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

• Published in: Journal of proteome research Vol. 18; no. 12; pp. 4206 - 4214
• Main Authors: Archakov, Alexander I, Aseev, Alexander L, Bykov, Victor A, Grigoriev, Anatoly I, Govorun, Vadim M, Ilgisonis, Ekaterina V, Ivanov, Yuri D, Ivanov, Vadim T, Kiseleva, Olga I, Kopylov, Arthur T, Lisitsa, Andrey V, Mazurenko, Sergey N, Makarov, Alexander A, Naryzhny, Stanislav N, Pleshakova, Tatiana O, Ponomarenko, Elena A, Poverennaya, Ekaterina V, Pyatnitskii, Mikhail A, Sagdeev, Renad Z, Skryabin, Konstantin G, Zgoda, Victor G
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 06.12.2019
• Subjects: mass-spectrometry; fractionation; missing proteins; human proteome; low-abundant proteins; proteoforms; sensitivity; Chromosome-Centric Human Proteome Project (C-HPP); atomic force microscopy
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.9b00358

This manuscript collects all the efforts of the 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 forming 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. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.