#include <OpenMS/QC/PSMExplainedIonCurrent.h>

Inheritance diagram for PSMExplainedIonCurrent:

Collaboration diagram for PSMExplainedIonCurrent:

Classes
struct	Statistics
	Structure for storing results: average and variance over all PSMs. More...

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

virtual	~PSMExplainedIonCurrent ()=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 PSMExplainedIonCurrent (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 PSMExplainedIonCurrent (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	requires () 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 double	annotatePSMExplainedIonCurrent_ (PeptideIdentification &pep_id, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, WindowMower &filter, PSMExplainedIonCurrent::ToleranceUnit tolerance_unit, double tolerance)

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::PSMExplainedIonCurrent::Statistics

struct OpenMS::PSMExplainedIonCurrent::Statistics

Structure for storing results: average and variance over all PSMs.

Collaboration diagram for PSMExplainedIonCurrent::Statistics:

[legend]

Class Members
double	average_correctness
double	variance_correctness

Constructor & Destructor Documentation

◆ PSMExplainedIonCurrent()

PSMExplainedIonCurrent ( )

default

Default constructor.

◆ ~PSMExplainedIonCurrent()

virtual ~PSMExplainedIonCurrent ( )

virtualdefault

Destructor.

Member Function Documentation

◆ annotatePSMExplainedIonCurrent_()

static double annotatePSMExplainedIonCurrent_	(	PeptideIdentification &	pep_id,
		const MSExperiment &	exp,
		const QCBase::SpectraMap &	map_to_spectrum,
		WindowMower &	filter,
		PSMExplainedIonCurrent::ToleranceUnit	tolerance_unit,
		double	tolerance
	)

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 PSMExplainedIonCurrent (only of the first PeptideHit of each PepID)

To calculate PSMExplainedIonCurrent the theoretical spectrum is generated and matched with the original one. After that: PSMExplainedIonCurrent = sum of matched peaks intensity / total intensity

Stores average and variance of PSMExplainedIonCurrent as a struct and stores it in the results vector (can be accessed by getResults()). Each PSMExplainedIonCurrent is also stored in the first PeptideHit of the corresponding PeptideIdentification as metavalue "PSM_correctness".

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	Search window for matching peaks; distance has to be lower than tolerance value
tolerance_unit	Tolerance in ppm or Dalton (if auto was chosen, the unit and value will taken from FeatureMap metadata)

Exceptions

Exceptions::MissingInformation	If fragment mass tolerance is missing in metadata of FeatureMap (& no ToleranceUnit is given)
Exception::InvalidParameter	PeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgument	Spectrum for a PepID has ms-level of 1
Exception::MissingInformation	If PSMExplainedIonCurrent couldn't be calculated for any spectrum. (i.e. all spectra are: empty, contain only peaks with intensity 0 or the matching pep_id has no hits)
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 PSMExplainedIonCurrent (only of the first PeptideHit of each PepID)

Same as above, but with PeptideIdentification + SearchParameter input instead of FeatureMap

Parameters

pep_ids	Input peptide identifications for annotation and data for theoretical spectra
search_params	Input search parameters from ID-search that generated the peptide identifications from @pep_ids
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	Search window for matching peaks; distance has to be lower than tolerance value
tolerance_unit	Tolerance in ppm or Dalton (if auto was chosen, the unit and value will taken from FeatureMap metadata)

Exceptions

Exceptions::MissingInformation	If fragment mass tolerance is missing in metadata of FeatureMap (& no ToleranceUnit is given)
Exception::InvalidParameter	PeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgument	Spectrum for a PepID has ms-level of 1
Exception::MissingInformation	If PSMExplainedIonCurrent couldn't be calculated for any spectrum. (i.e. all spectra are: empty, contain only peaks with intensity 0 or the matching pep_id has no hits)
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

◆ requires()

QCBase::Status requires ( ) 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