TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform

  • Mehdi Mirzaei
  • Dana Pascovici
  • Jemma X. Wu
  • Joel Chick
  • Yunqi Wu
  • Brett Cooke
  • Paul Haynes
  • Mark P. Molloy
Part of the Methods in Molecular Biology book series (MIMB, volume 1549)


In this chapter we describe the workflow we use for labeled quantitative proteomics analysis using tandem mass tags (TMT) starting with the sample preparation and ending with the multivariate analysis of the resulting data. We detail the step-by-step process from sample processing, labeling, fractionation, and data processing using Proteome Discoverer through to data analysis and interpretation in the context of a multi-run experiment. The final analysis and data interpretation rely on an R package we call TMTPrepPro, which are deployed on a local GenePattern server, and used for generating various outputs which are also outlined herein.

Key words

Quantitative shotgun proteomics TMT Software workflow 


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Mehdi Mirzaei
    • 1
  • Dana Pascovici
    • 2
  • Jemma X. Wu
    • 2
  • Joel Chick
    • 3
  • Yunqi Wu
    • 1
  • Brett Cooke
    • 2
  • Paul Haynes
    • 1
  • Mark P. Molloy
    • 1
    • 2
  1. 1.Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular SciencesMacquarie UniversitySydneyAustralia
  2. 2.Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis FacilityMacquarie UniversitySydneyAustralia
  3. 3.Department of Cell BiologyHarvard Medical SchoolBostonUSA

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