Efficiency improvement of peptide identification for an organism without complete genome sequence, using expressed sequence tag database and tandem mass spectral data

We compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) p...

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Bibliographic Details
Published in:Proteomics (Weinheim) 2003-12, Vol.3 (12), p.2305-2309
Main Authors: Kwon, Kyung-Hoon, Kim, Mioak, Kim, Jin Young, Kim, Kyung Wook, Kim, Seung Il, Park, Young Mok, Yoo, Jong Shin
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Computational Biology
Database search
Databases, Protein
de novo sequencing
Expressed Sequence Tag
Expressed Sequence Tags
Genome
Molecular Sequence Data
Peptides - genetics
Plants - chemistry
Plants - genetics
Proteomics
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Tandem Mass Spectrum
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Summary:We compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) protein DB of green plants using either the MASCOT or SEQUEST software program, it was confirmed that the former is as accurate as the latter. Peptides identified from EST DB were twice as many as those from the nr protein DB, in spite of the fact that the EST DB has less data (26 222 EST) than the NCBI nr protein DB (224 238). This study demonstrates that EST DB with tandem mass spectra can be used reliably for high‐throughput proteomics studies in an organism without genome information.
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.200300620