| OpenMS 2.5.0

Public Member Functions | Private Member Functions | Private Attributes | List of all members
MzCalibration Class Reference

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

`#include <OpenMS/QC/MzCalibration.h>`

Inheritance 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...

## 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_
String | name_

## Additional Inherited Members

Public Types inherited from QCBase
enum | Requires : UInt64 { FAIL, RAWMZML, POSTFDRFEAT, PREFDRFEAT, CONTAMINANTS, TRAFOALIGN, SIZE_OF_REQUIRES }
| Enum to encode a file type as a bit. More...
Static Public Member Functions inherited from QCBase
template<typename MAP , typename T >
static void | iterateFeatureMap (MAP &fmap, T lambda)
| function, which iterates through all PeptideIdentifications of a given FeatureMap and applies a given lambda function More...
Static Public Attributes inherited from QCBase
static const std::string | names_of_requires []
| strings corresponding to enum Requires 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 | ( |  | ) |

virtual default

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

override virtual

Returns the name of the metric.

Implements QCBase.

## ◆ requires()

Status requires | ( |  | ) | const

override virtual

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

## ◆ name_

String name_

private

## ◆ no_mzml_

bool no_mzml_

private