Practical integration of multi-run iTRAQ data

Dana Pascovici, Xiaomin Song, Jemma Wu, Thiri Zaw, Mark Molloy*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


In this chapter, we describe some of the approaches we employ in the analysis of iTRAQ data in our group, with an emphasis on practical issues that can occur in larger multi-run projects. Our pipeline starts with a well-established iTRAQ workflow, makes use of protein level quantitation using ProteinPilot, and continues either via a global analysis in the presence of a common reference, or by identifying pairwise comparisons of interest and applying a method taking the protein ratios and protein ratio confidence measures into consideration. Additionally we describe what issues can occur in the more subtle scenarios involving composite databases in multi-run situations, and an approach applicable in that setting.

Original languageEnglish
Title of host publicationMass spectrometry of proteins
Subtitle of host publicationmethods and protocols
EditorsCaroline A. Evans, Phillip C. Wright, Josselin Noirel
Place of PublicationNew York
PublisherHumana Press
Number of pages17
ISBN (Electronic)9781493992324
ISBN (Print)9781493992317
Publication statusPublished - 2019

Publication series

NameMethods in Molecular Biology
PublisherHumana Press
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Mass spectrometry
  • Quantitative proteomics
  • iTRAQ
  • Data processing
  • Replication


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