Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics
- 16 May 2008
- journal article
- other
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 320 (5878), 938-941
- https://doi.org/10.1126/science.1157956
Abstract
We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.This publication has 28 references indexed in Scilit:
- A Combined Proteome and Transcriptome Analysis of Developing Medicago truncatula SeedsMolecular & Cellular Proteomics, 2007
- PRIDE: new developments and new datasetsNucleic Acids Research, 2007
- PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectraBioinformatics, 2007
- The minimum information about a proteomics experiment (MIAPE)Nature Biotechnology, 2007
- Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designsNature Biotechnology, 2007
- Computational prediction of proteotypic peptides for quantitative proteomicsNature Biotechnology, 2006
- Improving gene annotation using peptide mass spectrometryGenome Research, 2006
- Protein oxidation and agingFree Radical Research, 2006
- Scoring proteomes with proteotypic peptide probesNature Reviews Molecular Cell Biology, 2005
- Analysis of Shotgun Proteomics and RNA Profiling Data from Arabidopsis thaliana ChloroplastsJournal of Proteome Research, 2005