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iTRAQ 4-plex set

iTRAQ4.Rd

This instance of class "ReporterIons" corresponds to the iTRAQ 4-plex set, i.e the 114, 115, 116 and 117 isobaric tags. In the iTRAQ5 data set, an unfragmented tag, i.e reporter and attached isobaric tag, is also included at MZ 145. These objects are used to plot the reporter ions of interest in an MSMS spectra (see "Spectrum2") as well as for quantification (see quantify).

Usage

iTRAQ4
iTRAQ5
iTRAQ8
iTRAQ9

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.

See also

TMT6.

Examples

iTRAQ4
#> Object of class "ReporterIons"
#> iTRAQ4: '4-plex iTRAQ' with 4 reporter ions
#>  - [iTRAQ4.114] 114.1112 +/- 0.05 (red)
#>  - [iTRAQ4.115] 115.1083 +/- 0.05 (green)
#>  - [iTRAQ4.116] 116.1116 +/- 0.05 (blue)
#>  - [iTRAQ4.117] 117.115 +/- 0.05 (yellow)
iTRAQ4[1:2]
#> Object of class "ReporterIons"
#> iTRAQ4[1:2]: 'subset of 4-plex iTRAQ' with 2 reporter ions
#>  - [iTRAQ4.114] 114.1112 +/- 0.05 (red)
#>  - [iTRAQ4.115] 115.1083 +/- 0.05 (green)

newReporter <- new("ReporterIons",
                   description="an example",
                   name="my reporter ions",
                   reporterNames=c("myrep1","myrep2"),
                   mz=c(121,122),
                   col=c("red","blue"),
                   width=0.05)
newReporter
#> Object of class "ReporterIons"
#> my reporter ions: 'an example' with 2 reporter ions
#>  - [myrep1] 121 +/- 0.05 (red)
#>  - [myrep2] 122 +/- 0.05 (blue)