#include <OpenMS/QC/FragmentMassError.h>

Inheritance diagram for FragmentMassError:

Collaboration diagram for FragmentMassError:

Classes
struct	Statistics
	Structure for storing results: average and variance of all FragmentMassErrors in ppm. More...

Public Member Functions
	FragmentMassError ()=default
	Default constructor. More...

virtual	~FragmentMassError ()=default
	Destructor. More...

void	compute (FeatureMap &fmap, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, ToleranceUnit tolerance_unit=ToleranceUnit::AUTO, double tolerance=20)
	computes FragmentMassError (FME) in ppm and Dalton (only of the first PeptideHit of each PepID) More...

void	compute (std::vector< PeptideIdentification > &pep_ids, const ProteinIdentification::SearchParameters &search_params, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, ToleranceUnit tolerance_unit=ToleranceUnit::AUTO, double tolerance=20)
	computes FragmentMassError (FME) in ppm and Dalton (only of the first PeptideHit of each PepID) More...

const String &	getName () const override
	returns the name of the metric More...

const std::vector< Statistics > &	getResults () const
	returns results More...

QCBase::Status	requirements () const override
	Returns the input data requirements of the compute(...) function. More...

Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Static Private Member Functions
static void	calculateFME_ (PeptideIdentification &pep_id, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, bool &print_warning, double tolerance, FragmentMassError::ToleranceUnit tolerance_unit, double &accumulator_ppm, UInt32 &counter_ppm, WindowMower &window_mower_filter)

static void	calculateVariance_ (FragmentMassError::Statistics &result, const PeptideIdentification &pep_id, const UInt num_ppm)

Private Attributes
std::vector< Statistics >	results_
	container that stores results More...

Additional Inherited Members
Public Types inherited from QCBase
enum class	Requires : UInt64 { NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT , CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...

enum class	ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }

using	Status = FlagSet< Requires >

Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...

template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ? More...

Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...

static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit More...

Class Documentation

◆ OpenMS::FragmentMassError::Statistics

struct OpenMS::FragmentMassError::Statistics

Structure for storing results: average and variance of all FragmentMassErrors in ppm.

Collaboration diagram for FragmentMassError::Statistics:

[legend]

Class Members
double	average_ppm
double	variance_ppm

Constructor & Destructor Documentation

◆ FragmentMassError()

FragmentMassError ( )

default

Default constructor.

◆ ~FragmentMassError()

virtual ~FragmentMassError ( )

virtualdefault

Destructor.

Member Function Documentation

◆ calculateFME_()

static void calculateFME_	(	PeptideIdentification &	pep_id,
		const MSExperiment &	exp,
		const QCBase::SpectraMap &	map_to_spectrum,
		bool &	print_warning,
		double	tolerance,
		FragmentMassError::ToleranceUnit	tolerance_unit,
		double &	accumulator_ppm,
		UInt32 &	counter_ppm,
		WindowMower &	window_mower_filter
	)

staticprivate

◆ calculateVariance_()

static void calculateVariance_	(	FragmentMassError::Statistics &	result,
		const PeptideIdentification &	pep_id,
		const UInt	num_ppm
	)

staticprivate

◆ compute() [1/2]

void compute	(	FeatureMap &	fmap,
		const MSExperiment &	exp,
		const QCBase::SpectraMap &	map_to_spectrum,
		ToleranceUnit	tolerance_unit = `ToleranceUnit::AUTO`,
		double	tolerance = `20`
	)

computes FragmentMassError (FME) in ppm and Dalton (only of the first PeptideHit of each PepID)

Stores average FME over all spectra (one for each PeptideIdentification) and its variance in ppm as a struct in a vector. Each FME (in ppm) is stored at the first PeptideHit of the corresponding PeptideIdentification as metavalue Constants::UserParam::FRAGMENT_ERROR_PPM_METAVALUE_USERPARAM and contains the FME for each peak in the corresponding spectrum. Same is done for the FME in Da - as metavalue Constants::UserParam::FRAGMENT_ERROR_DA_METAVALUE_USERPARAM. For both tolerance units the variance of FMEs over the spectrum is also stored as a metavalue with the extension "_variance" to the metavalue name. Note: Variance will not be written if 1 or less FMEs were calculated. Note: If the metavalues already exist, they will be overwritten.

