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*

*Corresponding author for this work

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

23 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationProteome Bioinformatics
Subtitle of host publicationMethods in Molecular Biology
EditorsShivakumar Keerthikumar, Suresh Mathivanan
Place of PublicationNew York
PublisherHumana Press Inc.
Number of pages22
ISBN (Electronic)9781493967407
ISBN (Print)9781493967384
Publication statusPublished - 2017

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • quantitative shotgun proteomics
  • software workflow
  • TMT


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