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An evaluation for cross‐species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data
Author(s) -
Huang Mei,
Chen Tong,
Chan ZhuLong
Publication year - 2006
Publication title -
rapid communications in mass spectrometry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.528
H-Index - 136
eISSN - 1097-0231
pISSN - 0951-4198
DOI - 10.1002/rcm.2631
Subject(s) - mascot , chemistry , tandem mass spectrometry , database search engine , proteomics , tandem , computational biology , sequence (biology) , peptide , protein sequencing , sequence database , peptide mass fingerprinting , database , mass spectrometry , peptide sequence , search engine , chromatography , information retrieval , biochemistry , computer science , biology , gene , materials science , political science , law , composite material
With 1383 tandem mass spectra derived from 120 individual protein spots separated by the two‐dimensional (2‐D) gel electrophoresis of protein samples from three different species, comparative analyses were performed by searching the Expressed Sequence Tag (EST) database (DB) and the NCBI non‐redundant (nr) DB of green plants, respectively, which uses the Mascot search engine to establish a statistical basis. It was confirmed that the former could identify more peptides manually validated by de novo sequencing (DNS) from fewer species in more closely phylogenetic relationships than the latter in a statistically significant manner. Our data demonstrated that correct peptide identifications were given low Mascot scores (e.g. 6–14) and incorrect peptide identifications were given high Mascot scores (e.g. 68–83). Our data also showed that the current evaluation approaches to protein assignments are unsatisfactory because a few ‘false‐positive’ proteins are recognized and several ‘false‐negative’ proteins are rescued by manual validation. Copyright © 2006 John Wiley & Sons, Ltd.