NDLI: pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in <i>Arabidopsis thaliana</i>

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pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana

Content Provider	Royal Society of Chemistry (RSC)
Author	Baginsky, Sacha Hirsch-Hoffmann, Matthias Gruissem, Wilhelm Baerenfaller, Katja Hull, Roger Bischof, Sylvain Russenberger, Doris Lu, Qingtao Svozil, Julia
Copyright Year	2011
Abstract	pep2pro is a comprehensive proteome analysis database specifically suitable for flexible proteome data analysis. The pep2pro database schema offers solutions to the various challenges of developing a proteome data analysis database and because data integrated in pep2pro are in relational format, it enables flexible and detailed data analysis. The information provided here will facilitate building proteome data analysis databases for other organisms or applications. The capacity of the pep2pro database for the integration and analysis of large proteome datasets was demonstrated by creating the pep2pro dataset, which is an organ-specific characterisation of the Arabidopsis thaliana proteome containing 14 522 identified proteins based on 2.6 million peptide spectrum assignments. This dataset provides evidence of protein expression and reveals organ-specific processes. The high coverage and density of the dataset are essential for protein quantification by normalised spectral counting and allowed us to extract information that is usually not accessible in low-coverage datasets. With this quantitative protein information we analysed organ- and organelle-specific sub-proteomes. In addition we matched spectra to regions in the genome that were not predicted to have protein coding capacity and provide PCR validation for selected revised gene models. Furthermore, we analysed the peptide features that distinguish detected from non-detected peptides and found substantial disagreement between predicted and detected proteotypic peptides, suggesting that large-scale proteomics data are essential for efficient selection of proteotypic peptides in targeted proteomics surveys. The pep2pro dataset is available as a resource for plant systems biology at http://www.pep2pro.ethz.ch.
Starting Page	225
Ending Page	237
Page Count	13
File Format	HTM / HTML PDF
ISSN	17579694
Volume Number	3
Issue Number	3
Journal	Integrative Biology
DOI	10.1039/c0ib00078g
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Proteome Arabidopsis thaliana Protein primary structure Protein Label-free quantification Genome Polymerase chain reaction DNA sequencing Proteomics Systems biology
Content Type	Text
Resource Type	Article
Subject	Medicine Biochemistry Biophysics

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