6. Conclusion

The idea to manage the theoretical proteomes and link them with experimental, 2DE-based data has been tried to realize in another online database, DynaProt 2D [58]. It was developed for dynamic access to proteomes and 2DE gels. Here, a 2DE gel could serve as a reference map and as a tool for navigation of the database [58]. Integrated into 2DE database a complete theoretical proteome could provide a powerful tool allowing simply linking newly identified spots to the already available appropriate theoretical data [58]. But this idea was tried for one

If we plot experimentally measured physicochemical parameters of proteoforms (pI or Mw) against the theoretical ones, the general view of the proteome according to the diversity of proteoforms is revealed (Figure 6). Here, the dots are distributed along the diagonal in the graph, if experimentally detected parameters match or are close to the theoretical values. Otherwise, dots are distributed above or below the diagonal, and the bigger the difference between theoretical and experimental parameters, the bigger the deviation of the dot position from the diagonal. In particular, in case of pI, the location of proteoform dots above the diagonal shows that the experimental pIs of this proteoform is smaller than the theoretical

Figure 7. The examples of variety of proteoforms in HepG2 cells (top) and human plasma (bottom). The arrow shows the predicted location of the master polypeptide (polypeptide coded by the canonical sequence). Adapted from Naryzhny

et al. [29].

organism only, Lactococcus lactis, and stopped in realization.

100 Electrophoresis - Life Sciences Practical Applications

The continuing evolution of the detection technique (mostly mass spectrometry) and usage of it in combination with optimum protein separation techniques will finally allow us to reach the main aim of the HUPO—image of the whole human proteome. A union of such a classic proteomics method for separation of proteins as 2DE with bottom-up mass spectrometry (shot-gun analysis of peptides by ESI LC-MS/MS) is an efficient approach for increasing the productivity of tandem mass-spectrometry. Additionally, this union of top-down and bottomup approaches allows very convenient visual representation (profiling) of information about diverse proteoforms. As 2DE maps are a convenient and effective way to represent information about proteomes and navigate around all its proteoforms, it will allow the construction of a knowledge base for an inventory of all human protein species/proteoforms, that is, visually attractive, clear, easy to search and perceptive.

Particularly, the development of chromosome-centric interactive virtual 2DE maps of proteins coded by specific genes in combination with experimental 2DE protein maps will allow executing more effectively C-HPP, to estimate more accurately the number of proteoforms and could be a basis for the knowledge base of human proteins. The development of such inventory will be based on existing databases like http://world-2dpage.expasy.org/, https://www.nextprot.org/, http://www.uniprot.org/ and http://atlas.topdownproteomics.org.
