window, const bool ms1=false, const int ms1_isotopes=0)
	Prepare the extraction coordinates from a LightTargetedExperiment.
template<typename TransitionExpT >
static void	return_chromatogram (const std::vector< OpenSwath::ChromatogramPtr > &chromatograms, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, TransitionExpT &transition_exp_used, SpectrumSettings settings, std::vector< OpenMS::MSChromatogram > &output_chromatograms, bool ms1, double im_extraction_width=0.0)
	This converts the ChromatogramPtr to MSChromatogram and adds meta-information.

Private Member Functions
template<class SpectrumSettingsT , class ChromatogramT >
void	prepareSpectra_ (SpectrumSettingsT &settings, std::vector< ChromatogramT > &chromatograms, OpenMS::TargetedExperiment &transition_exp)
	This populates the chromatograms vector with empty chromatograms (but sets their meta-information)
bool	outsideExtractionWindow_ (const ReactionMonitoringTransition &transition, double current_rt, const TransformationDescription &trafo, double rt_extraction_window)
int	getFilterNr_ (const std::string &filter)
void	populatePeptideRTMap_ (OpenMS::TargetedExperiment &transition_exp, double rt_extraction_window)

Static Private Member Functions
template<typename TransitionExpT >
static std::string	extract_id_ (TransitionExpT &transition_exp_used, const std::string &id, int &prec_charge)
	Extracts id (peptide sequence or compound name) for a compound.

Private Attributes
std::map< std::string, double >	PeptideRTMap_

Additional Inherited Members
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

The ChromatogramExtractor extracts chromatograms (intensity vs retention time) from mass spectrometry data.

This class provides functionality to extract chromatographic traces from mass spectrometry data based on specified coordinates (m/z, retention time, and optionally ion mobility values).

The primary interface uses a set of ExtractionCoordinates that specify the exact coordinates for extraction. The static prepare_coordinates() helper generates these coordinates from an OpenSwath::LightTargetedExperiment for common MS1 and MS2 extraction scenarios. Callers working with an OpenMS::TargetedExperiment should first convert it to a LightTargetedExperiment via OpenSwathDataAccessHelper::convertTargetedExp().

Key features:

• Supports both MS1 and MS2 level extractions
• Configurable extraction window sizes in m/z dimension (absolute or ppm)
• Multiple filter types available (Bartlett, tophat) for signal processing
• Handles ion mobility data when available
• Optimized for SWATH/DIA (Data Independent Acquisition) experiments
• Progress logging capabilities through ProgressLogger base class

For MS2 extractions, the input data is expected to come from a SWATH/DIA experiment where precursor ions are fragmented in wide isolation windows, allowing for extraction of fragment ion chromatograms.

See also

ChromatogramExtractorAlgorithm For the underlying extraction algorithm implementation

ExtractionCoordinates For the coordinate specification format

Member Typedef Documentation

ExtractionCoordinates

typedef ChromatogramExtractorAlgorithm::ExtractionCoordinates ExtractionCoordinates

Member Function Documentation

extract_id_()

template<typename TransitionExpT >

static std::string extract_id_ ( TransitionExpT &  transition_exp_used, const std::string &  id, int &  prec_charge  )

staticprivate

Extracts id (peptide sequence or compound name) for a compound.

Parameters

[in]	transition_exp_used	The transition experiment used as input (LightTargetedExperiment)
[in]	id	The identifier of the compound or peptide
[out]	prec_charge	The charge state of the precursor (filled by this function)

extractChromatograms() [1/2]

void extractChromatograms ( const OpenSwath::SpectrumAccessPtr  input, std::vector< OpenSwath::ChromatogramPtr > &  output, const std::vector< ExtractionCoordinates > &  extraction_coordinates, double  mz_extraction_window, bool  ppm, const std::string &  filter  )

inline

Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.

Parameters

[in]	input	The input spectra from which to extract chromatograms
[out]	output	The output vector in which to store the chromatograms (needs to be of the same length as the extraction coordinates, use prepare_coordinates)
[in]	extraction_coordinates	The extraction coordinates (m/z, RT, ion mobility)
[in]	mz_extraction_window	Extracts a window of this size in m/z dimension (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
[in]	ppm	Whether mz windows in ppm
[in]	filter	Which filter to use (bartlett or tophat)

References ChromatogramExtractorAlgorithm::extractChromatograms().

extractChromatograms() [2/2]

void extractChromatograms ( const OpenSwath::SpectrumAccessPtr  input, std::vector< OpenSwath::ChromatogramPtr > &  output, const std::vector< ExtractionCoordinates > &  extraction_coordinates, double  mz_extraction_window, bool  ppm, double  im_extraction_window, const std::string &  filter  )

inline

Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.

