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Open AccessArticle

Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins

1
Institute of Biomedical Chemistry, Moscow 119121, Russia
2
Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
3
V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117198, Russia
4
V.L. Talrose Institute for Energy Problems of Chemical Physics, Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
5
Moscow Institute of Physics and Technology (State University), Dolgoprudny 141700, Russia
6
Blokhin Russian Cancer Research Center, Moscow 115478, Russia
*
Author to whom correspondence should be addressed.
Proteomes 2020, 8(2), 12; https://doi.org/10.3390/proteomes8020012
Received: 24 April 2020 / Revised: 18 May 2020 / Accepted: 19 May 2020 / Published: 23 May 2020
(This article belongs to the Special Issue Human Proteomics)
Despite direct or indirect efforts of the proteomic community, the fraction of blind spots on the protein map is still significant. Almost 11% of human genes encode missing proteins; the existence of which proteins is still in doubt. Apparently, proteomics has reached a stage when more attention and curiosity need to be exerted in the identification of every novel protein in order to expand the unusual types of biomaterials and/or conditions. It seems that we have exhausted the current conventional approaches to the discovery of missing proteins and may need to investigate alternatives. Here, we present an approach to deciphering missing proteins based on the use of non-standard methodological solutions and encompassing diverse MS/MS data, obtained for rare types of biological samples by members of the Russian Proteomic community in the last five years. These data were re-analyzed in a uniform manner by three search engines, which are part of the SearchGUI package. The study resulted in the identification of two missing and five uncertain proteins detected with two peptides. Moreover, 149 proteins were detected with a single proteotypic peptide. Finally, we analyzed the gene expression levels to suggest feasible targets for further validation of missing and uncertain protein observations, which will fully meet the requirements of the international consortium. The MS data are available on the ProteomeXchange platform (PXD014300). View Full-Text
Keywords: human proteome; missing proteins; uncertain proteins; neXtProt; proteotypic peptide; mass spectrometry; Chromosome-Centric Human Proteome Project (C-HPP) human proteome; missing proteins; uncertain proteins; neXtProt; proteotypic peptide; mass spectrometry; Chromosome-Centric Human Proteome Project (C-HPP)
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MDPI and ACS Style

Poverennaya, E.; Kiseleva, O.; Ilgisonis, E.; Novikova, S.; Kopylov, A.; Ivanov, Y.; Kononikhin, A.; Gorshkov, M.; Kushlinskii, N.; Archakov, A.; Ponomarenko, E. Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. Proteomes 2020, 8, 12.

AMA Style

Poverennaya E, Kiseleva O, Ilgisonis E, Novikova S, Kopylov A, Ivanov Y, Kononikhin A, Gorshkov M, Kushlinskii N, Archakov A, Ponomarenko E. Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. Proteomes. 2020; 8(2):12.

Chicago/Turabian Style

Poverennaya, Ekaterina; Kiseleva, Olga; Ilgisonis, Ekaterina; Novikova, Svetlana; Kopylov, Arthur; Ivanov, Yuri; Kononikhin, Alexei; Gorshkov, Mikhail; Kushlinskii, Nikolay; Archakov, Alexander; Ponomarenko, Elena. 2020. "Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins" Proteomes 8, no. 2: 12.

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