OpenMS
MzCalibration Class Reference

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

#include <OpenMS/QC/MzCalibration.h>

Inheritance diagram for MzCalibration:
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Collaboration diagram for MzCalibration:
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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 requirements () const override
 
const StringgetName () 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()

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
featuresFeatureMap with m/z-values of PeptideIdentification after calibration, meta values are added here
expPeakMap of the original experiment. Can be empty (i.e. not available).
map_to_spectrumMap to find index of spectrum given by meta value at PepID
Exceptions
Exception::InvalidParameterPeptideID is missing meta value 'spectrum_reference'
Exception::IllegalArgumentSpectrum for a PepID has MSLevel of 1
Exception::MissingInformationMeta value 'mz_raw' missing from MSExperiment

◆ getName()

const String& getName ( ) const
overridevirtual

Returns the name of the metric.

Implements QCBase.

◆ requirements()

Status requirements ( ) 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