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

doi:10.1007/978-1-4939-6740-7_5

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

Australian Proteome Analysis Facility (APAF)

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

29 Citations (Scopus)

Abstract

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 language	English
Title of host publication	Proteome Bioinformatics
Subtitle of host publication	Methods in Molecular Biology
Editors	Shivakumar Keerthikumar, Suresh Mathivanan
Place of Publication	New York
Publisher	Humana Press Inc.
Pages	45-66
Number of pages	22
Volume	1549
ISBN (Electronic)	9781493967407
ISBN (Print)	9781493967384
DOIs	https://doi.org/10.1007/978-1-4939-6740-7_5
Publication status	Published - 2017

Publication series

Name	Methods in Molecular Biology
Volume	1549
ISSN (Print)	1064-3745

Keywords

quantitative shotgun proteomics
software workflow
TMT

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10.1007/978-1-4939-6740-7_5

Cite this

Mirzaei, M., Pascovici, D., Wu, J. X., Chick, J., Wu, Y., Cooke, B., Haynes, P., & Molloy, M. P. (2017). TMT one-stop shop: from reliable sample preparation to computational analysis platform. In S. Keerthikumar, & S. Mathivanan (Eds.), Proteome Bioinformatics: Methods in Molecular Biology (Vol. 1549, pp. 45-66). (Methods in Molecular Biology; Vol. 1549). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-6740-7_5

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abstract = "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.",

keywords = "quantitative shotgun proteomics, software workflow, TMT",

author = "Mehdi Mirzaei and Dana Pascovici and Wu, {Jemma X.} and Joel Chick and Yunqi Wu and Brett Cooke and Paul Haynes and Molloy, {Mark P.}",

year = "2017",

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language = "English",

isbn = "9781493967384",

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Mirzaei, M , Pascovici, D, Wu, JX, Chick, J, Wu, Y, Cooke, B, Haynes, P & Molloy, MP 2017, TMT one-stop shop: from reliable sample preparation to computational analysis platform. in S Keerthikumar & S Mathivanan (eds), Proteome Bioinformatics: Methods in Molecular Biology. vol. 1549, Methods in Molecular Biology, vol. 1549, Humana Press Inc., New York, pp. 45-66. https://doi.org/10.1007/978-1-4939-6740-7_5

TMT one-stop shop: from reliable sample preparation to computational analysis platform. / Mirzaei, Mehdi ; Pascovici, Dana; Wu, Jemma X. et al.
Proteome Bioinformatics: Methods in Molecular Biology. ed. / Shivakumar Keerthikumar; Suresh Mathivanan. Vol. 1549 New York: Humana Press Inc., 2017. p. 45-66 (Methods in Molecular Biology; Vol. 1549).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

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TMT one-stop shop: from reliable sample preparation to computational analysis platform

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