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Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.

Proteomics, the systematic identification of proteins, has become an important asset for the study of cellular processes in a systems biology context. During the last few years significant technological improvements have been reported for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. With the maturation of proteomics technology, scientists now aim at proteome-wide protein identification to complement data from genome-wide transcriptional profiling and metabolomics experiments. A complete map of the proteome is expected to provide important information on genome activities and gene structures. Peptides identified in proteomics experiments are extremely valuable because they manifest the expression of a gene and thus complement the annotation of open reading frames and confirm or correct gene structure prediction. Furthermore, knowledge of repeatedly identified peptides in large-scale proteomics experiments allows peptide arrays with a selected set of proteotypic peptides for absolute protein quantification to be designed. Last but not least, knowledge of protein abundance, posttranslational modification and localisation is the key to a better understanding of the molecular mechanisms of cell functioning and pathway compartmentalisation. In this chapter, we will briefly highlight the current status of Arabidopsis proteomics and discuss existing limitations and anticipated new developments in plant proteomics.