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On the utility of ultrafast MS1-only proteomics in drug target discovery studies based on thermal proteome profiling method

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Abstract

Advances in high-throughput high-resolution mass spectrometry and the development of thermal proteome profiling approach (TPP) have made it possible to accelerate a drug target search. Since its introduction in 2014, TPP quickly became a method of choice in chemical proteomics for identifying drug-to-protein interactions on a proteome-wide scale and mapping the pathways of these interactions, thus further elucidating the unknown mechanisms of action of a drug under study. However, the current TPP implementations based on tandem mass spectrometry (MS/MS), associated with employing lengthy peptide separation protocols and expensive labeling techniques for sample multiplexing, limit the scaling of this approach for the ever growing variety of drug-to-proteomes. A variety of ultrafast proteomics methods have been developed in the last couple of years. Among them, DirectMS1 provides MS/MS-free quantitative proteome-wide analysis in 5-min time scale, thus opening the way for sample-hungry applications, such as TPP. In this work, we demonstrate the first implementation of the TPP approach using the ultrafast proteome-wide analysis based on DirectMS1. Using a drug topotecan, which is a known topoisomerase I (TOP1) inhibitor, the feasibility of the method for identifying drug targets at the whole proteome level was demonstrated for an ovarian cancer cell line.

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Funding

This work was supported by Russian Science Foundation (grant № 20–14-00229-P).

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Authors and Affiliations

  1. V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Leninsky Pr. 38, Bld.2, 119334, Moscow, Russia

    Ivan I. Fedorov, Julia A. Bubis, Elizaveta M. Kazakova, Anna A. Lobas, Mark V. Ivanov, Daria D. Emekeeva, Irina A. Tarasova & Mikhail V. Gorshkov

  2. Moscow Center for Advanced Studies, Kulakova Str. 20, 123592, Moscow, Russia

    Ivan I. Fedorov

  3. Faculty of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991, Moscow, Russia

    Alexey A. Nazarov

  4. Faculty of Chemistry of the National Research University Higher School of Economics, Vavilova Str. 7, 101000, Moscow, Russia

    Alexey A. Nazarov

Authors
  1. Ivan I. Fedorov
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  2. Julia A. Bubis
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  3. Elizaveta M. Kazakova
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  4. Anna A. Lobas
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  5. Mark V. Ivanov
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  6. Daria D. Emekeeva
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  7. Irina A. Tarasova
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  8. Alexey A. Nazarov
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  9. Mikhail V. Gorshkov
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Contributions

Ivan I. Fedorov: data curation; formal analysis; visualization; writing, original draft preparation; writing, review and editing. Julia A. Bubis: methodology, investigation, laboratory work. Elizaveta M. Kazakova: investigation, laboratory work, data curation. Anna A. Lobas: methodology. Mark V. Ivanov: software, resources. Daria D. Emekeeva: investigation, laboratory work. Irina A. Tarasova: resources, formal analysis, supervision. Alexey A. Nazarov: investigation, laboratory work. Mikhail V. Gorshkov: conceptualization, supervision, funding acquisition, project administration, writing—review and editing. All authors discussed the results and commented on the manuscript. All authors have given approval to the final version of the manuscript.

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Correspondence to Mikhail V. Gorshkov.

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Fedorov, I.I., Bubis, J.A., Kazakova, E.M. et al. On the utility of ultrafast MS1-only proteomics in drug target discovery studies based on thermal proteome profiling method. Anal Bioanal Chem (2024). https://doi.org/10.1007/s00216-024-05330-9

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  • DOI: https://doi.org/10.1007/s00216-024-05330-9

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