| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ITRAQLabeler Class Reference

Simulate iTRAQ experiments. More...

`#include <OpenMS/SIMULATION/LABELING/ITRAQLabeler.h>`

Inheritance diagram for ITRAQLabeler:

## Public Types

typedef ItraqConstants::ChannelInfo | ChannelInfo
typedef ItraqConstants::ChannelMapType | ChannelMapType
typedef ItraqConstants::IsotopeMatrices | IsotopeMatrices

## Public Member Functions

| ITRAQLabeler ()
| default constructor More...
| ~ITRAQLabeler () override
| destructor More...
void | preCheck (Param &param) const override
| Checks the (simulation) params passed if they are consistent with the labeling technique. More...
void | setUpHook (SimTypes::FeatureMapSimVector &) override
| Hook to prepare the simulation process. More...
void | postDigestHook (SimTypes::FeatureMapSimVector &) override
| Labeling between digestion and rt simulation. More...
void | postRTHook (SimTypes::FeatureMapSimVector &) override
| Labeling after rt simulation. More...
void | postDetectabilityHook (SimTypes::FeatureMapSimVector &) override
| Labeling after detectability simulation. More...
void | postIonizationHook (SimTypes::FeatureMapSimVector &) override
| Labeling after ionization. More...
void | postRawMSHook (SimTypes::FeatureMapSimVector &) override
| Labeling after raw signal generation. More...
void | postRawTandemMSHook (SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) override
| Labeling after Tandem MS (e.g. iTRAQ) More...
Public Member Functions inherited from BaseLabeler
| BaseLabeler ()
| constructor More...
| ~BaseLabeler () override
| destructor More...
virtual Param | getDefaultParameters () const
| Returns the default parameters. Re-implement. More...
virtual void | setRnd (SimTypes::MutableSimRandomNumberGeneratorPtr rng)
| Set the random number generator. More...
ConsensusMap & | getConsensus ()
const String & | getDescription () const
| Get short description of the labeler (e.g., channels used) More...
String | getChannelIntensityName (const Size channel_index) const
| to ensure standardized meta value names across labelers for channel intensity 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...

## Static Public Member Functions

static BaseLabeler * | create ()
| create new object (needed by Factory) More...
static const String | getProductName ()
| name of the model (needed by Factory) More...
Static Public Member Functions inherited from BaseLabeler
static void | registerChildren ()
| register all derived classes here (implemented in file BaseLabeler_impl.h) More...

## Protected Member Functions

void | addModificationToPeptideHit_ (Feature &feature, const String &modification, const Size &pos) const
| Modify the first peptide hit of the feature with a modification at `pos`. More...
void | labelPeptide_ (const Feature &feature, SimTypes::FeatureMapSim &result) const
| tag a feature with iTRAQ modifications More...
Feature | mergeFeatures_ (Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const
void | updateMembers_ () override
| Synchronize members with param class. More...
double | getRTProfileIntensity_ (const Feature &f, const double MS2_RT_time) const
EigenMatrixXdPtr | getItraqIntensity_ (const Feature &f, const double MS2_RT_time) const
| convert meta information from feature into intensity values for iTRAQ More...
Protected Member Functions inherited from BaseLabeler
SimTypes::FeatureMapSim | mergeProteinIdentificationsMaps_ (const SimTypes::FeatureMapSimVector &maps)
| Creates an empty FeatureMap with the merged ProteinIdentifications from all FeatureMaps contained in `maps`. More...
void | mergeProteinAccessions_ (Feature &target, const Feature &source) const
| join all protein references of two features More...
void | recomputeConsensus_ (const SimTypes::FeatureMapSim &simulated_features)
| Based on the stored consensus recompute the associations for the passed features, assuming that the features where derived from the features stored in the consensus. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

Int | itraq_type_
| set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX More...
ChannelMapType | channel_map_
IsotopeMatrices | isotope_corrections_
| Matrices with isotope correction values (one for each plex-type) More...
double | y_labeling_efficiency_
| efficiency of "Y" labeling More...
Protected Attributes inherited from BaseLabeler
ConsensusMap | consensus_
SimTypes::MutableSimRandomNumberGeneratorPtr | rng_
String | channel_description_
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

Simulate iTRAQ experiments.

