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viQC: Visual and Intuitive Quality Control for Mass Spectrometry-Based Proteome Analysis

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Abstract

Mass spectrometry-based bottom-up proteomics becomes a method of choice in a broad range of biomedical studies. However, because of the growing complexity of the mass spectrometers employed in these studies, there is an increasing need in robust and rapid quality control over the instrument performance. A variety of quality control tools targeting all aspects of LC–MS instrument operation have been developed recently. These tools are typically loaded heavily with a large number of metrics. Many of these metrics are difficult for interpretation for regular users without extensive instrumentation and/or data processing experience. In this work, we introduced a set of simple and intuitively understandable metrics for assessing the quality of proteomic analysis, including the total experimental time and the number of spectral scans, ion accumulation time and intensity in both MS and MS/MS spectra, charge state distribution for precursor peptide ions, and the number of sequential MS/MS scans, etc. These metrics are implemented as an open-source utility, viQC, freely available at hg.theorchromo.ru/viQC. The developed tool has been tested experimentally using data from three different Orbitrap instruments and demonstrated its capability for assessing the possible flaws in the instrument’s operation and subsequent improving the efficiency of proteomic analysis.

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ACKNOWLEDGMENTS

The authors are grateful to Prof. S.A. Moshkovskii and I.Yu. Ilina for help in sample preparation, and the facilities of United Pushchino Center for Mass Spectrometry (584307) for help with experiments. We also thank Drs. I.A. Tarasova and M.V. Ivanov, as well as Yu.A. Bubis for a fruitful discussion of the test results of the developed software and the proposed metrics for analyzing the quality of the proteomic experiment.

Funding

The software for implementing the viQC algorithm was developed with the financial support of the Russian Foundation for Basic Research, project no. 18-29-13015. The experimental data used in the work were obtained in the framework of the Program for Basic Research of State Academies of Sciences for 2013–2020 (topic no. ААА-А18-118112090111-4).

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Authors and Affiliations

  1. Moscow Institute of Physics and Technology (State University), 141700, Dolgoprudny, Moscow oblast, Russia

    E. M. Solovyeva

  2. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia

    E. M. Solovyeva, A. A. Lobas, L. I. Levitsky & M. V. Gorshkov

  3. Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290, Pushchino, Moscow oblast, Russia

    A. K. Surin

  4. Microbiology & Biotechnology, 142279, Obolensk, Moscow oblast, Russia

    A. K. Surin

  5. University of Southern Denmark, 5230, Odense, Denmark

    V. A. Gorshkov

Authors
  1. E. M. Solovyeva
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  2. A. A. Lobas
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  3. A. K. Surin
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  4. L. I. Levitsky
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  5. V. A. Gorshkov
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  6. M. V. Gorshkov
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Corresponding author

Correspondence to M. V. Gorshkov.

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The authors declare that there is no conflict of interest.

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Translated by O. Zhukova

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Solovyeva, E.M., Lobas, A.A., Surin, A.K. et al. viQC: Visual and Intuitive Quality Control for Mass Spectrometry-Based Proteome Analysis. J Anal Chem 74, 1363–1370 (2019). https://doi.org/10.1134/S1061934819140119

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  • DOI: https://doi.org/10.1134/S1061934819140119

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