| OpenMS 2.5.0

Classes | Public Types | Static Public Member Functions | Static Public Attributes | List of all members
ItraqConstants Class Reference

Some constants used throughout iTRAQ classes. More...

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

## 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 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

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 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_type | Which matrix to stringify. Should be of values from enum ITRAQ_TYPES
  isotope_corrections | Vector 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_type | Should be of values from enum ITRAQ_TYPES
  map | Storage 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_type | Should be of values from enum ITRAQ_TYPES
  isotope_corrections | isotope 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_channels | StringList with channel and description
  map | Storage 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_type | Which matrix to stringify. Should be of values from enum ITRAQ_TYPES
  channels | New channel isotope values as strings
  isotope_corrections | Vector 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)