ItraqConstants Class Reference

Some constants used throughout iTRAQ classes. More...

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

Collaboration diagram for ItraqConstants:

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.

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Class Documentation

OpenMS::ItraqConstants::ChannelInfo

struct OpenMS::ItraqConstants::ChannelInfo

stores information on an iTRAQ channel

Collaboration diagram for ItraqConstants::ChannelInfo:

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)