Parameters

[in]	input	The input spectra from which to extract chromatograms
[out]	output	The output vector in which to store the chromatograms (needs to be of the same length as the extraction coordinates, use prepare_coordinates)
[in]	extraction_coordinates	The extraction coordinates (m/z, RT, ion mobility)
[in]	mz_extraction_window	Extracts a window of this size in m/z dimension (e.g. a window of 50 ppm means an extraction of 25 ppm on either side)
[in]	ppm	Whether mz windows in ppm
[in]	im_extraction_window	Extracts a window of this size in ion mobility
[in]	filter	Which filter to use (bartlett or tophat)

Note

: whenever possible, please use this ChromatogramExtractorAlgorithm implementation

References ChromatogramExtractorAlgorithm::extractChromatograms().

getFilterNr_()

int getFilterNr_ ( const std::string &  filter )

private

Note

: TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

outsideExtractionWindow_()

bool outsideExtractionWindow_ ( const ReactionMonitoringTransition &  transition, double  current_rt, const TransformationDescription &  trafo, double  rt_extraction_window  )

private

Note

: TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

populatePeptideRTMap_()

void populatePeptideRTMap_ ( OpenMS::TargetedExperiment &  transition_exp, double  rt_extraction_window  )

private

Note

: TODO deprecate this function (use ChromatogramExtractorAlgorithm instead)

prepare_coordinates()

static void prepare_coordinates ( std::vector< OpenSwath::ChromatogramPtr > &  output_chromatograms, std::vector< ExtractionCoordinates > &  coordinates, const OpenSwath::LightTargetedExperiment &  transition_exp_used, const double  rt_extraction_window, const bool  ms1 = false, const int  ms1_isotopes = 0  )

static

Prepare the extraction coordinates from a LightTargetedExperiment.

Will fill the coordinates vector with the appropriate extraction coordinates (transitions for MS2 extraction, peptide m/z for MS1 extraction). The output will be sorted by m/z.

Parameters

[in]	output_chromatograms	An empty vector which will be initialized correctly
[out]	coordinates	An empty vector which will be filled with the appropriate extraction coordinates in m/z and rt and sorted by m/z (to be used as input to extractChromatograms)
[in]	transition_exp_used	The transition experiment used as input
[in]	rt_extraction_window	If non-negative, full RT extraction window, centered on the first RT value (rt_end - rt_start will equal this window size). If negative, rt_end will be set to -1 and rt_start to 0 (i.e. full RT range). If NaN, the compound's rt_start and rt_end fields are used directly (must be pre-populated, e.g. via OpenSwathDataAccessHelper::convertTargetedExp() from a compound whose rts vector contains exactly two entries).
[in]	ms1	Whether to extract for MS1 (peptide level) or MS2 (transition level)
[in]	ms1_isotopes	Number of isotopes to include in coordinates when in MS1 mode

Exceptions

Exception::IllegalArgument

if RT values are expected (depending on rt_extraction_window) but not provided

prepareSpectra_()

template<class SpectrumSettingsT , class ChromatogramT >

void prepareSpectra_ ( SpectrumSettingsT &  settings, std::vector< ChromatogramT > &  chromatograms, OpenMS::TargetedExperiment &  transition_exp  )

inlineprivate

This populates the chromatograms vector with empty chromatograms (but sets their meta-information)

It extracts 1) the target m/z 2) the isolation window (upper/lower) 3) the peptide sequence 4) the fragment m/z 5) Copy the meta-data, e.g. InstrumentSettings, AcquisitionInfo, sourceFile and DataProcessing 6) the native ID from the transition

References ReactionMonitoringTransition::getCompoundRef(), TargetedExperiment::getCompounds(), ReactionMonitoringTransition::getNativeID(), ReactionMonitoringTransition::getPeptideRef(), TargetedExperiment::getPeptides(), ReactionMonitoringTransition::getPrecursorMZ(), ReactionMonitoringTransition::getProductMZ(), TargetedExperiment::getTransitions(), PeptideCompound::id, Peptide::sequence, Precursor::setIsolationWindowLowerOffset(), Precursor::setIsolationWindowUpperOffset(), MetaInfoInterface::setMetaValue(), Peak1D::setMZ(), and Product::setMZ().

return_chromatogram()

template<typename TransitionExpT >

static void return_chromatogram ( const std::vector< OpenSwath::ChromatogramPtr > &  chromatograms, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &  coordinates, TransitionExpT &  transition_exp_used, SpectrumSettings  settings, std::vector< OpenMS::MSChromatogram > &  output_chromatograms, bool  ms1, double  im_extraction_width = 0.0  )

inlinestatic

This converts the ChromatogramPtr to MSChromatogram and adds meta-information.

It sets 1) the target m/z 2) the isolation window (upper/lower) 3) the peptide sequence 4) the fragment m/z 5) the meta-data, e.g. InstrumentSettings, AcquisitionInfo, sourceFile and DataProcessing 6) the native ID from the transition 7) ion mobility extraction target and window (lower/upper)

References SpectrumSettings::getAcquisitionInfo(), ChromatogramSettings::getDataProcessing(), SpectrumSettings::getDataProcessing(), SpectrumSettings::getInstrumentSettings(), SpectrumSettings::getPrecursors(), SpectrumSettings::getSourceFile(), ChromatogramExtractorAlgorithm::ExtractionCoordinates::id, ChromatogramExtractorAlgorithm::ExtractionCoordinates::ion_mobility, ChromatogramExtractorAlgorithm::ExtractionCoordinates::mz, ChromatogramSettings::setAcquisitionInfo(), Precursor::setCharge(), ChromatogramSettings::setChromatogramType(), Precursor::setDriftTime(), Precursor::setDriftTimeWindowLowerOffset(), Precursor::setDriftTimeWindowUpperOffset(), ChromatogramSettings::setInstrumentSettings(), Precursor::setIsolationWindowLowerOffset(), Precursor::setIsolationWindowUpperOffset(), MetaInfoInterface::setMetaValue(), Peak1D::setMZ(), Product::setMZ(), ChromatogramSettings::setNativeID(), ChromatogramSettings::setPrecursor(), ChromatogramSettings::setProduct(), and ChromatogramSettings::setSourceFile().

Member Data Documentation

PeptideRTMap_

std::map<std::string, double> PeptideRTMap_

private