Research Report 2010 - MDC

has become a standardized data flow and initial sets ofall encoded proteins can be generated in a computerassistedand automated way.The integration of metabolomic and proteomics technologiesinto the annotation process gives an experimentalvalidation of in silico gene models as well as toimproved accuracy of existing gene models.BIMSB systems databaseGuido Mastrobuoni, Matthias Pietzke and ChristophDieterichModern “-omics” technologies like transcriptomics, proteomicsand metabolomics are established at BIMSB.Those techniques generate large amounts of data andcover a wide range of biological processes. To analyzeand store such large amounts of data from these technologieswe are establishing the BIMSB systems database.The database will consist of several modules fordata input and subsequent data analysis and comparison,thus it will connect the analytical platforms withcomputational biologists (see figure 2). It will help tostructure and synchronize large datasets from multipleanalytical platforms and will build up the basis for integrativeanalyses.Figure 1. Functional categories of identified planarian proteins. Totalprotein extract from whole worm was enzymatically digested andthe resulting peptide mixture analyzed by LC-MS/MS on an Orbitrapmass spectrometer. The first analysis allowed the matching ofaround 35% of MS/MS peptide fragmentation spectra to proteinsequences from a database of predicted gene products.Selected PulicationsMay P, Christian JO, Kempa S and Walther D (2009) ChlamyCyc: anintegrative systems biology database and web-portal forChlamydomonas reinhardtii. BMC Genomics 4;10:209Kempa S, Hummel J, Schwemmer T, Pietzke M, Strehmel N, Wienkoop S,Kopka J and Weckwerth W (2009) An automated GCxGC-TOF-MS protocolfor batch-wise extraction and alignment of mass isotopomer matrixesfrom differential 13C-labelling experiments: a case study forphotoautotroph-mixotroph grown Chlamydomonas reinhardtii cells. JBasic Microbiol. 49(1):82-91Kempa S, May P, Wienkoop S, Usadel B, Christian N, Rupprecht J, Weiss J,Recuenco Munoz L, Ebenhöh O, Weckwerth W and Walther D (2008)Metabolomics and Proteomics Assisted Genome Annotation andAnalysis of the Draft Metabolic Network of Chlamydomonas reinhardtii.Genetics 179: 1–10Kempa S, Krasensky J, Dal Santo S, Kopka J and Jonak C (2008) A centralrole of abscisic acid in stress regulated carbohydrate metabolism. PLoSONE 3(12):e3935Kempa S, Rozhon W, Šamaj J, Erban A, Baluška F, Becker T, Haselmayer J,Schleiff E, Kopka J, Hirt H and Jonak C (2007) A plastid localized glycogensynthase kinase 3 modulates stress tolerance and carbohydratemetabolism. Plant J. 49(6):1076-90Figure 2. Scheme of BIMSB systems database. The database consists ofseveral modules from data input, analysis, storage and subsequentanalyses. It will be a tool to analyze large datasets from different analyticalplatforms and will allow interspecies comparison on a quantitativelevel. The aim of the database is to connect the analytical platformswith the computational biologists at the BIMSB.Berlin Institute of Medical Systems Biology 197