Abstract Body

Background: Mass Spectrometry has become an indispensable technique for studying proteins in biological systems. Thousands of proteins can be identified and quantified with state-of-the art instruments in a single experiment. Global changes in the proteome and certain post translational modifications can now be routinely characterized due to dramatic improvements in speed and sensitivity of mass spectrometric instruments and data analysis software. However, there are still areas of proteomics where analysis can be not as straight forward or need extra care in sample preparation. Examples are the characterization of disease specific circulating antibodies and the detection of virus-host protein protein interactions. Conclusions: Protein-Protein interactions are critical for all cellular processes. Understanding with which host proteins the virus interacts is crucial for understanding the mechanism of infection. Current strategies of affinity purifications of tagged viral proteins, chemical cross-linking of host-virus proteins as well as changes in post translational modifications (i.e. phosphorylation) upon infection will be presented. Common problems of affinity purifications and characterizing infection dependent post translational modifications will be discussed with special emphasis on sample preparation strategies. Establishing antibody repertoires of infected individuals by high throughput DNA sequencing has been rapidly advancing, yet the antibody composition in the blood of infected individuals remains largely unknown. Here, mass spectrometry is emerging as an enabling technology in combination with a match personal antibody database. Characterizing and quantifying the circulating antibodies in the blood of infected individuals is however not a trivial task. The majority of the antibody is structurally identical and it is therefore difficult to unambiguously identify which antibody is present in the sera of individuals. The majority of antibody derived peptides will be identical and shared between many different antibodies. Here, current strategies for identifying antibody specific peptides are described.