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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

Public Types

typedef ItraqConstants::ChannelMapType ChannelMapType
 
- Public Types inherited from ItraqConstants
enum  ITRAQ_TYPES { FOURPLEX = 0, EIGHTPLEX, TMT_SIXPLEX, SIZE_OF_ITRAQ_TYPES }
 
typedef Map< Int, ChannelInfoChannelMapType
 maps iTRAQ channel (e.g. 117) to more information More...
 
typedef std::vector< Matrix< double > > IsotopeMatrices
 (user defined?) isotope correction matrix in (-2, -1, +1, +2) row style More...
 

Public Member Functions

 ItraqChannelExtractor ()
 Constructor (assuming 4plex) More...
 
 ItraqChannelExtractor (Int itraq_type)
 Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) More...
 
 ItraqChannelExtractor (Int itraq_type, const Param &param)
 Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param. More...
 
 ItraqChannelExtractor (const ItraqChannelExtractor &cp)
 copy constructor More...
 
ItraqChannelExtractoroperator= (const ItraqChannelExtractor &rhs)
 assignment operator More...
 
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 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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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_ ()
 
void updateMembers_ ()
 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 init_ ()
 initialize More...
 

Private Attributes

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

Additional Inherited Members

- Static Public Member Functions inherited from ItraqConstants
static StringList getIsotopeMatrixAsStringList (const int itraq_type, const IsotopeMatrices &isotope_corrections)
 convert isotope correction matrix to stringlist More...
 
static void updateIsotopeMatrixFromStringList (const int itraq_type, const StringList &channels, IsotopeMatrices &isotope_corrections)
 convert strings to isotope correction matrix rows More...
 
static void initChannelMap (const int itraq_type, ChannelMapType &map)
 information about an iTRAQ channel More...
 
static void updateChannelMap (const StringList &active_channels, ChannelMapType &map)
 activate & annotate channels More...
 
static Matrix< doubletranslateIsotopeMatrix (const int &itraq_type, const IsotopeMatrices &isotope_corrections)
 translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format More...
 
- Static Public Attributes inherited from ItraqConstants
static const Int CHANNEL_COUNT []
 
static const Int CHANNELS_FOURPLEX [4][1]
 channel names for 4plex( 114, 115, 116, 117) More...
 
static const Int CHANNELS_EIGHTPLEX [8][1]
 channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121) More...
 
static const Int CHANNELS_TMT_SIXPLEX [6][1]
 channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131) More...
 
static const double ISOTOPECORRECTIONS_FOURPLEX [4][4]
 default isotope correction matrix (4 plex) More...
 
static const double ISOTOPECORRECTIONS_EIGHTPLEX [8][4]
 default isotope correction matrix (8 plex) More...
 
static const double ISOTOPECORRECTIONS_TMT_SIXPLEX [6][4]
 default isotope correction matrix (6 plex TMT) More...
 
- 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< Stringsubsections_
 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

[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 post-processing 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

Constructor & Destructor Documentation

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.

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_dataRaw data to read
consensus_map
void setDefaultParams_ ( )
protected
void updateMembers_ ( )
protectedvirtual

implemented for DefaultParamHandler

Reimplemented from DefaultParamHandler.

Member Data Documentation

ChannelMapType channel_map_
private

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

Int itraq_type_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:39 using doxygen 1.8.9.1