Proteome data analysis of hairy root of Panax ginseng : use of expressed sequence tag data of Ginseng for the protein identification = 인삼 모상근 프로테옴 데이터 분석 : 인삼 EST database와의 통합 분석에 의한 단백질 동정

Cited 0 time in scopus
Metadata Downloads
Title
Proteome data analysis of hairy root of Panax ginseng : use of expressed sequence tag data of Ginseng for the protein identification = 인삼 모상근 프로테옴 데이터 분석 : 인삼 EST database와의 통합 분석에 의한 단백질 동정
Author(s)
K H Kwon; S I Kim; K W Kim; E A Kim; K Cho; J Y Kim; Y H Kim; D C Yang; Cheol Goo Hur; J S Yoo; Y M Park
Bibliographic Citation
Korean Journal of Plant Biotechnology (Tissue Culture), vol. 29, no. 3, pp. 161-170
Publication Year
2002
Abstract
For the hairy root of Panax ginseng, we have got mass spectrums from MALDI/ TOF/MS analysis and Tandem mass spectrums from ESI/Q-TOF/MS analysis. While mass spectrum provides the molecular weights of peptide fragments digested by protease such as trypsin, tandem mass spectrum produces amino acid sequence of digested peptides. Each amino acid sequences can be a query sequence in BLAST search to identify proteins. For the specimens of animals or plants of which genome sequences were known, we can easily identify expressed proteins from mass spectrums with high accuracy. However, for the other specimens such as ginseng, it is difficult to identify proteins with accuracy since all the protein sequences are not available yet. Here we compared the mass spectrums and the peptide amino acid sequences with ginseng expressed sequence tag (EST) DB. The matched EST sequence was used as a query in BLAST search for protein identification. They could offer the correct protein information by the sequence alignment with EST sequences. 90% of peptide sequences of ESI/Q-TOF/MS are matched with EST sequences. Comparing 68% matches of the same sequences with the nr database of NCBI, we got more matches by 22% from ginseng EST sequence search. In case of peptide mass fingerprinting from MALDI/TOF/MS, only about 19% (9 proteins of 47 spots) among peptide matches from nr DB were correlated with ginseng EST DB. From these results, we suggest that amino acid sequencing using tandem mass spectrum analysis may be necessary for protein identification in ginseng proteome analysis.
Keyword
databaseexpressed sequence tagmass spectrometerPanax ginsengproteome
ISSN
1015-5880
Publisher
South Korea
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.