[Frontiers in Bioscience 17, 1599-1612, January 1, 2012]

CD proteome and beyond - technologies for targeting the immune cell surfaceome

Thomas Bock 1,2,3, Damaris Bausch-Fluck 1,2, Andreas Hofmann 1,2, Bernd Wollscheid1,2

1National Center of Competence in Research (NCCR), Neuro Center for Proteomics, UZH/ ETH Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland, 2Swiss Federal Institute of Technology (ETH) Zurich, Department of Biology, Institute of Molecular Systems Biology, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland, 3ZNZ International PhD Program in Neuroscience, University of Zurich (UZH) / ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland

TABLE OF CONTENTS

1. Abstract
2. Introduction
2.1. Information processing by cell surface proteins during the immune response
2.2. Challenges in the detection of cell surface proteins by classical immunological tools
3. A proteomic view of the immunological surfaceome
3.1. Mass spectrometry-based proteomic technology
3.2. Biochemical cell surface protein enrichment strategies
3.3. Carbohydrate-based affinity enrichment strategies
3.3.1. Lectin affinity-based glycoprotein enrichment and analysis
3.3.2. Chemical enrichment and analysis of N-glycopeptides
3.4. Targeted verification strategy: selected reaction monitoring
4. Summary and perspective
5. Acknowledgements
6. References

1. ABSTRACT

Communication between cells of the immune system and the organism is dependent on information processing mediated by proteins of the cell surface. The cell surface proteome consists of a group of functionally diverse proteins, which not only enables but also limits the interaction capacities of cells within their particular microenvironment. Although these proteins represent a highly important proteome for immunological research, most routinely used technologies for their detection only allow for a fragmented view of the ensemble of cell surface located proteins. A major bottleneck is the limited availability of high quality antibodies against cell surface protein targets that altogether impedes a Systems Biology view on the cell surface proteome (surfaceome) and its concerted functions during signal processing. Recent developments in mass spectrometry-based technologies enable now complementary approaches for the qualitative and quantitative analysis of the surfaceome. Here, we highlight recent progress in the field towards the identification and quantification of the surfaceome as an important subproteome forming the information gateway of the cell.