Scripps VIVO scripps research logo

  • Index
  • Log in
  • Home
  • People
  • Organizations
  • Research
  • Events
Search form

Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method

Academic Article
uri icon
  • Overview
  • Research
  • Identity
  • Additional Document Info
  • View All
scroll to property group menus

Overview

authors

  • Rauniyar, N.
  • Gao, B. B.
  • McClatchy, D. B.
  • Yates III, John

publication date

  • February 2013

journal

  • Journal of Proteome Research  Journal

abstract

  • Stable isotope labeling via isobaric derivatization of peptides is a universally applicable approach that enables concurrent identification and quantification of proteins in different samples using tandem mass spectrometry. In this study, we evaluated the performance of amine-reactive isobaric tandem mass tag (TMT), available as duplex and sixplex sets, with regard to their ability to elucidate protein expression changes. Using rat brain tissue from two different developmental time points, postnatal day 1 (p1) and 45 (p45), as a model system, we compared the protein expression ratios (p45/p1) observed using duplex TMT tags in triplicate measurements versus sixplex tag in a single LC-MS/MS analysis. A correlation of 0.79 in relative protein abundance was observed in the proteins quantified by these two sets of reagents. However, more proteins passed the criteria for significant fold change (-1.0 ≤ log(2) ratio (p45/p1) ≥ +1.0 and p < 0.05) in the sixplex analysis. Nevertheless, in both methods most proteins showing significant fold change were identified by multiple spectra, increasing their quantification precision. Additionally, the fold change in p45 rats against p1, observed in TMT experiments, was corroborated by a metabolic labeling strategy where relative quantification of differentially expressed proteins was obtained using (15)N-labeled p45 rats as an internal standard.

subject areas

  • Animals
  • Animals, Newborn
  • Brain Chemistry
  • Chromatography, Liquid
  • Gene Expression Regulation, Developmental
  • Isotope Labeling
  • Nerve Tissue Proteins
  • Peptide Fragments
  • Proteomics
  • Rats
  • Rats, Sprague-Dawley
  • Staining and Labeling
  • Tandem Mass Spectrometry
scroll to property group menus

Research

keywords

  • MudPIT
  • SILAM
  • TMT
  • isobaric tag
  • mass spectrometry
  • metabolic labeling
  • quantitative proteomics
  • tandem mass tag
scroll to property group menus

Identity

PubMed Central ID

  • PMC3751587

International Standard Serial Number (ISSN)

  • 1535-3893

Digital Object Identifier (DOI)

  • 10.1021/pr3008896

PubMed ID

  • 23214967
scroll to property group menus

Additional Document Info

start page

  • 1031

end page

  • 1039

volume

  • 12

issue

  • 2

©2021 The Scripps Research Institute | Terms of Use | Powered by VIVO

  • About
  • Contact Us
  • Support