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TMT 6/10-plex sets

TMT6.Rd

This instance of class "ReporterIons" corresponds to the TMT 6-plex set, i.e the 126, 127, 128, 129, 130 and 131 isobaric tags. In the TMT7 data set, an unfragmented tag, i.e reporter and attached isobaric tag, is also included at MZ 229. A second TMT6b has slightly different values.

The TMT10 instance corresponds to the 10-plex version. There are spectific HCD (TMT10HCD, same as TMT10) and ETD (TMT10ETD) sets.

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

TMT6
TMT6b
TMT7
TMT7b
TMT10
TMT10ETD
TMT10HCD
TMT11
TMT11HCD

References

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.

See also

iTRAQ4.

Examples

TMT6
#> Object of class "ReporterIons"
#> TMT6: '6-plex TMT tags' with 6 reporter ions
#>  - [TMT6.126] 126.1277 +/- 0.05 (red)
#>  - [TMT6.127] 127.1311 +/- 0.05 (purple)
#>  - [TMT6.128] 128.1344 +/- 0.05 (blue)
#>  - [TMT6.129] 129.1378 +/- 0.05 (steelblue)
#>  - [TMT6.130] 130.1411 +/- 0.05 (green)
#>  - [TMT6.131] 131.1382 +/- 0.05 (yellow)
TMT6[1:2]
#> Object of class "ReporterIons"
#> TMT6[1:2]: 'subset of 6-plex TMT tags' with 2 reporter ions
#>  - [TMT6.126] 126.1277 +/- 0.05 (red)
#>  - [TMT6.127] 127.1311 +/- 0.05 (purple)

TMT10
#> Object of class "ReporterIons"
#> TMT10HCD: '10-plex TMT HCD' with 10 reporter ions
#>  - [126] 126.1277 +/- 0.002 (#8DD3C7)
#>  - [127N] 127.1248 +/- 0.002 (#FFFFB3)
#>  - [127C] 127.1311 +/- 0.002 (#BEBADA)
#>  - [128N] 128.1281 +/- 0.002 (#FB8072)
#>  - [128C] 128.1344 +/- 0.002 (#80B1D3)
#>  - [129N] 129.1315 +/- 0.002 (#FDB462)
#>  - [129C] 129.1378 +/- 0.002 (#B3DE69)
#>  - [130N] 130.1348 +/- 0.002 (#FCCDE5)
#>  - [130C] 130.1411 +/- 0.002 (#D9D9D9)
#>  - [131] 131.1382 +/- 0.002 (#BC80BD)

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)