Execute all steps in an OpenSwath analysis. More...

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

Inheritance diagram for OpenSwathWorkflow:

Collaboration diagram for OpenSwathWorkflow:

Public Member Functions
	OpenSwathWorkflow (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)
	Constructor. More...

void	performExtraction (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription &trafo, const ChromExtractParams &chromatogram_extraction_params, const ChromExtractParams &ms1_chromatogram_extraction_params, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &assay_library, FeatureMap &result_featureFile, bool store_features_in_featureFile, OpenSwathTSVWriter &result_tsv, OpenSwathOSWWriter &result_osw, Interfaces::IMSDataConsumer *result_chromatograms, int batchSize, int ms1_isotopes, bool load_into_memory)
	Execute OpenSWATH analysis on a set of SwathMaps and transitions. 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 () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Member Functions
void	writeOutFeaturesAndChroms_ (std::vector< OpenMS::MSChromatogram > &chromatograms, std::vector< MSChromatogram > &ms1_chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer)
	Write output features and chromatograms. More...

void	scoreAllChromatograms_ (const std::vector< OpenMS::MSChromatogram > &ms2_chromatograms, const std::vector< OpenMS::MSChromatogram > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, const TransformationDescription &trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, int nr_ms1_isotopes=0, bool ms1only=false) const
	Perform scoring on a set of chromatograms. More...

void	selectCompoundsForBatch_ (const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t batch_idx)
	Select which compounds to analyze in the next batch (and copy to output) More...

void	copyBatchTransitions_ (const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output)
	Helper function for selectCompoundsForBatch_() 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...

Private Types
typedef OpenSwath::LightTransition	TransitionType

typedef MRMTransitionGroup< MSChromatogram, TransitionType >	MRMTransitionGroupType

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

The workflow will perform a complete OpenSWATH analysis. Optionally, a calibration of m/z and retention time (mapping peptides to normalized space and correcting m/z error) can be performed beforehand using the OpenSwathCalibrationWorkflow class.

For diaPASEF workflows where ion mobility windows are overlapping, precursors may be found in multiple SWATHs. In this case, precursors are only extracted from the SWATH in which they are most centered across ion mobility (Provided -pasef flag is set).

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

Obtain precursor ion chromatograms (if enabled) through MS1Extraction_()
Perform scoring of precursor ion chromatograms if no MS2 is given
Iterate through each SWATH-MS window:
- Select which transitions to extract (proceed in batches) using OpenSwathHelper::selectSwathTransitions()
- Iterate through each batch of transitions:
  - Extract current batch of transitions from current SWATH window:
    - Select transitions for current batch (see selectCompoundsForBatch_())
    - Prepare transition extraction (see prepareExtractionCoordinates_())
    - Extract transitions using ChromatogramExtractor::extractChromatograms()
    - Convert data to OpenMS format using ChromatogramExtractor::return_chromatogram()
  - Score extracted transitions (see scoreAllChromatograms_())
  - Write scored chromatograms and peak groups to disk (see writeOutFeaturesAndChroms_())

Member Typedef Documentation

◆ MRMTransitionGroupType

typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType

private

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

◆ OpenSwathWorkflow()

OpenSwathWorkflow	(	bool	use_ms1_traces,
		bool	use_ms1_ion_mobility,
		bool	prm,
		bool	pasef,
		int	threads_outer_loop
	)

inline

Constructor.

Parameters

use_ms1_traces	Whether to use MS1 data
use_ms1_ion_mobility	Whether to use ion mobility extraction on MS1 traces
threads_outer_loop	How many threads should be used for the outer loop (-1 will use all threads in the outer loop)
prm	Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows

Note: The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).

Member Function Documentation

◆ copyBatchTransitions_()

void copyBatchTransitions_	(	const std::vector< OpenSwath::LightCompound > &	used_compounds,
		const std::vector< OpenSwath::LightTransition > &	all_transitions,
		std::vector< OpenSwath::LightTransition > &	output
	)

protected

Helper function for selectCompoundsForBatch_()

Copy all transitions matching to one of the compounds in the selected peptide vector from all_transitions to the output.

Parameters

used_compounds	Which peptides or metabolites to be used
all_transitions	Transitions vector from which to select transitions
output	Output vector containing matching transitions (taken from all_transitions)

◆ performExtraction()

void performExtraction	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const TransformationDescription &	trafo,
		const ChromExtractParams &	chromatogram_extraction_params,
		const ChromExtractParams &	ms1_chromatogram_extraction_params,
		const Param &	feature_finder_param,
		const OpenSwath::LightTargetedExperiment &	assay_library,
		FeatureMap &	result_featureFile,
		bool	store_features_in_featureFile,
		OpenSwathTSVWriter &	result_tsv,
		OpenSwathOSWWriter &	result_osw,
		Interfaces::IMSDataConsumer *	result_chromatograms,
		int	batchSize,
		int	ms1_isotopes,
		bool	load_into_memory
	)

Execute OpenSWATH analysis on a set of SwathMaps and transitions.

See OpenSwathWorkflow class for a detailed description of this function.

