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
Corresponding Authorhuxiangyang@mail.kib.ac.cn
2011-09-01
Source PublicationPLANT OMICS
ISSN1836-0661
Volume4Issue:5Pages:257-263
AbstractThe 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.
KeywordCross-species Protein Database Peptide Mass Fingerprinting Protein Identification Proteomics
Subject AreaPlant Sciences
Indexed BySCI
Language英语
WOS Research AreaPlant Sciences
WOS SubjectPlant Sciences
WOS IDWOS:000295958300004
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/3960
Collection中国科学院东亚植物多样性与生物地理学重点实验室
Affiliation1.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
Recommended Citation
GB/T 7714
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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