title: An improvement of shotgun proteomics analysis by adding next-generation sequencing transcriptome data in orange.
abstract: BACKGROUND
  Shotgun proteomics data analysis usually relies on database search. Because commonly employed protein sequence databases of most species do not contain sufficient protein information, the application of shotgun proteomics to the research of protein sequence profile remains a big challenge, especially to the species whose genome has not been sequenced yet.
  
  
  RESULTS
  In this paper, we present a workflow with integrated database to partly address this problem. First, we downloaded the homologous species database. Next, we identified the transcriptome of the sample, created a protein sequence database based on the transcriptome data, and integtrated it with homologous species database. Lastly, we developed a workflow for identifying peptides simultaneously from shotgun proteomics data.
  
  
  CONCLUSIONS
  We used datasets from orange leaves samples to demonstrate our workflow. The results showed that the integrated database had great advantage on orange shotgun proteomics data analysis compared to the homologous species database, an 18.5% increase in number of proteins identification.
authors: The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, PR China.
authors: Jiaping
authors: J
authors: Song
authors: Renjie
authors: R
authors: Sun
authors: Dazhi
authors: D
authors: Li
authors: Fengji
authors: F
authors: Tan
authors: Xin
authors: X
authors: Li
authors: Pingping
authors: P
authors: Jiang
authors: Xinjie
authors: X
authors: Huang
authors: Liang
authors: L
authors: Lin
authors: Ziniu
authors: Z
authors: Deng
authors: Yong
authors: Y
authors: Zhang
mesh_terms: D032084:Citrus sinensis / Q000235:genetics* / Q000378:metabolism*; D030541:Databases, Genetic; D030562:Databases, Protein; D018506:Gene Expression Regulation, Plant; D058977:Molecular Sequence Annotation; D010455:Peptides / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010455:Peptides; D010940:Plant Proteins