A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science
- Author(s)
- Reinhard Turetschek, David Lyon, Getinet Desalegn, Hans-Peter Kaul, Stefanie Wienkoop
- Abstract
The proteomic study of non-model organisms, such as many crop plants, is challenging due to the lack of comprehensive genome information. Changing environmental conditions require the study and selection of adapted cultivars. Mutations, inherent to cultivars, hamper protein identification and thus considerably complicate the qualitative and quantitative comparison in large-scale systems biology approaches. With this workflow, cultivar-specific mutations are detected from high-throughput comparative MS analyses, by extracting sequence polymorphisms with de novo sequencing. Stringent criteria are suggested to filter for confidential mutations. Subsequently, these polymorphisms complement the initially used database, which is ready to use with any preferred database search algorithm. In our example, we thereby identified 26 specific mutations in two cultivars of Pisum sativum and achieved an increased number (17 %) of peptide spectrum matches.
- Organisation(s)
- External organisation(s)
- Universität für Bodenkultur Wien
- Journal
- Methods in Molecular Biology
- Volume
- 1394
- Pages
- 233-243
- No. of pages
- 11
- ISSN
- 1064-3745
- DOI
- https://doi.org/10.1007/978-1-4939-3341-9_17
- Publication date
- 12-2015
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 106037 Proteomics, 106030 Plant ecology
- Keywords
- ASJC Scopus subject areas
- Genetics, Molecular Biology
- Portal url
- https://ucris.univie.ac.at/portal/en/publications/a-proteomic-workflow-using-highthroughput-de-novo-sequencing-towards-complementation-of-genome-information-for-improved-comparative-crop-science(0b8d794b-254d-49ee-a12c-89ce5fdd226c).html