Practical integration of multi-run iTRAQ data

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

Abstract

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.

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
Chapter13
Pages199-215
Number of pages17
ISBN (Electronic)9781493992324
ISBN (Print)9781493992317
DOIs
Publication statusPublished - 2019

Publication series

NameMethods in Molecular Biology
PublisherHumana Press
Volume1977
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Proteins
Workflow
Databases

Keywords

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

Cite this

Pascovici, D., Song, X., Wu, J., Zaw, T., & Molloy, M. (2019). Practical integration of multi-run iTRAQ data. In C. A. Evans, P. C. Wright, & J. Noirel (Eds.), Mass spectrometry of proteins: methods and protocols (pp. 199-215). (Methods in Molecular Biology; Vol. 1977). New York: Humana Press. https://doi.org/10.1007/978-1-4939-9232-4_13
Pascovici, Dana ; Song, Xiaomin ; Wu, Jemma ; Zaw, Thiri ; Molloy, Mark. / Practical integration of multi-run iTRAQ data. Mass spectrometry of proteins: methods and protocols. editor / Caroline A. Evans ; Phillip C. Wright ; Josselin Noirel. New York : Humana Press, 2019. pp. 199-215 (Methods in Molecular Biology).
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Pascovici, D, Song, X, Wu, J, Zaw, T & Molloy, M 2019, Practical integration of multi-run iTRAQ data. in CA Evans, PC Wright & J Noirel (eds), Mass spectrometry of proteins: methods and protocols. Methods in Molecular Biology, vol. 1977, Humana Press, New York, pp. 199-215. https://doi.org/10.1007/978-1-4939-9232-4_13

Practical integration of multi-run iTRAQ data. / Pascovici, Dana; Song, Xiaomin; Wu, Jemma; Zaw, Thiri; Molloy, Mark.

Mass spectrometry of proteins: methods and protocols. ed. / Caroline A. Evans; Phillip C. Wright; Josselin Noirel. New York : Humana Press, 2019. p. 199-215 (Methods in Molecular Biology; Vol. 1977).

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

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Pascovici D, Song X, Wu J, Zaw T, Molloy M. Practical integration of multi-run iTRAQ data. In Evans CA, Wright PC, Noirel J, editors, Mass spectrometry of proteins: methods and protocols. New York: Humana Press. 2019. p. 199-215. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9232-4_13