Inventory of proteoforms as a current challenge of proteomics: Some technical aspects

The main intricacy in the human proteome is that it is tremendously complex and composed from diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances in the technology of so called "Top-Down" mass spectrometry based proteomics, have been made. However, the scale of performance of this approach is still far behind the "Bottom-Up", peptide-centric techniques. The classical two-dimensional electrophoresis (2-DE) as the most powerful and convenient method for separation of proteoforms remains as a superior method in "Top-Down" proteomics. Here, some aspects of approaches for establishing an inventory of proteoforms based on 2-DE and mass spectrometry are discussed. BIOLOGICAL SIGNIFICANCE: The systematic efforts in the Human Proteome project to map the entire human proteome greatly depend on currently available and emerging techniques and approaches. Here, the possibilities of a visual representation of the human proteome by combination of virtual/experimental 2-DE with protein identification by mass spectrometry or immunologically is discussed. By application of this approach on several profiles of gene products we show its convenience in informative representation of the whole proteome and single gene products, proteoforms (protein species). This approach could be very helpful in the emerging global inventory of all human proteoforms.