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
2016
Peer reviewed
Yes
Austrian Fields of Science 2012
106037 Proteomics, 106030 Plant ecology
Keywords
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