Seminar, 1 November 2012, C. Dieterich

1 November 2012, 16:15
Ernst-Abbe-Platz 2, seminar room 3423

Towards proteome wide absolute protein abundance estimation

Dr. Christoph Dieterich (Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany)

Shotgun proteomics data is typically generated by an LC-­MS/MS approach. Herein, proteins are digested to yield peptides, which are then ionized and fragmented in a mass spectrometer.
The observed peptide intensities are the outcome of a poorly understood process with many hidden variables. Evidently, we are interested in estimating absolute protein abundances from the observed peptide intensities. I will introduce the most relevant aspects of this problem and discuss our preliminary approach to protein quantification.
We propose a model where each peptide abundance is essentially determined by the sum of protein abundances in which this peptide occurs. However, different peptides are neither produced with the same efficiency nor possess the same ionization properties. That is why, we resort to a Gibbs sampling strategy to estimate the three unknowns: protein abundance, tryptic digestion and peptide ionization efficiency.