Adds reporter ion intensities to MS/MS scans. Supports custom channel allocation and isotope matrices.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
iTRAQ | string | 4plex | 4plex, 8plex | 4plex or 8plex iTRAQ?
reporter_mass_shift | float | 0.1 | min: 0.0 max: 0.5 | Allowed shift (uniformly distributed - left to right) in Da from the expected position (of e.g. 114.1, 115.1)
channel_active_4plex | string list | [114:myReference] |  | Four-plex only: Each channel that was used in the experiment and its description (114-117) in format :, e.g. "114:myref","115:liver".
channel_active_8plex | string list | [113:myReference] |  | Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format :, e.g. "113:myref","115:liver","118:lung".
isotope_correction_values_4plex | string list | [114:0.0/1.0/5.9/0.2, 115:0.0/2.0/5.6/0.1, 116:0.0/3.0/4.5/0.1, 117:0.1/4.0/3.5/0.1] |  | override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'
isotope_correction_values_8plex | string list | [113:0.0/0.0/6.89/0.22, 114:0.0/0.94/5.9/0.16, 115:0.0/1.88/4.9/0.1, 116:0.0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0.0, 118:0.09/4.71/1.88/0.0, 119:0.14/5.66/0.87/0.0, 121:0.27/7.44/0.18/0.0] |  | override default values (see Documentation); use the following format: :<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2'
Y_contamination | float | 0.3 | min: 0.0 max: 1.0 | Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Member Typedef Documentation

## ◆ ChannelInfo

typedef ItraqConstants::ChannelInfo ChannelInfo

## ◆ ChannelMapType

typedef ItraqConstants::ChannelMapType ChannelMapType

## ◆ IsotopeMatrices

typedef ItraqConstants::IsotopeMatrices IsotopeMatrices

## Constructor & Destructor Documentation

## ◆ ITRAQLabeler()

ITRAQLabeler | ( |  | ) |

default constructor

## ◆ ~ITRAQLabeler()

~ITRAQLabeler | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addModificationToPeptideHit_()

void addModificationToPeptideHit_ | ( | Feature & | feature,
|  | const String & | modification,
|  | const Size & | pos
| ) |  | const

protected

Modify the first peptide hit of the feature with a modification at `pos`.

## ◆ create()

static BaseLabeler* create | ( |  | ) |

inline static

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

## ◆ getItraqIntensity_()

EigenMatrixXdPtr getItraqIntensity_ | ( | const Feature & | f,
|  | const double | MS2_RT_time
| ) |  | const

protected

convert meta information from feature into intensity values for iTRAQ

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

## ◆ getRTProfileIntensity_()

double getRTProfileIntensity_ | ( | const Feature & | f,
|  | const double | MS2_RT_time
| ) |  | const

protected

## ◆ labelPeptide_()

void labelPeptide_ | ( | const Feature & | feature,
|  | SimTypes::FeatureMapSim & | result
| ) |  | const

protected

tag a feature with iTRAQ modifications

This might produce several features, due to incomplete labeling of "Y" residues. The resulting features are exact copies, except for their intensity and modification state.

## ◆ mergeFeatures_()

Feature mergeFeatures_ | ( | Feature & | labeled_channel_feature,
|  | const AASequence & | unmodified_sequence,
|  | std::map< AASequence, Feature > & | unlabeled_features_index
| ) |  | const

protected

## ◆ postDetectabilityHook()

void postDetectabilityHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Labeling after detectability simulation.

Implements BaseLabeler.

## ◆ postDigestHook()

void postDigestHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Labeling between digestion and rt simulation.

Implements BaseLabeler.

## ◆ postIonizationHook()

void postIonizationHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Labeling after ionization.

Implements BaseLabeler.

## ◆ postRawMSHook()

void postRawMSHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Labeling after raw signal generation.

Implements BaseLabeler.

## ◆ postRawTandemMSHook()

void postRawTandemMSHook | ( | SimTypes::FeatureMapSimVector & | ,
|  | SimTypes::MSSimExperiment & |
| ) |  |

override virtual

Labeling after Tandem MS (e.g. iTRAQ)

Implements BaseLabeler.

## ◆ postRTHook()

void postRTHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Labeling after rt simulation.

Implements BaseLabeler.

## ◆ preCheck()

void preCheck | ( | Param & | param | ) | const

override virtual

Checks the (simulation) params passed if they are consistent with the labeling technique.

Parameters

  param | Param object containing the simulation parameters

Exceptions

  Exception::InvalidParameter | if the given parameters are not consistent with the labeling technique

Implements BaseLabeler.

## ◆ setUpHook()

void setUpHook | ( | SimTypes::FeatureMapSimVector & |  | ) |

override virtual

Hook to prepare the simulation process.

Implements BaseLabeler.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ channel_map_

ChannelMapType channel_map_

protected

map the channel-name (e.g. 114) onto its description and the centroid mass the channel-name is also the id-string in the mapList section of the ConsensusMap

## ◆ isotope_corrections_

IsotopeMatrices isotope_corrections_

protected

Matrices with isotope correction values (one for each plex-type)

## ◆ itraq_type_

Int itraq_type_

protected

set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX

## ◆ y_labeling_efficiency_

double y_labeling_efficiency_

protected

efficiency of "Y" labeling