Number of detected proteins as the function of the sensitivity of proteomic technology in human liver cells

Vavilov, N. E.; Ilgisonis, E. V.; Lisitsa, A. V.; Ponomarenko, E. A.; Farafonova, T. E.; Tikhonova, O. V.; Zgoda, V. G.; Archakov, A. I.

doi:10.1101/2021.11.24.469687

bioRxiv · 10.1101/2021.11.24.469687

Number of detected proteins as the function of the sensitivity of proteomic technology in human liver cells

Vavilov, N. E.·Ilgisonis, E. V.·Lisitsa, A. V.·Ponomarenko, E. A.·Farafonova, T. E.·Tikhonova, O. V.·Zgoda, V. G.·Archakov, A. I.

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Abstract

The main goal of the Russian part of C-HPP is to detect and functionally annotate missing proteins (PE2-PE4) encoded by human chromosome 18. However, identifying such proteins in a complex biological mixture using mass spectrometry (MS)-based methods is difficult due to the insufficient sensitivity of proteomic analysis methods. In this study, we determined the proteomic technology sensitivity using a standard set of UPS1 proteins as an example. The results revealed that 100% of proteins in a mixture could only be identified at a concentration of at least 10-9 M. The decrease in concentration leads to protein losses associated with technology sensitivity, and no UPS1 protein is detected at a concentration of 10-13 M. Therefore, two-dimensional fractionation of samples was applied to improve sensitivity. The human liver tissue was examined by selected reaction monitoring and shotgun methods of MS analysis using one-dimensional and two-dimensional fractionation to identify the proteins encoded by human chromosome 18. A total of 134 proteins were identified. The overlap between proteomic and transcriptomic data in human liver tissue was ~50%. This weak convergence is due to the low sensitivity of proteomic technology compared to transcriptomic approaches. Data is available via ProteomeXchange with identifier PXD026997.

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Vavilov, N. E., Ilgisonis, E. V., Lisitsa, A. V., Ponomarenko, E. A., Farafonova, T. E., Tikhonova, O. V., Zgoda, V. G., Archakov, A. I.. 2021-11-25. Number of detected proteins as the function of the sensitivity of proteomic technology in human liver cells. https://doi.org/10.1101/2021.11.24.469687

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