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  • Title: TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform.
    Author: Mirzaei M, Pascovici D, Wu JX, Chick J, Wu Y, Cooke B, Haynes P, Molloy MP.
    Journal: Methods Mol Biol; 2017; 1549():45-66. PubMed ID: 27975283.
    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.
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