A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science

peer-reviewed · Methods in Molecular Biology · 2016

peer-reviewed · Methods in Molecular Biology · 2016. Reinhard Turetschek et al. The proteomic study of non-model organisms, such as many crop plants, is challenging due to the lack of…
Date 2016-01-01
Type peer-reviewed
Venue Methods in Molecular Biology
Publisher Springer New York
Contribution downstream-application
DOI 10.1007/978-1-4939-3341-9_17
Citations (OpenAlex) 11
Venue 2-year citedness 1.14

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.

Authors

  1. Reinhard Turetschek
  2. David Lyon · University of Copenhagen
  3. Getinet Desalegn
  4. Hans-Peter Kaul
  5. Stefanie Wienkoop

Methods and tools

  • High-throughput de novo for crop proteomics: A proteomic workflow built on high-throughput de novo sequencing for non-model crop plants, where the genome information needed for a database search is missing and cultivars have to be compared anyway.

Cites (10)

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