The "ReporterIons" Class

The ReporterIons class allows to define a set of isobaric reporter ions that are used for quantification in MSMS mode, e.g. iTRAQ (isobaric tag for relative and absolute quantitation) or TMT (tandem mass tags). ReporterIons instances can them be used when quantifying "MSnExp" data of plotting the reporters peaks based on in "Spectrum2" ojects.

Some reporter ions are provided with MSnbase an can be loaded with the data function. These reporter ions data sets are:

iTRAQ4:: ReporterIon object for the iTRAQ 4-plex set. Load with data(iTRAQ4).
iTRAQ5:: ReporterIon object for the iTRAQ 4-plex set plus the isobaric tag. Load with data(iTRAQ5).
TMT6:: ReporterIon object for the TMT 6-plex set. Load with data(TMT6).
TMT7:: ReporterIon object for the TMT 6-plex set plus the isobaric tag. Load with data(TMT6).

Objects from the Class

Objects can be created by calls of the form new("ReporterIons", ...).

Slots

name:: Object of class "character" to identify the ReporterIons instance.
reporterNames:: Object of class "character" naming each individual reporter of the ReporterIons instance. If not provided explicitely, they are names by concatenating the ReporterIons name and the respective MZ values.
description:: Object of class "character" to describe the ReporterIons instance.
mz:: Object of class "numeric" providing the MZ values of the reporter ions.
col:: Object of class "character" providing colours to highlight the reporters on plots.
width:: Object of class "numeric" indicating the width around the individual reporter ions MZ values were to search for peaks. This is dependent on the mass spectrometer's resolution and is used for peak picking when quantifying the reporters. See quantify for more details about quantification.
.__classVersion__:: Object of class "Versions" indicating the version of the ReporterIons instance. Intended for developer use and debugging.

Extends

Class "Versioned", directly.

Methods

show(object): Displays object content as text.
object[]: Subsets one or several reporter ions of the ReporterIons object and returns a new instance of the same class.
length(object): Returns the number of reporter ions in the instance.
mz(object, ...): Returns the expected mz values of reporter ions. Additional arguments are currently ignored.
reporterColours(object) or reporterColors(object): Returns the colours used to highlight the reporter ions.
reporterNames(object): Returns the name of the individual reporter ions. If not specified or is an incorrect number of names is provided at initialisation, the names are generated automatically by concatenating the instance name and the reporter's MZ values.
reporterNames(object) <- value: Sets the reporter names to value, which must be a character of the same length as the number of reporter ions.
width(object): Returns the widths in which the reporter ion peaks are expected.
names(object): Returns the name of the ReporterIons object.
description(object): Returns the description of the ReporterIons object.

References

Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents." Mol Cell Proteomics, 2004 Dec;3(12):1154-69. Epub 2004 Sep 22. PubMed PMID: 15385600.

Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C. "Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS." Anal Chem. 2003 Apr 15;75(8):1895-904. Erratum in: Anal Chem. 2006 Jun 15;78(12):4235. Mohammed, A Karim A [added] and Anal Chem. 2003 Sep 15;75(18):4942. Johnstone, R [added]. PubMed PMID: 12713048.

Author

Laurent Gatto

Examples

## Code used for the iTRAQ4 set
ri <- new("ReporterIons",
          description="4-plex iTRAQ",
          name="iTRAQ4",
          reporterNames=c("iTRAQ4.114","iTRAQ4.115",
                          "iTRAQ4.116","iTRAQ4.117"),
          mz=c(114.1,115.1,116.1,117.1),
          col=c("red","green","blue","yellow"),
          width=0.05)
ri
#> Object of class "ReporterIons"
#> iTRAQ4: '4-plex iTRAQ' with 4 reporter ions
#>  - [iTRAQ4.114] 114.1 +/- 0.05 (red)
#>  - [iTRAQ4.115] 115.1 +/- 0.05 (green)
#>  - [iTRAQ4.116] 116.1 +/- 0.05 (blue)
#>  - [iTRAQ4.117] 117.1 +/- 0.05 (yellow)
reporterNames(ri)
#> [1] "iTRAQ4.114" "iTRAQ4.115" "iTRAQ4.116" "iTRAQ4.117"
ri[1:2]
#> Object of class "ReporterIons"
#> iTRAQ4[1:2]: 'subset of 4-plex iTRAQ' with 2 reporter ions
#>  - [iTRAQ4.114] 114.1 +/- 0.05 (red)
#>  - [iTRAQ4.115] 115.1 +/- 0.05 (green)