TMT one-stop shop:from reliable sample preparation to computational analysis platform
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| Title: | TMT one-stop shop:from reliable sample preparation to computational analysis platform |
|---|---|
| Authors: | Mirzaei, Mehdi, Pascovici, Dana, Wu, Jemma X., Chick, Joel, Wu, Yunqi, Cooke, Brett, Haynes, Paul, Molloy, Mark P. |
| Contributors: | Keerthikumar, Shivakumar, Mathivanan, Suresh |
| Source: | 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 , Methods in Molecular Biology , vol. 1549 , New York , pp. 45-66 . https://doi.org/10.1007/978-1-4939-6740-7_5 |
| Publication Year: | 2017 |
| Subject Terms: | quantitative shotgun proteomics, software workflow, TMT |
| Description: | 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. |
| Document Type: | book part |
| Language: | English |
| ISBN: | 978-1-4939-6738-4 1-4939-6738-X |
| Relation: | urn:ISBN:9781493967384 |
| DOI: | 10.1007/978-1-4939-6740-7_5 |
| Availability: | https://researchers.mq.edu.au/en/publications/fa70f13c-08d8-4eab-b096-16c8afe3cbbe https://doi.org/10.1007/978-1-4939-6740-7_5 http://www.scopus.com/inward/record.url?scp=85006374960&partnerID=8YFLogxK |
| Rights: | info:eu-repo/semantics/closedAccess |
| Accession Number: | edsbas.C45CF363 |
| Database: | BASE |
Nájsť tento článok vo Web of Science | 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. |
|---|---|
| ISBN: | 9781493967384 149396738X |
| DOI: | 10.1007/978-1-4939-6740-7_5 |