title: TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform.
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.
authors.affiliation: Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirzaei
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia.
authors.forename: Dana
authors.initials: D
authors.lastname: Pascovici
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia.
authors.forename: Jemma X
authors.initials: JX
authors.lastname: Wu
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Chick
authors.affiliation: Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
authors.forename: Yunqi
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia.
authors.forename: Brett
authors.initials: B
authors.lastname: Cooke
authors.affiliation: Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Haynes
authors.affiliation: Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia. mmolloy@proteome.org.au.|Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, E8C310, Research Park Drive, Sydney, NSW, 2109, Australia. mmolloy@proteome.org.au.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Molloy
mesh_terms: D002853:Chromatography, Liquid; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D011499:Protein Processing, Post-Translational; D059748:Proteolysis; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012984:Software; D013194:Staining and Labeling; D013223:Statistics as Topic / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*; D064878:Web Browser; D057188:Workflow
chemical_list: D020543:Proteome
keywords: Quantitative shotgun proteomics; Software workflow; TMT