Subproteomic tools to increase genome annotation complexity

Comprehensive and precise annotations of short protein-coding genes are always a challenging task. Here we propose a new design to facilitate the characterization of previously overlooked short protein-coding genes by integrating a shotgun proteomics method and oligonucleotide array analysis. Using...

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Published in:Proteomics (Weinheim) 2008-10, Vol.8 (20), p.4209-4213
Main Authors: Wei, Candong, Peng, Junping, Xiong, Zhaohui, Yang, Jian, Wang, Jing, Jin, Qi
Format: Article
Language:English
Subjects:
2‐D LC‐MS/MS
Analytical, structural and metabolic biochemistry
Bacterial Proteins - analysis
Bacterial Proteins - isolation & purification
Biological and medical sciences
Chromatography, Liquid
Computational Biology - methods
Fundamental and applied biological sciences. Psychology
Genome, Bacterial
Miscellaneous
Oligonucleotide array
Oligonucleotide Array Sequence Analysis - methods
Open Reading Frames
Proteins
Proteomics - methods
Shigella flexneri - chemistry
Software
Subproteomic
Tandem Mass Spectrometry
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cited_by cdi_FETCH-LOGICAL-c3976-16c2e0e8b8a8c8d33255f609afbc401d9aebca322912daafd461654ae349d6563
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container_end_page 4213
container_issue 20
container_start_page 4209
container_title Proteomics (Weinheim)
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creator Wei, Candong
Peng, Junping
Xiong, Zhaohui
Yang, Jian
Wang, Jing
Jin, Qi
description Comprehensive and precise annotations of short protein-coding genes are always a challenging task. Here we propose a new design to facilitate the characterization of previously overlooked short protein-coding genes by integrating a shotgun proteomics method and oligonucleotide array analysis. Using Shigella flexneri as a model, we validate 163 annotated ORFs and 51 hypothetical or putative transcripts at the protein level, and discover four novel short ORFs. This strategy will contribute significantly to comprehensive and accurate genome-wide annotation, and to our understanding of prokaryotic genome structure.
doi_str_mv 10.1002/pmic.200800226
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source Wiley-Blackwell Read & Publish Collection
subjects 2‐D LC‐MS/MS
Analytical, structural and metabolic biochemistry
Bacterial Proteins - analysis
Bacterial Proteins - isolation & purification
Biological and medical sciences
Chromatography, Liquid
Computational Biology - methods
Fundamental and applied biological sciences. Psychology
Genome, Bacterial
Miscellaneous
Oligonucleotide array
Oligonucleotide Array Sequence Analysis - methods
Open Reading Frames
Proteins
Proteomics - methods
Shigella flexneri - chemistry
Software
Subproteomic
Tandem Mass Spectrometry
title Subproteomic tools to increase genome annotation complexity
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