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ItraqConstants Class Reference

Some constants used throughout iTRAQ classes. More...

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

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Classes

struct  ChannelInfo
 stores information on an iTRAQ channel More...
 

Public Types

enum  ITRAQ_TYPES { FOURPLEX = 0 , EIGHTPLEX , TMT_SIXPLEX , SIZE_OF_ITRAQ_TYPES }
 
typedef std::map< Int, ChannelInfo > ChannelMapType
 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...
 

Static Public Member Functions

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< double > translateIsotopeMatrix (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

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...
 

Detailed Description

Some constants used throughout iTRAQ classes.

Constants for iTRAQ experiments and a ChannelInfo structure to store information about a single channel.

Class Documentation

◆ OpenMS::ItraqConstants::ChannelInfo

struct OpenMS::ItraqConstants::ChannelInfo

stores information on an iTRAQ channel

Collaboration diagram for ItraqConstants::ChannelInfo:
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Class Members
bool active channel actually added to the experiment?
CoordinateType center expected centroid of peak in MZ
String description description given by experimentalist (e.g. lung tissue)
Int id 0-4 or 0-8
Int name 114-117 or 113 to 121

Member Typedef Documentation

◆ ChannelMapType

typedef std::map<Int, ChannelInfo> ChannelMapType

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

◆ IsotopeMatrices

typedef std::vector<Matrix<double> > IsotopeMatrices

(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style

Member Enumeration Documentation

◆ ITRAQ_TYPES

enum ITRAQ_TYPES
Enumerator
FOURPLEX 
EIGHTPLEX 
TMT_SIXPLEX 
SIZE_OF_ITRAQ_TYPES 

Member Function Documentation

◆ getIsotopeMatrixAsStringList()

static StringList getIsotopeMatrixAsStringList ( const int  itraq_type,
const IsotopeMatrices &  isotope_corrections 
)
static

convert isotope correction matrix to stringlist

Each line is converted into a string of the format <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' Useful for creating parameters or debug output.

Parameters
itraq_typeWhich matrix to stringify. Should be of values from enum ITRAQ_TYPES
isotope_correctionsVector of the two matrices (4plex, 8plex).

◆ initChannelMap()

static void initChannelMap ( const int  itraq_type,
ChannelMapType &  map 
)
static

information about an iTRAQ channel

State, name and expected mz-position of iTRAQ channels are initialized.

Parameters
itraq_typeShould be of values from enum ITRAQ_TYPES
mapStorage to initialize

◆ translateIsotopeMatrix()

static Matrix<double> translateIsotopeMatrix ( const int &  itraq_type,
const IsotopeMatrices &  isotope_corrections 
)
static

translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format

Translates e.g. ItraqConstants::ISOTOPECORRECTIONS_EIGHTPLEX matrix into a 8x8 matrix which maps how channel (row) distributes its tags onto other channels (columns).

Parameters
itraq_typeShould be of values from enum ITRAQ_TYPES
isotope_correctionsisotope correction matrix in -2...+2 form

◆ updateChannelMap()

static void updateChannelMap ( const StringList &  active_channels,
ChannelMapType &  map 
)
static

activate & annotate channels

State and description of iTRAQ channels are updated. Each input string must have the format <channel>:<description>, e.g. "114:myref","115:liver"

Parameters
active_channelsStringList with channel and description
mapStorage to update

◆ updateIsotopeMatrixFromStringList()

static void updateIsotopeMatrixFromStringList ( const int  itraq_type,
const StringList &  channels,
IsotopeMatrices &  isotope_corrections 
)
static

convert strings to isotope correction matrix rows

Each string of format <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' is parsed and the corresponding channel(row) in the matrix is updated. Not all channels need to be present, missing channels will be left untouched. Useful to update the matrix with user isotope correction values.

Parameters
itraq_typeWhich matrix to stringify. Should be of values from enum ITRAQ_TYPES
channelsNew channel isotope values as strings
isotope_correctionsVector of the two matrices (4plex, 8plex).

Member Data Documentation

◆ CHANNEL_COUNT

const Int CHANNEL_COUNT[]
static

◆ CHANNELS_EIGHTPLEX

const Int CHANNELS_EIGHTPLEX[8][1]
static

channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121)

◆ CHANNELS_FOURPLEX

const Int CHANNELS_FOURPLEX[4][1]
static

channel names for 4plex( 114, 115, 116, 117)

◆ CHANNELS_TMT_SIXPLEX

const Int CHANNELS_TMT_SIXPLEX[6][1]
static

channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131)

◆ ISOTOPECORRECTIONS_EIGHTPLEX

const double ISOTOPECORRECTIONS_EIGHTPLEX[8][4]
static

default isotope correction matrix (8 plex)

◆ ISOTOPECORRECTIONS_FOURPLEX

const double ISOTOPECORRECTIONS_FOURPLEX[4][4]
static

default isotope correction matrix (4 plex)

◆ ISOTOPECORRECTIONS_TMT_SIXPLEX

const double ISOTOPECORRECTIONS_TMT_SIXPLEX[6][4]
static

default isotope correction matrix (6 plex TMT)