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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.

The world existed before me. I am a visitor, a temporary visitor, in the infinity of existence. The reality lived by those who visited before me has congealed into its own pastness. Yet it is ever present in the present that I am living, contained “within” it. The future, still awaiting its realisation, is open: packed full of tomorrows.

I am here and I am there, about to arrive and at the same time somewhere else. Is it possible in this dense forest of time to see what lies behind or ahead? Who is there behind me? Or in front of me? If I indeed know myself, do I know these other mes? If the answer is in the affirmative, has someone betrayed someone? What is truth, and whose property is it?

Let the murmuring pasts speak out.

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.

The world existed before me. I am a visitor, a temporary visitor, in the infinity of existence. The reality lived by those who visited before me has congealed into its own pastness. Yet it is ever present in the present that I am living, contained “within” it. The future, still awaiting its realisation, is open: packed full of tomorrows.

I am here and I am there, about to arrive and at the same time somewhere else. Is it possible in this dense forest of time to see what lies behind or ahead? Who is there behind me? Or in front of me? If I indeed know myself, do I know these other mes? If the answer is in the affirmative, has someone betrayed someone? What is truth, and whose property is it?

Let the murmuring pasts speak out.

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.

The world existed before me. I am a visitor, a temporary visitor, in the infinity of existence. The reality lived by those who visited before me has congealed into its own pastness. Yet it is ever present in the present that I am living, contained “within” it. The future, still awaiting its realisation, is open: packed full of tomorrows.

I am here and I am there, about to arrive and at the same time somewhere else. Is it possible in this dense forest of time to see what lies behind or ahead? Who is there behind me? Or in front of me? If I indeed know myself, do I know these other mes? If the answer is in the affirmative, has someone betrayed someone? What is truth, and whose property is it?

Let the murmuring pasts speak out.

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.