TMT6: TMT 6/10-plex sets

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description

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, Sch\"afer 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
TMT6[1:2]

TMT10

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

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.16.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

    trimws

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)
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)
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)
Object of class "ReporterIons"
my reporter ions: 'an example' with 2 reporter ions
 - [myrep1] 121 +/- 0.05 (red)
 - [myrep2] 122 +/- 0.05 (blue)

MSnbase documentation built on Jan. 23, 2021, 2 a.m.