Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Martin von Bergen
Helmholtz Centre for Environmental Research, Germany
Posters-Accepted Abstracts: J Proteomics Bioinform
The steady increase of sequencing data enabled the detection of non-coding transcripts as a normal component in the RNA ensemble of every eukaryotic cell. Beside a wide variety of shorter RNA sub-types there are also long and very long ncRNAs described. Based on new findings from ribosome profiling and bioinformatic analyses it has been proposed that some shorter sequence stretches show coding potential. Here we will present recent studies on proteogenomic analyses of microbes like Dehalococcoides and Helicobacter. In these studies the simple search of mass spectrometric data against the six frame translation of the genomic sequence is sufficient to unravel novel proteins or coding sequences. The experimental approach has also been supported by novel prediction tools like RNAcode. The validation has been done by SRM measurements. For typical model systems and especially those with very large genomes like human the bioinformatics challenge is much harder. We developed a stepwise filtering by using transcriptome data instead of genomic information and substraction of already known coding sequences. In this study we used transcriptomic data from polarized human immune cells and detected up to 300 novel coding sequences which some also are correlating with different immune cell sub-types. For a proper detection of novel coding sequences the stringency of the database search and the way of validation are critical issues and we will show the several layers in this process. In summary, the combination of proteomics and bioinformatics will enable the further development of the field of proteogenomics in the future.
Email: martin.vonbergen@ufz.de