Parameters

fmap	Input FeatureMap for annotation and data for theoretical spectra
exp	Input MSExperiment for MS2 spectra; spectra should be sorted (ascending RT)
map_to_spectrum	Map to find index of spectrum given by meta value at PepID
tolerance_unit	Tolerance in ppm or Dalton (if auto was chosen, the unit and value will taken from FeatureMap metadata)
tolerance	Search window for matching peaks; distance has to be lower than tolerance value (Will be overwritten if tolerance_unit AUTO is chosen)

Exceptions

Exceptions::MissingInformation	If fragment mass tolerance is missing in metadata of FeatureMap
Exception::InvalidParameter	PeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgument	Spectrum for a PepID has ms-level of 1
Exception::MissingInformation	If no fragmentation method given in a MS2 precursor
Exception::InvalidParameter	If the fragmentation method is not ECD, ETD, CID or HCD

◆ compute() [2/2]

void compute	(	std::vector< PeptideIdentification > &	pep_ids,
		const ProteinIdentification::SearchParameters &	search_params,
		const MSExperiment &	exp,
		const QCBase::SpectraMap &	map_to_spectrum,
		ToleranceUnit	tolerance_unit = `ToleranceUnit::AUTO`,
		double	tolerance = `20`
	)

computes FragmentMassError (FME) in ppm and Dalton (only of the first PeptideHit of each PepID)

Stores average FME over all spectra and its variance in ppm as a struct in a vector. Each FME (in ppm) is stored at the first PeptideHit of the corresponding PeptideIdentification as metavalue Constants::UserParam::FRAGMENT_ERROR_PPM_METAVALUE_USERPARAM and contains the FME for each peak in the corresponding spectrum. Same is done for the FME in Da - as metavalue Constants::UserParam::FRAGMENT_ERROR_DA_METAVALUE_USERPARAM. For both tolerance units the variance of FMEs over the spectrum is also stored as a metavalue with the extension "_variance" to the metavalue name. Note: Variance will not be written if 1 or less FMEs were calculated. Note: If the metavalues already exist, they will be overwritten.

Parameters

pep_ids	Input vector of peptide identifications for annotation and data for theoretical spectra
search_params	Input search parameters (corresponding to ID search that generated `pep_ids`) for finding fragment mass tolerance and unit automatically
exp	Input MSExperiment for MS2 spectra; spectra should be sorted (ascending RT)
map_to_spectrum	Map to find index of spectrum given by meta value at PepID
tolerance_unit	Tolerance in ppm or Dalton (if auto was chosen, the unit and value will taken from FeatureMap metadata)
tolerance	Search window for matching peaks; distance has to be lower than tolerance value (Will be overwritten if tolerance_unit AUTO is chosen)

Exceptions

Exceptions::MissingInformation	If fragment mass tolerance is missing in `search_params`
Exception::InvalidParameter	PeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgument	Spectrum for a PepID has ms-level of 1
Exception::MissingInformation	If no fragmentation method given in a MS2 precursor
Exception::InvalidParameter	If the fragmentation method is not ECD, ETD, CID or HCD

◆ getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

◆ getResults()

const std::vector<Statistics>& getResults ( ) const

returns results

◆ requirements()

QCBase::Status requirements ( ) const

overridevirtual

Returns the input data requirements of the compute(...) function.

Returns: Status for RAWMZML and POSTFDRFEAT

Implements QCBase.

Member Data Documentation

◆ results_

std::vector<Statistics> results_

private

container that stores results

Classes

Public Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members