MSnbase: iTRAQ4 – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

iTRAQ4

iTRAQ 4-plex set

Description

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.

Examples

iTRAQ4
iTRAQ4[1:2]

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

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release