Literature DB >> 18578521

A statistical model for iTRAQ data analysis.

Elizabeth G Hill1, John H Schwacke, Susana Comte-Walters, Elizabeth H Slate, Ann L Oberg, Jeanette E Eckel-Passow, Terry M Therneau, Kevin L Schey.   

Abstract

We describe biological and experimental factors that induce variability in reporter ion peak areas obtained from iTRAQ experiments. We demonstrate how these factors can be incorporated into a statistical model for use in evaluating differential protein expression and highlight the benefits of using analysis of variance to quantify fold change. We demonstrate the model's utility based on an analysis of iTRAQ data derived from a spike-in study.

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Year:  2008        PMID： 18578521      PMCID： PMC2722948          DOI： 10.1021/pr070520u

Source DB:  PubMed          Journal:  J Proteome Res        ISSN： 1535-3893            Impact factor:   4.466


  15 in total

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2.  Assessing gene significance from cDNA microarray expression data via mixed models.

Authors:  R D Wolfinger; G Gibson; E D Wolfinger; L Bennett; H Hamadeh; P Bushel; C Afshari; R S Paules
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3.  Analysis of variance for gene expression microarray data.

Authors:  M K Kerr; M Martin; G A Churchill
Journal:  J Comput Biol       Date:  2000       Impact factor: 1.479

4.  Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.

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Journal:  Bioinformatics       Date:  2003-10-12       Impact factor: 6.937

5.  Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells.

Authors:  Richard D Unwin; Andrew Pierce; Rod B Watson; David W Sternberg; Anthony D Whetton
Journal:  Mol Cell Proteomics       Date:  2005-04-22       Impact factor: 5.911

6.  Quantitative analysis of protein expression using amine-specific isobaric tags in Escherichia coli cells expressing rhsA elements.

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Journal:  Proteomics       Date:  2005-06       Impact factor: 3.984

7.  Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype.

Authors:  Venkateshwar G Keshamouni; George Michailidis; Catherine S Grasso; Shalini Anthwal; John R Strahler; Angela Walker; Douglas A Arenberg; Raju C Reddy; Sudhakar Akulapalli; Victor J Thannickal; Theodore J Standiford; Philip C Andrews; Gilbert S Omenn
Journal:  J Proteome Res       Date:  2006-05       Impact factor: 4.466

8.  Identification of differentiating neural progenitor cell markers using shotgun isobaric tagging mass spectrometry.

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Journal:  Proteomics       Date:  2006-10       Impact factor: 3.984

10.  Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.

Authors:  Philip L Ross; Yulin N Huang; Jason N Marchese; Brian Williamson; Kenneth Parker; Stephen Hattan; Nikita Khainovski; Sasi Pillai; Subhakar Dey; Scott Daniels; Subhasish Purkayastha; Peter Juhasz; Stephen Martin; Michael Bartlet-Jones; Feng He; Allan Jacobson; Darryl J Pappin
Journal:  Mol Cell Proteomics       Date:  2004-09-22       Impact factor: 5.911
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  50 in total

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Authors:  Phillip D Kim; Bhavinkumar B Patel; Anthony T Yeung
Journal:  J Biomol Tech       Date:  2012-04

Review 2.  Overcoming key technological challenges in using mass spectrometry for mapping cell surfaces in tissues.

Authors:  Noelle M Griffin; Jan E Schnitzer
Journal:  Mol Cell Proteomics       Date:  2010-06-14       Impact factor: 5.911

3.  Tight binding of proteins to membranes from older human cells.

Authors:  Roger J W Truscott; Susana Comte-Walters; Zsolt Ablonczy; John H Schwacke; Yoke Berry; Anastasia Korlimbinis; Michael G Friedrich; Kevin L Schey
Journal:  Age (Dordr)       Date:  2010-12-23

4.  Relative quantification: characterization of bias, variability and fold changes in mass spectrometry data from iTRAQ-labeled peptides.

Authors:  Douglas W Mahoney; Terry M Therneau; Carrie J Heppelmann; Leeann Higgins; Linda M Benson; Roman M Zenka; Pratik Jagtap; Gary L Nelsestuen; H Robert Bergen; Ann L Oberg
Journal:  J Proteome Res       Date:  2011-08-02       Impact factor: 4.466

5.  AKAP signaling in reinstated cocaine seeking revealed by iTRAQ proteomic analysis.

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Journal:  J Neurosci       Date:  2011-04-13       Impact factor: 6.167

6.  Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVA.

Authors:  Ann L Oberg; Douglas W Mahoney; Jeanette E Eckel-Passow; Christopher J Malone; Russell D Wolfinger; Elizabeth G Hill; Leslie T Cooper; Oyere K Onuma; Craig Spiro; Terry M Therneau; H Robert Bergen
Journal:  J Proteome Res       Date:  2008-01-04       Impact factor: 4.466

7.  Proteome changes in Oncidium sphacelatum (Orchidaceae) at different trophic stages of symbiotic germination.

Authors:  R B S Valadares; S Perotto; E C Santos; M R Lambais
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8.  Evaluation of normalization methods to pave the way towards large-scale LC-MS-based metabolomics profiling experiments.

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Journal:  OMICS       Date:  2013-06-29

9.  Quantification of protein expression changes in the aging left ventricle of Rattus norvegicus.

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Review 10.  Quality assessment for clinical proteomics.

Authors:  David L Tabb
Journal:  Clin Biochem       Date:  2012-12-12       Impact factor: 3.281
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