Parameters

swath_maps	The raw data (swath maps)
rt_trafo	Retention time transformation description (translating this runs' RT to normalized RT space)
chromatogram_extraction_params	Parameter set for the chromatogram extraction
ms1_chromatogram_extraction_params	Parameter set for the chromatogram extraction of the MS1 data
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
assay_library	The set of assays to be extracted and scored
result_featureFile	Output feature map to store identified features
store_features_in_featureFile	Whether features should be appended to the output feature map (if this is false, then out_featureFile will be empty)
result_tsv	TSV Writer object to store identified features in csv format (set store_features to false if using this option)
result_osw	OSW Writer object to store identified features in SQLite format (set store_features to false if using this option)
result_chromatograms	Chromatogram consumer object to store the extracted chromatograms
batchSize	Size of the batches which should be extracted and scored
int	ms1_isotopes Number of MS1 isotopes to extract (zero means only monoisotopic peak)
load_into_memory	Whether to cache the current SWATH map in memory

Note: Speed and memory performance can be influenced by batchSize and load_into_memory where larger batch sizes increase memory and potentially decrease the utility of parallelization while loading data into memory will increase memory usage but decrease execution time.

◆ scoreAllChromatograms_()

void scoreAllChromatograms_	(	const std::vector< OpenMS::MSChromatogram > &	ms2_chromatograms,
		const std::vector< OpenMS::MSChromatogram > &	ms1_chromatograms,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		const Param &	feature_finder_param,
		const TransformationDescription &	trafo,
		const double	rt_extraction_window,
		FeatureMap &	output,
		OpenSwathTSVWriter &	tsv_writer,
		OpenSwathOSWWriter &	osw_writer,
		int	nr_ms1_isotopes = `0`,
		bool	ms1only = `false`
	)		const

protected

Perform scoring on a set of chromatograms.

This will generate a new object of type MRMTransitionGroup for each compound or peptide in the provided assay library and link the transition meta information with the extracted chromatograms. This will then be used to perform peak picking and peak scoring through MRMTransitionGroupPicker and MRMFeatureFinderScoring. The assay library is provided as transition_exp and the chromatograms in ms2_chromatograms.

The overall execution flow is as follows:

Iterate over all assays (compounds / peptides) in the transition_exp
- Create a new MRMTransitionGroup
- Iterate over all transitions in an assay
  - Find the relevant chromatogram for the given transition, convert it and filter it by RT
  - Add the chromatogram and transition to the MRMTransitionGroup
- Add a single MS1 chromatogram of the mono-isotopic precursor to the MRMTransitionGroup, if available (named "groupId_Precursor_i0")
- Find peakgroups in the chromatogram set (see MRMTransitionGroupPicker::pickTransitionGroup)
- Score peakgroups in the chromatogram set (see MRMFeatureFinderScoring::scorePeakgroups)
- Add the identified peak groups to the TSV writer (tsv_writer) and the SQL-based output format (osw_writer)

Parameters

ms2_chromatograms	Input chromatograms (MS2 level)
ms1_chromatograms	Input chromatograms (MS1-level)
swath_maps	Set of swath map(s) for the current swath window (for SONAR multiple maps are provided)
transition_exp	The transition experiment (assay library)
feature_finder_param	Parameters for the MRMFeatureFinderScoring
trafo	RT Transformation function
rt_extraction_window	RT extraction window
output	Output map
tsv_writer	TSV writer for storing output (on the fly)
osw_writer	OSW Writer object to store identified features in SQLite format
ms1only	If true, will only score on MS1 level and ignore MS2 level

◆ selectCompoundsForBatch_()

void selectCompoundsForBatch_	(	const OpenSwath::LightTargetedExperiment &	transition_exp_used_all,
		OpenSwath::LightTargetedExperiment &	transition_exp_used,
		int	batch_size,
		size_t	batch_idx
	)

protected

Select which compounds to analyze in the next batch (and copy to output)

This function will select which compounds or peptides should be analyzed in the current batch (with index "batch_idx"). The selected compounds will be copied into the output structure. The output will contain "batch_size" compounds or peptides.

Parameters

transition_exp_used_all	The full set of transitions (this will be used to select transitions from)
transition_exp_used	The selected set of transitions (will contain only transitions for the next batch)
batch_size	How many compounds or peptides should be used per batch
batch_idx	Current batch index (only compounds or peptides from batch_idxbatch_size to batch_idxbatch_size+batch_size will be copied)

Note: The proteins will be copied completely without checking for a match

◆ writeOutFeaturesAndChroms_()

void writeOutFeaturesAndChroms_	(	std::vector< OpenMS::MSChromatogram > &	chromatograms,
		std::vector< MSChromatogram > &	ms1_chromatograms,
		const FeatureMap &	featureFile,
		FeatureMap &	out_featureFile,
		bool	store_features,
		Interfaces::IMSDataConsumer *	chromConsumer
	)

protected

Write output features and chromatograms.

Writes output chromatograms to the provided chromatogram consumer (presumably to disk) and output features to the provided FeatureMap.

Parameters

chromatograms	Output chromatograms to be passed to the consumer
featureFile	Features to be appended to the output FeatureMap
out_featureFile	Output FeatureMap to which the features will be appended
store_features	Whether features should be appended to the output feature map (if this is false, then out_featureFile will be empty)
chromConsumer	Chromatogram consumer object to store the extracted chromatograms

Note: This should be wrapped in an OpenMP critical block

Public Member Functions

Protected Member Functions

Private Types

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ MRMTransitionGroupType

◆ TransitionType

Constructor & Destructor Documentation

◆ OpenSwathWorkflow()

Member Function Documentation

◆ copyBatchTransitions_()

◆ performExtraction()

◆ scoreAllChromatograms_()

◆ selectCompoundsForBatch_()

◆ writeOutFeaturesAndChroms_()