| OpenMS 2.5.0

Classes | Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
IsobaricChannelExtractor Class Reference

Extracts individual channels from MS/MS spectra for isobaric labeling experiments. More...

`#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricChannelExtractor.h>`

Inheritance diagram for IsobaricChannelExtractor:

## Classes

struct | PuritySate_
| Small struct to capture the current state of the purity computation. More...

## Public Member Functions

| IsobaricChannelExtractor (const IsobaricQuantitationMethod *const quant_method)
| C'tor to create a new channel extractor for the given quantitation method. More...
| IsobaricChannelExtractor (const IsobaricChannelExtractor &other)
| Copy c'tor. More...
IsobaricChannelExtractor & | operator= (const IsobaricChannelExtractor &rhs)
| Assignment operator. More...
void | extractChannels (const PeakMap &ms_exp_data, ConsensusMap &consensus_map)
| Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map. More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Protected Member Functions

void | setDefaultParams_ ()
| implemented for DefaultParamHandler More...
void | updateMembers_ () override
| implemented for DefaultParamHandler More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Private Member Functions

void | registerChannelsInOutputMap_ (ConsensusMap &consensus_map)
| add channel information to the map after it has been filled More...
bool | isValidPrecursor_ (const Precursor &precursor) const
| Checks if the given precursor fulfills all constraints for extractions. More...
bool | hasLowIntensityReporter_ (const ConsensusFeature &cf) const
| Checks whether the given ConsensusFeature contains a channel that is below the given intensity threshold. More...
double | computePrecursorPurity_ (const PeakMap::ConstIterator &ms2_spec, const PuritySate_ &pState) const
| Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum. More...
double | computeSingleScanPrecursorPurity_ (const PeakMap::ConstIterator &ms2_spec, const PeakMap::SpectrumType &precursor_spec) const
| Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference to the potential precursor spectrum. More...
String | getActivationMethod_ (const PeakMap::SpectrumType &s) const
| Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum. More...

## Private Attributes

const IsobaricQuantitationMethod * | quant_method_
| The used quantitation method (itraq4plex, tmt6plex,..). More...
String | selected_activation_
| Used to select only specific types of spectra for the channel extraction. More...
Peak2D::CoordinateType | reporter_mass_shift_
| Allowed deviation between the expected and observed reporter ion m/z. More...
Peak2D::IntensityType | min_precursor_intensity_
| Minimum intensity of the precursor to be considered for quantitation. More...
bool | keep_unannotated_precursor_
| Flag if precursor with missing intensity value or missing precursor spectrum should be included or not. More...
Peak2D::IntensityType | min_reporter_intensity_
| Minimum reporter ion intensity to be considered for quantitation. More...
bool | remove_low_intensity_quantifications_
| Flag if complete quantification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ . More...
double | min_precursor_purity_
| Minimum precursor purity to accept the spectrum for quantitation. More...
double | max_precursor_isotope_deviation_
| Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor. More...
bool | interpolate_precursor_purity_
| Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan. More...

## Additional Inherited Members

Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Detailed Description

Extracts individual channels from MS/MS spectra for isobaric labeling experiments.

In addition to extracting the channel information this class can also filter the extracted channel information according to several parameters, i.e., discard channel information if certain criteria are not met.

- Precursor activation method (e.g., select only HCD scans).
- Minimum precursor intensity.
- Minimum reporter intensity (i.e., remove reporter channels below a certain intensity)
- Precursor purity (i.e., fraction of TIC in the precursor window that can be assigned to the precursor)

The precursor purity computation uses the interpolation approach described in: Savitski MM, Sweetman G, Askenazi M, et al. (2011). Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers. Analytical chemistry 83: 8959-67. http://www.ncbi.nlm.nih.gov/pubmed/22017476

Note
  Centroided MS and MS/MS data is required.

## Constructor & Destructor Documentation

## ◆ IsobaricChannelExtractor() [1/2]

IsobaricChannelExtractor | ( | const IsobaricQuantitationMethod *const | quant_method | ) |

explicit

C'tor to create a new channel extractor for the given quantitation method.

Parameters

  quant_method | IsobaricQuantitationMethod providing the necessary information which channels should be extracted.

## ◆ IsobaricChannelExtractor() [2/2]

IsobaricChannelExtractor | ( | const IsobaricChannelExtractor & | other | ) |

Copy c'tor.

## Member Function Documentation

## ◆ computePrecursorPurity_()

double computePrecursorPurity_ | ( | const PeakMap::ConstIterator & | ms2_spec,
|  | const PuritySate_ & | pState
| ) |  | const

private

Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and one to the precursor spectrum.

