MzCalibration Class Reference

QC metric calculating (un)calibrated m/z error. More...

#include <OpenMS/QC/MzCalibration.h>

Inheritance diagram for MzCalibration:

Collaboration diagram for MzCalibration:

Public Member Functions
	MzCalibration ()
	Constructor. More...
virtual	~MzCalibration ()=default
	Destructor. More...
void	compute (FeatureMap &features, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum)
	Writes results as meta values to the PeptideIdentification of the given FeatureMap. More...
Status	requires () const override
const String &	getName () const override
	Returns the name of the metric. More...
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Member Functions
void	addMzMetaValues_ (PeptideIdentification &peptide_ID, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum)
	calculate the m/z values and m/z errors and add them to the PeptideIdentification More...

Private Attributes
double	mz_raw_
double	mz_ref_
bool	no_mzml_

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...

Detailed Description

QC metric calculating (un)calibrated m/z error.

The metric sets m/z-values of the original experiment and the calculated reference m/z-values, uncalibrated m/z error (ppm) and calibrated m/z error (ppm) as metavalues of all PeptideIdentifications in a FeatureMap.

For full functionality a PeakMap/MSExperiment with original m/z-values before m/z calibration generated by InternalCalibration has to be given. It's also possible to use this without an MzML File, but then only uncalibrated m/z error (ppm) will be reported. A FeatureMap after FDR is always required.

Constructor & Destructor Documentation

MzCalibration()

MzCalibration

(

)

Constructor.

~MzCalibration()

virtual ~MzCalibration ( )

virtualdefault

Destructor.

Member Function Documentation

addMzMetaValues_()

void addMzMetaValues_ ( PeptideIdentification &  peptide_ID, const MSExperiment &  exp, const QCBase::SpectraMap &  map_to_spectrum  )

private

calculate the m/z values and m/z errors and add them to the PeptideIdentification

compute()

void compute	(	FeatureMap &	features,
		const MSExperiment &	exp,
		const QCBase::SpectraMap &	map_to_spectrum
	)

Writes results as meta values to the PeptideIdentification of the given FeatureMap.

Parameters

features	FeatureMap with m/z-values of PeptideIdentification after calibration, meta values are added here
exp	PeakMap of the original experiment. Can be empty (i.e. not available).
map_to_spectrum	Map to find index of spectrum given by meta value at PepID

Exceptions

Exception::InvalidParameter	PeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgument	Spectrum for a PepID has MSLevel of 1
Exception::MissingInformation	Meta value 'mz_raw' missing from MSExperiment

getName()

const String& getName ( ) const

overridevirtual

Returns the name of the metric.

Implements QCBase.

requires()

Status requires ( ) const

overridevirtual

define the required input files only FeatureXML after FDR is ultimately necessary

Implements QCBase.

Member Data Documentation

mz_raw_

double mz_raw_

private

mz_ref_

double mz_ref_

private

no_mzml_

bool no_mzml_

private