Showing papers by "Jens Allmer published in 2010"

Systematic computational analysis of potential RNAi regulation in Toxoplasma gondii

Abstract: RNA interference (RNAi) is the mechanism through which RNA interferes with the production of other RNAs in a sequence specific manner. Micro RNA (miRNA) is a type of RNA which is transcribed as pri-miRNAs and processed to pre-miRNAs in the nucleus. These pre-miRNAs are then exported from the nucleus and processed in the cytoplasm to double stranded RNA with one strand providing target specificity‥Toxoplasma gondii is a parasitic apicomplexan which causes several diseases. T. gondii is a good candidate for computational efforts with its small and publicly available genome files and extensive information about its gene structure. Although the existence of RNA interference in T. gondii is being debated, establishment of its complete potential RNAi regulatory network may be beneficial for further investigations into the topic.

Label-free quantitation, an extension to 2DB

Abstract: Determining the differential expression of proteins under different conditions is of major importance in proteomics Since mass spectrometry-based proteomics is often used to quantify proteins, several labelling strategies have been developed While these are generally more precise than label-free quantitation approaches, they imply specifically designed experiments which also require knowledge about peptides that are expected to be measured and need to be modified We recently designed the 2DB database which aids storage, analysis, and publication of data from mass spectrometric experiments to identify proteins This database can aid identifying peptides which can be used for quantitation Here an extension to the database application, named MSMAG, is presented which allows for more detailed analysis of the distribution of peptides and their associated proteins over the fractions of an experiment Furthermore, given several biological samples in the database, label-free quantitation can be performed Thus, interesting proteins, which may warrant further investigation, can be identified en passant while performing high-throughput proteomics studies

Relative protein quantitation with post translational modifications in mass spectrometry based proteomics

Abstract: Mass spectrometry has become the tool of choice for most investigations in proteomics. Identification of proteins from complex mixtures has long been achieved and is now routinely used in countless high throughput studies. Quantitation by mass spectrometry is comparably newer and many different strategies have been proposed. One such strategy quantitates the difference in protein expression level among samples via extracted ion chromatograms, or spectral counts or a combination thereof. Another strategy involves mass modifications of the analytes in one or more of the samples under investigation. MSMAG has been developed as an extension to 2DB and it has been shown that it can aid in quantitation of data from experiments employing label-free quantitation. Recently, it has been extended to allow for analysis of data based on labelling strategies. This also makes it possible to quickly visualize and investigate inherent mass differences as presented by post translational modifications.