Parameters

  ms2_spec | Iterator pointing to the MS2 spectrum.
  precursor | Iterator pointing to the precursor spectrum of ms2_spec.

Returns
  Fraction of the total intensity in the isolation window of the precursor spectrum that was assigned to the precursor.

## ◆ computeSingleScanPrecursorPurity_()

double computeSingleScanPrecursorPurity_ | ( | const PeakMap::ConstIterator & | ms2_spec,
|  | const PeakMap::SpectrumType & | precursor_spec
| ) |  | const

private

Computes the purity of the precursor given an iterator pointing to the MS/MS spectrum and a reference to the potential precursor spectrum.

Parameters

  ms2_spec | Iterator pointing to the MS2 spectrum.
  precursor | Iterator pointing to the precursor spectrum of ms2_spec.

Returns
  Fraction of the total intensity in the isolation window of the precursor spectrum that was assigned to the precursor.

## ◆ extractChannels()

void extractChannels | ( | const PeakMap & | ms_exp_data,
|  | ConsensusMap & | consensus_map
| ) |  |

Extracts the isobaric channels from the tandem MS data and stores intensity values in a consensus map.

Parameters

  ms_exp_data | Raw data to search for isobaric quantitation channels.
  consensus_map | Output map containing the identified channels and the corresponding intensities.

## ◆ getActivationMethod_()

String getActivationMethod_ | ( | const PeakMap::SpectrumType & | s | ) | const

inline private

Get the first (of potentially many) activation methods (HCD,CID,...) of this spectrum.

Parameters

  s | The spectrum

Returns
  Entry from Precursor::NamesOfActivationMethod or empty string.

References SpectrumSettings::getPrecursors(), and Precursor::NamesOfActivationMethod.

## ◆ hasLowIntensityReporter_()

bool hasLowIntensityReporter_ | ( | const ConsensusFeature & | cf | ) | const

private

Checks whether the given ConsensusFeature contains a channel that is below the given intensity threshold.

Parameters

  cf | The ConsensusFeature to check.

Returns
  $true$ if a low intensity reporter is contained, $false$ otherwise.

## ◆ isValidPrecursor_()

bool isValidPrecursor_ | ( | const Precursor & | precursor | ) | const

private

Checks if the given precursor fulfills all constraints for extractions.

Parameters

  precursor | The precursor to test.

Returns
  $true$ if the precursor can be used for extraction, $false$ otherwise.

## ◆ operator=()

IsobaricChannelExtractor& operator= | ( | const IsobaricChannelExtractor & | rhs | ) |

Assignment operator.

## ◆ registerChannelsInOutputMap_()

void registerChannelsInOutputMap_ | ( | ConsensusMap & | consensus_map | ) |

private

add channel information to the map after it has been filled

## ◆ setDefaultParams_()

void setDefaultParams_ | ( |  | ) |

protected

implemented for DefaultParamHandler

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ interpolate_precursor_purity_

bool interpolate_precursor_purity_

private

Flag if precursor purity will solely be computed based on the precursor scan (false), or interpolated between the precursor- and the following MS1 scan.

## ◆ keep_unannotated_precursor_

bool keep_unannotated_precursor_

private

Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.

## ◆ max_precursor_isotope_deviation_

double max_precursor_isotope_deviation_

private

Max. allowed deviation between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.

## ◆ min_precursor_intensity_

Peak2D::IntensityType min_precursor_intensity_

private

Minimum intensity of the precursor to be considered for quantitation.

## ◆ min_precursor_purity_

double min_precursor_purity_

private

Minimum precursor purity to accept the spectrum for quantitation.

## ◆ min_reporter_intensity_

Peak2D::IntensityType min_reporter_intensity_

private

Minimum reporter ion intensity to be considered for quantitation.

## ◆ quant_method_

const IsobaricQuantitationMethod* quant_method_

private

The used quantitation method (itraq4plex, tmt6plex,..).

## ◆ remove_low_intensity_quantifications_

bool remove_low_intensity_quantifications_

private

Flag if complete quantification should be discarded if a single reporter ion has an intensity below the threshold given in IsobaricChannelExtractor::min_reporter_intensity_ .

## ◆ reporter_mass_shift_

Peak2D::CoordinateType reporter_mass_shift_

private

Allowed deviation between the expected and observed reporter ion m/z.

## ◆ selected_activation_

String selected_activation_

private

Used to select only specific types of spectra for the channel extraction.