title: A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science.
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.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, 1090, Austria.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Turetschek
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, 1090, Austria.
authors.forename: David
authors.initials: D
authors.lastname: Lyon
authors.affiliation: Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria.
authors.forename: Getinet
authors.initials: G
authors.lastname: Desalegn
authors.affiliation: Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Austria.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Kaul
authors.affiliation: Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, 1090, Austria. stefanie.wienkoop@univie.ac.at.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wienkoop
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods; D018556:Crops, Agricultural / Q000235:genetics* / Q000378:metabolism*; D030541:Databases, Genetic; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D040901:Proteomics / Q000379:methods*; D049490:Systems Biology / Q000379:methods*; D053719:Tandem Mass Spectrometry
keywords: Crop science; Cultivars; De novo sequencing; Mass spectrometry; Pisum sativum; Polymorphism; Proteomics