Improved protein identification using a species- specific protein/peptide database derived from expressed sequence tags
Chen, Jinhui2,3; Shi, Jisen3; Tian, Dagang2; Yang, Liming2; Luo, Yuming2; Yin, Denghua2; Hu, Xiangyang1
2011-09-01
发表期刊PLANT OMICS
ISSN1836-0661
卷号4期号:5页码:257-263
摘要The use of peptide mass fingerprinting data obtained by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry in conjunction with protein database searching is a fast, high-throughput method that is widely used to identify proteins in a proteome. The success of a search is limited, however, by the number of proteins represented in the database. When the fully sequenced genome of an organism is not available, cross-species databases are usually used, which can compromise the reliability of the results. Databases containing expressed sequence tag sequences are available and are potentially invaluable resources for proteomic studies. For the study reported herein, we developed a proteomic approach that incorporates a species-specific protein/peptide database constructed from expressed sequence tag sequences, and we validated this approach by accurately retrieving proteins from this database that matched, on the basis of the masses of their in silico-generated tryptic peptides, experimentally isolated proteins derived from a wheat stem proteome. We also compared the results obtained using the wheat database with those obtained using the same peptide mass fingerprints and a cross-species protein database search. Given the reliability of the results and the improved scoring obtained with the wheat database study in comparison with the cross-species database study, species-specific databases derived from expressed sequence tags may replace cross-species databases for proteomic studies involving organisms for which a completely sequenced genome is unavailable.
关键词Cross-species Protein Database Peptide Mass Fingerprinting Protein Identification Proteomics
资助信息National Science Foundation of China[30901156, 31170619, 30930077, 30871704, 30971452, 31170256]; Chinese National Forest Bureau[2009-4-24]; Natural Science Foundation of Jiangsu University[09KJA220001]
学科领域Plant Sciences
收录类别SCI
语种英语
WOS研究方向Plant Sciences
WOS类目Plant Sciences
WOS记录号WOS:000295958300004
引用统计
被引频次:4[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/3960
专题中国科学院东亚植物多样性与生物地理学重点实验室
作者单位1.Chinese Acad Sci, Key Lab Biodivers & Biogeog, Kunming Inst Bot, Inst Tibet Plateau Res Kunming, Kunming 650204, Peoples R China
2.Huaiyin Normal Univ, Sch Life Sci, Jiangsu Key Lab Ecoagr Biotechnol Hongze Lake, Huaian 223300, Jiangsu, Peoples R China
3.Nanjing Forestry Univ, Key Lab Forest Genet & Biotechnol, Minist Educ, Nanjing 210037, Peoples R China
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Chen, Jinhui,Shi, Jisen,Tian, Dagang,et al. Improved protein identification using a species- specific protein/peptide database derived from expressed sequence tags[J]. PLANT OMICS,2011,4(5):257-263.
APA Chen, Jinhui.,Shi, Jisen.,Tian, Dagang.,Yang, Liming.,Luo, Yuming.,...&Hu, Xiangyang.(2011).Improved protein identification using a species- specific protein/peptide database derived from expressed sequence tags.PLANT OMICS,4(5),257-263.
MLA Chen, Jinhui,et al."Improved protein identification using a species- specific protein/peptide database derived from expressed sequence tags".PLANT OMICS 4.5(2011):257-263.
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