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ItraqChannelExtractor Class Reference

[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map More...

#include <OpenMS/ANALYSIS/QUANTITATION/ItraqChannelExtractor.h>

Inheritance diagram for ItraqChannelExtractor:
DefaultParamHandler ItraqConstants

List of all members.

Public Types

typedef
ItraqConstants::ChannelMapType 		ChannelMapType
 maps iTRAQ channel (e.g. 117) to more information

Public Member Functions

 ItraqChannelExtractor ()
 Constructor (assuming 4plex).
 ItraqChannelExtractor (Int itraq_type)
 Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES).
 ItraqChannelExtractor (Int itraq_type, const Param &param)
 Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param.
 ItraqChannelExtractor (const ItraqChannelExtractor &cp)
 copy constructor
ItraqChannelExtractor & operator= (const ItraqChannelExtractor &rhs)
 assignment operator
void run (const MSExperiment< Peak1D > &ms_exp_data, ConsensusMap &consensus_map)
 extracts the iTRAQ channels from the tandem MS data and stores intensity values in a consensus map

Protected Member Functions

void setDefaultParams_ ()
void updateMembers_ ()
 implemented for DefaultParamHandler

Private Member Functions

void init_ ()
 initialize

Private Attributes

Int itraq_type_
 set to either ItraqConstants::FOURPLEX, ItraqConstants::EIGHTPLEX, or ItraqConstants::TMT_SIXPLEX
ChannelMapType channel_map_

Detailed Description

[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a consensus map

[experimental class] This class supports 4 and 8 channel iTRAQ and 6 channel TMT and will optionally do peak picking before the quantitation step. Quantitation is done by adding all signals within a small delta around the expected m/z of each channel. When all channels are found to be empty, the ConsensusFeature is not created. No postprocessing is done here. Use ItraqQuantifier for that!

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
select_activation stringHigh-energy collision-induced dissociation Collision-induced dissociation, Post-source decay, Plasma desorption, Surface-induced dissociation, Blackbody infrared radiative dissociation, Electron capture dissociation, Infrared multiphoton dissociation, Sustained off-resonance irradiation, High-energy collision-induced dissociation, Low-energy collision-induced dissociation, Photodissociation, Electron transfer dissociation, Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering.
reporter_mass_shift float0.1 min: 1e-08 max: 0.5Allowed shift (left to right) in Da from the expected position.
channel_active string list[114:liver, 117:lung]  Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format :, e.g. "114:myref","115:liver".

Note:

Member Typedef Documentation

typedef ItraqConstants::ChannelMapType ChannelMapType

maps iTRAQ channel (e.g. 117) to more information

Reimplemented from ItraqConstants.

Constructor & Destructor Documentation

ItraqChannelExtractor (  ) 

Constructor (assuming 4plex).

ItraqChannelExtractor ( Int  itraq_type  )  [explicit]

Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES).

ItraqChannelExtractor ( Int  itraq_type,
const Param &  param 
)

Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param.

ItraqChannelExtractor ( const ItraqChannelExtractor &  cp  ) 

copy constructor

Member Function Documentation

void init_ (  )  [private]

initialize

ItraqChannelExtractor& operator= ( const ItraqChannelExtractor &  rhs  ) 

assignment operator

void run ( const MSExperiment< Peak1D > &  ms_exp_data,
ConsensusMap &  consensus_map 
)

extracts the iTRAQ channels from the tandem MS data and stores intensity values in a consensus map

Parameters:
ms_exp_data Raw data to read
consensus_map 
void setDefaultParams_ (  )  [protected]
void updateMembers_ (  )  [protected]

implemented for DefaultParamHandler

Member Data Documentation

ChannelMapType channel_map_ [private]

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

Int itraq_type_ [private]

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

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1