Challenges of the Human Proteome Project: 10-year Experience of the Russian Consortium

This manuscript collects all the efforts of Russian Consortium, bottlenecks revealed in the course of the C-HPP realization and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins formed the «dark part» of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. For the systematic analysis of the functional features of a number of proteins (CP50 Challenge), we crea...