title: Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots.
abstract: OBJECTIVE
  To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants.
  
  
  RESULTS
  A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.
  
  
  CONCLUSIONS
  The in-house protein database is a feasible and innovative strategy for proteomic research on non-model plants.
authors.affiliation: Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou, 510631, China.
authors.forename: Chanjuan
authors.initials: C
authors.lastname: Ning
authors.affiliation: Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou, 510631, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Qin
authors.affiliation: Cooperative Wildlife Research Laboratory and Department of Zoology, Southern Illinois University Carbondale, Carbondale, IL, 62901, USA.
authors.forename: Da
authors.initials: D
authors.lastname: Chen
authors.affiliation: Department of Biology, Molecular Cell Biology, Lund University, 22467, Lund, Sweden.
authors.forename: Lars Olof
authors.initials: LO
authors.lastname: Björn
authors.affiliation: Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou, 510631, China. lishsh@scnu.edu.cn.
authors.forename: Shaoshan
authors.initials: S
authors.lastname: Li
mesh_terms: D030562:Databases, Protein; D023281:Genomics / Q000379:methods*; D019216:Metals, Heavy / Q000633:toxicity*; D019697:Onions / Q000187:drug effects* / Q000378:metabolism; D018517:Plant Roots / Q000187:drug effects* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*
chemical_list: D019216:Metals, Heavy
keywords: In-house database; Non-model plants; Proteomic research; Restriction enzyme map; Unigenes