Technologien & Ressourcen
A Linux server running RStudio (https://www.rstudio.com/) is used for the efficient processing and analysis of large metabolomics datasets. 1TB RAM and 144 cpus allow for fast and parallelized computation of tasks in R from mass spectrometry raw file to result. Practically, we produce peaktables from raw data of our mass spectrometer (GC-MS and high resolution LC-MS) using the R packages TargetSearch (Cuadros-Inostroza et al., 2009), xcms (Smith et al., 2006) and CAMERA (Kuhl et al., 2012). To interpret mass spectral data beyond the possibilities provided by commercial software, tasks like database queries, de-novo sum formula annotation, structure determination by processing and automatized interpretation of MS/MS spectra or statistical cross-omics analyses combining metabolomic with genomic, transcriptional and phenomic data are executed using innovative self-developed R-scripts.
Example publications containing advanced analysis of mass spectrometry data:
Riewe, D., J. Wiebach, T. Altmann (2017) Structure annotation and quantification of wheat seed oxidized lipids by high resolution LC-MS/MS. Plant Physiology, epub ahead of print. 10.1104/pp.17.00470 (open access).
Knoch, D., Riewe, D., Meyer, R.C., Boudichevskaia, A., Schmidt, R., Altmann, T. (2017) Genetic dissection of metabolite variation in Arabidopsis seeds: evidence for mQTL hotspots and a master regulatory locus of seed metabolism. J. Exp. Bot. 68 1655-1667. 10.1093/jxb/erx049 (open access).
Biomek® FXP workstation
Currently a new Biomek FXP pipetting workstation from Beckman is installed at the IPK in the Department of Molecular Genetics (MOG) of Prof. Dr. Altmann.
With its large temperature-controlled deck capacity it expands the future needs for flexible laboratory solutions in all aspects of high throughput liquid handling – including pipetting, dilution, dispensing and integration – into a single, automated system.
The workstation contains a dual-pod pipetting system with a fixed 96-well multichannel pod and an independent span-8 flexible pod that can be used in parallel.
As one of the future central component in the MOG department the workstation is designed as a complete automated system, including extended labware storage, a BRT robotic labware transport system, plate incubation (0°C-70°C), plate washing and Bar-code reading for plates.
Additional components, like a fast capper-decapper-System (CapitAll), a WASP plate heat sealer, a magnetic beads station, a coolable Sigma zentrifuge and a separate and independend accessible Tecan Infinite M200 photometer are integrated and controlled by SAMI® Workstation EX software to maximize capacity and independend through-put of future assay handling.