Data processing for FIA-MS data. More...

#include <OpenMS/ANALYSIS/ID/FIAMSDataProcessor.h>

Inheritance diagram for FIAMSDataProcessor:

Collaboration diagram for FIAMSDataProcessor:

Public Member Functions
	FIAMSDataProcessor ()
	Constructor. More...

	~FIAMSDataProcessor () override=default
	Default destructor. More...

	FIAMSDataProcessor (const FIAMSDataProcessor &cp)=default
	Copy constructor. More...

FIAMSDataProcessor &	operator= (const FIAMSDataProcessor &fdp)=default
	Assignment. More...

bool	run (const MSExperiment &experiment, const float n_seconds, OpenMS::MzTab &output, const bool load_cached_spectrum=true)
	Run the full analysis for the experiment for the given time interval. More...

void	cutForTime (const MSExperiment &experiment, const float n_seconds, std::vector< MSSpectrum > &output)
	Cut the time axis of the experiment from 0 to @n_seconds. More...

MSSpectrum	mergeAlongTime (const std::vector< OpenMS::MSSpectrum > &input)
	Sum the spectra with different retention times into one. More...

MSSpectrum	extractPeaks (const MSSpectrum &input)
	Pick peaks from the summed spectrum. More...

FeatureMap	convertToFeatureMap (const MSSpectrum &input)
	Convert a spectrum to a feature map with the corresponding polarity. More...

MSSpectrum	trackNoise (const MSSpectrum &input)
	Estimate noise for each peak. More...

void	runAccurateMassSearch (FeatureMap &input, OpenMS::MzTab &output)
	Perform accurate mass search. More...

const std::vector< float > &	getMZs ()
	Get mass-to-charge ratios to base the summing the spectra along the time axis upon. More...

const std::vector< float > &	getBinSizes ()
	Get the sliding bin sizes for summing the spectra along the time axis. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

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

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Member Functions
void	storeSpectrum_ (const MSSpectrum &input, String filename)
	Store the spectrum to the given filepath. More...

Private Attributes
std::vector< float >	mzs_

std::vector< float >	bin_sizes_

SavitzkyGolayFilter	sgfilter_

PeakPickerHiRes	picker_

Additional Inherited Members
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. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

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

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Data processing for FIA-MS data.

Flow injection analysis (FIA) omits the separation step by removal of the column. It allows for much faster processing time with the cost of ambiguities in the data interpretation. The compounds are identified through the accurate mass search.

Flow injection analysis class implements the basic FIA-MS data processing steps such as: acquiring the data for the certain time interval, summing along the time axis, smoothing the peaks, peak picking and accurate mass search. The batch runs are to be managed with the FIAMSSchedule class that takes a simple csv file as an input.

The workflow is inspired by the data processing from Fuhrer et al https://pubs.acs.org/doi/10.1021/ac201267k though it is not the exact implementation.

Constructor & Destructor Documentation

◆ FIAMSDataProcessor() [1/2]

FIAMSDataProcessor ( )

Constructor.

◆ ~FIAMSDataProcessor()

~FIAMSDataProcessor ( )

overridedefault

Default destructor.

◆ FIAMSDataProcessor() [2/2]

FIAMSDataProcessor ( const FIAMSDataProcessor & cp )

default

Copy constructor.

Member Function Documentation

◆ convertToFeatureMap()

FeatureMap convertToFeatureMap ( const MSSpectrum & input )

Convert a spectrum to a feature map with the corresponding polarity.

Applies `SavitzkyGolayFilter` and `PeakPickerHiRes`

Parameters

input Input a picked spectrum

Returns: a feature map with the peaks converted to features and polarity from the parameters

◆ cutForTime()

void cutForTime	(	const MSExperiment &	experiment,
		const float	n_seconds,
		std::vector< MSSpectrum > &	output
	)

Cut the time axis of the experiment from 0 to @n_seconds.

Parameters

experiment	Input MSExperiment
n_seconds	Input number of seconds
output	[out] Spectra with retention time less than @n_seconds

◆ extractPeaks()

MSSpectrum extractPeaks ( const MSSpectrum & input )

Pick peaks from the summed spectrum.

Parameters

input Input vector of spectra

Returns: a spectrum with picked peaks

◆ getBinSizes()

const std::vector<float>& getBinSizes ( )

Get the sliding bin sizes for summing the spectra along the time axis.

◆ getMZs()

const std::vector<float>& getMZs ( )

Get mass-to-charge ratios to base the summing the spectra along the time axis upon.

◆ mergeAlongTime()

MSSpectrum mergeAlongTime ( const std::vector< OpenMS::MSSpectrum > & input )

Sum the spectra with different retention times into one.

The bin size for summing the intensities is defined as mz / (resolution*4) for all the mzs taken with the @bin_step defined in the parameters. Uses `SpectrumAddition::addUpSpectra` function with the sliding bin size parameter.

Parameters

input Input vector of spectra

Returns: a spectrum

◆ operator=()

FIAMSDataProcessor& operator= ( const FIAMSDataProcessor & fdp )

default

Assignment.

◆ run()

bool run	(	const MSExperiment &	experiment,
		const float	n_seconds,
		OpenMS::MzTab &	output,
		const bool	load_cached_spectrum = `true`
	)

Run the full analysis for the experiment for the given time interval.

The workflow steps are:

the time axis of the experiment is cut to the interval from 0 to n_seconds
the spectra are summed into one along the time axis with the bin size determined by mz and instrument resolution
data is smoothed by applying the Savitzky-Golay filter
peaks are picked
the accurate mass search for all the picked peaks is performed

The intermediate summed spectra and picked peaks can be saved to the filesystem. Also, the results of the accurate mass search and the signal-to-noise information of the resulting spectrum is saved.

Parameters

experiment	Input MSExperiment
n_seconds	Input number of seconds
load_cached_spectrum	Load the cached picked spectrum if exists
output	[out] Output of the accurate mass search results

Returns: a boolean indicating if the picked spectrum was loaded from the cached file

◆ runAccurateMassSearch()

void runAccurateMassSearch	(	FeatureMap &	input,
		OpenMS::MzTab &	output
	)

Perform accurate mass search.

Uses `AccurateMassSearchEngine`

Parameters

input	Input a feature map
output	[out] mzTab file with the accurate mass search results

◆ storeSpectrum_()

void storeSpectrum_	(	const MSSpectrum &	input,
		String	filename
	)

private

Store the spectrum to the given filepath.

◆ trackNoise()

MSSpectrum trackNoise ( const MSSpectrum & input )

Estimate noise for each peak.

Uses `SignalToNoiseEstimatorMedianRapid`

Parameters

input Input a picked spectrum

Returns: a spectrum object storing logSN information

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ bin_sizes_

std::vector<float> bin_sizes_

private

◆ mzs_

std::vector<float> mzs_

private

◆ picker_

PeakPickerHiRes picker_

private

◆ sgfilter_

SavitzkyGolayFilter sgfilter_

private

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FIAMSDataProcessor() [1/2]

◆ ~FIAMSDataProcessor()

◆ FIAMSDataProcessor() [2/2]

Member Function Documentation

◆ convertToFeatureMap()

◆ cutForTime()

◆ extractPeaks()

◆ getBinSizes()

◆ getMZs()

◆ mergeAlongTime()

◆ operator=()

◆ run()

◆ runAccurateMassSearch()

◆ storeSpectrum_()

◆ trackNoise()

◆ updateMembers_()

Member Data Documentation

◆ bin_sizes_

◆ mzs_

◆ picker_

◆ sgfilter_