| Chapter title |
TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform.
|
|---|---|
| Chapter number | 5 |
| Book title |
Proteome Bioinformatics
|
| Published in |
Methods in molecular biology, January 2017
|
| DOI | 10.1007/978-1-4939-6740-7_5 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6738-4, 978-1-4939-6740-7
|
| Authors |
Mehdi Mirzaei, Dana Pascovici, Jemma X. Wu, Joel Chick, Yunqi Wu, Brett Cooke, Paul Haynes, Mark P. Molloy, Mirzaei, Mehdi, Pascovici, Dana, Wu, Jemma X., Chick, Joel, Wu, Yunqi, Cooke, Brett, Haynes, Paul, Molloy, Mark P. |
| Editors |
Shivakumar Keerthikumar, Suresh Mathivanan |
| 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. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 19 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 5 | 26% |
| Professor > Associate Professor | 2 | 11% |
| Professor | 2 | 11% |
| Researcher | 2 | 11% |
| Student > Doctoral Student | 1 | 5% |
| Other | 1 | 5% |
| Unknown | 6 | 32% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 4 | 21% |
| Agricultural and Biological Sciences | 3 | 16% |
| Neuroscience | 3 | 16% |
| Immunology and Microbiology | 1 | 5% |
| Computer Science | 1 | 5% |
| Other | 2 | 11% |
| Unknown | 5 | 26% |