s obtained from a complex extract. Additionally, the sequencing of phosphopeptides is often difficult because the most widely used phosphopeptide fragmentation techniques in mass spectrometry induce dissociation primarily of the phosphate bond. This leads to the observation of a prominent loss of phosphate from the peptide but low fragmentation between amino acids, 
yielding low sequence information. In spite of these difficulties, the recent development of mass spectrometry-based phosphoproteomics technology that uses IMAC purification of phosphopeptides from complex mixtures has allowed rapid and large-scale identification of numerous in vivo phosphorylation sites. IMAC is based on the affinity of positively charged trivalent metal ions for negatively charged phosphate groups. The conversion of carboxylic acid groups to methyl esters prior to IMAC has greatly increased the specificity of phosphopeptide isolation. This modification reduces the binding of the otherwise acidic carboxyl groups to the metal ions. Several protocols have been used successfully for studying the phosphoproteome of Arabidopsis. Our data show that a protocol that was initially developed for the analysis of phosphorylation sites of yeast proteins, is very suitable for plant work. We have used the combination of IMAC and LC-MS/MS/MS to determine novel phosphorylation sites of intracellular Arabidopsis proteins, allowing the large-scale identification of phosphopeptides in a single LCMS/MS/MS run. As a proof of concept, we focused here on a group of highly phosphorylated proteins that are related to RNA metabolism. The data show that proteins containing RS domains are common targets of phosphorylation. Since these domains are present in many proteins in plants, these data may be generally applicable for other RS proteins. The conservation of the determined phosphorylation sites suggests that some of our results might even be extrapolated to other eukaryotes. In vivo phosphorylation of SR proteins By studying the nuclear and cytosolic phosphoproteomes of Arabidopsis globally, we determined 79 in vivo phosphorylation sites derived from 22 proteins involved in different aspects of RNA metabolism. SR proteins represented a prominent part of this group. Although several SR proteins have been shown to be phosphorylated in plants, none of the identified sites was described before. Our evidence shows that plant SR proteins, like their animal counterparts, are extensively phosphorylated at Ser residues in their RS domains. In extracts from PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19815280 a single cell type, 12 of the 19 SR proteins were identified as phosphoproteins. One peptide could not be assigned to either SRZ22/RSZ22 or RSZ22a, but since this peptide was detected six times it is possible that it is derived from both proteins. Although the other seven members may not be phosphoproteins, it is more likely that they are not expressed in the root cell culture used for our analysis or that they are of too low abundance to be detected. In total, we identified phosphorylation sites in the RS domains of 15 proteins. This indicates that RS domains of plant proteins are general targets of phosphorylation. The conservation of SR proteins suggests that our results can be extrapolated to other plant species. Since the RS domains of SR proteins are involved in proteinprotein interactions, which can be buy BCTC phosphorylation-dependent, the highly repetitive RS/SP motifs can possibly generate multiple protein-binding sites depending on the
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