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ITRAQLabeler Class Reference

Simulate iTRAQ experiments. More...

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

Inheritance diagram for ITRAQLabeler:
BaseLabeler DefaultParamHandler

List of all members.

Public Types

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

Public Member Functions

 ITRAQLabeler ()
 default constructor
virtual ~ITRAQLabeler ()
 destructor
void preCheck (Param &param) const
 Checks the (simulation) params passed if they are consistent with the labeling technique.
void setUpHook (FeatureMapSimVector &)
 Hook to prepare the simulation process.
void postDigestHook (FeatureMapSimVector &)
 Labeling between digestion and rt simulation.
void postRTHook (FeatureMapSimVector &)
 Labeling after rt simulation.
void postDetectabilityHook (FeatureMapSimVector &)
 Labeling after detectability simulation.
void postIonizationHook (FeatureMapSimVector &)
 Labeling after ionization.
void postRawMSHook (FeatureMapSimVector &)
 Labeling after raw signal generation.
void postRawTandemMSHook (FeatureMapSimVector &, MSSimExperiment &)
 Labeling after Tandem MS (e.g. iTRAQ).

Static Public Member Functions

static BaseLabeler * create ()
 create new object (needed by Factory)
static const String getProductName ()
 name of the model (needed by Factory)

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.
void labelPeptide_ (const Feature &feature, FeatureMapSim &result) const
 tag a feature with iTRAQ modifications
Feature mergeFeatures_ (Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const
void updateMembers_ ()
 Synchronize members with param class.
DoubleReal getRTProfileIntensity_ (const Feature &f, const DoubleReal MS2_RT_time) const
Matrix< SimIntensityType > getItraqIntensity_ (const Feature &f, const DoubleReal MS2_RT_time) const
 convert meta information from feature into intensity values for iTRAQ

Protected Attributes

Int itraq_type_
 set to either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
ChannelMapType channel_map_
IsotopeMatrices isotope_corrections_
 Matrices with isotope correction values (one for each plex-type).
DoubleReal y_labeling_efficiency_
 efficiency of "Y" labeling

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:

NameTypeDefaultRestrictionsDescription
iTRAQ string4plex 4plex, 8plex4plex or 8plex iTRAQ?
reporter_mass_shift float0.1 min: 0 max: 0.5Allowed 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[114:0/1/5.9/0.2, 115:0/2/5.6/0.1, 116:0/3/4.5/0.1, 117:0.1/4/3.5/0.1]  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[113:0/0/6.89/0.22, 114:0/0.94/5.9/0.16, 115:0/1.88/4.9/0.1, 116:0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0, 118:0.09/4.71/1.88/0, 119:0.14/5.66/0.87/0, 121:0.27/7.44/0.18/0]  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 float0.3 min: 0 max: 1Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling

Note:

Member Typedef Documentation

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

Constructor & Destructor Documentation

ITRAQLabeler (  ) 

default constructor

virtual ~ITRAQLabeler (  )  [virtual]

destructor

Member Function Documentation

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.

static BaseLabeler* create (  )  [inline, static]

create new object (needed by Factory)

Referenced by BaseLabeler::registerChildren().

Matrix<SimIntensityType> getItraqIntensity_ ( const Feature &  f,
const DoubleReal  MS2_RT_time 
) const [protected]

convert meta information from feature into intensity values for iTRAQ

static const String getProductName (  )  [inline, static]

name of the model (needed by Factory)

Referenced by BaseLabeler::registerChildren().

DoubleReal getRTProfileIntensity_ ( const Feature &  f,
const DoubleReal  MS2_RT_time 
) const [protected]
void labelPeptide_ ( const Feature &  feature,
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.

Feature mergeFeatures_ ( Feature &  labeled_channel_feature,
const AASequence &  unmodified_sequence,
std::map< AASequence, Feature > &  unlabeled_features_index 
) const [protected]
void postDetectabilityHook ( FeatureMapSimVector &   )  [virtual]

Labeling after detectability simulation.

Implements BaseLabeler.

void postDigestHook ( FeatureMapSimVector &   )  [virtual]

Labeling between digestion and rt simulation.

Implements BaseLabeler.

void postIonizationHook ( FeatureMapSimVector &   )  [virtual]

Labeling after ionization.

Implements BaseLabeler.

void postRawMSHook ( FeatureMapSimVector &   )  [virtual]

Labeling after raw signal generation.

Implements BaseLabeler.

void postRawTandemMSHook ( FeatureMapSimVector &  ,
MSSimExperiment &   
) [virtual]

Labeling after Tandem MS (e.g. iTRAQ).

Implements BaseLabeler.

void postRTHook ( FeatureMapSimVector &   )  [virtual]

Labeling after rt simulation.

Implements BaseLabeler.

void preCheck ( Param &  param  )  const [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.

void setUpHook ( FeatureMapSimVector &   )  [virtual]

Hook to prepare the simulation process.

Implements BaseLabeler.

void updateMembers_ (  )  [protected, virtual]

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

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

IsotopeMatrices isotope_corrections_ [protected]

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

Int itraq_type_ [protected]

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

DoubleReal y_labeling_efficiency_ [protected]

efficiency of "Y" labeling

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1