viQC: Visual and Intuitive Quality Control for Mass Spectrometry-Based Proteome Analysis
- Autores: Solovyeva E.1,2, Lobas A.2, Surin A.3,4, Levitsky L.2, Gorshkov V.5, Gorshkov M.2
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Afiliações:
- Moscow Institute of Physics and Technology (State University)
- Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
- Microbiology & Biotechnology
- University of Southern Denmark
- Edição: Volume 74, Nº 14 (2019)
- Páginas: 1363-1370
- Seção: Articles
- URL: https://journals.rcsi.science/1061-9348/article/view/183376
- DOI: https://doi.org/10.1134/S1061934819140119
- ID: 183376
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Resumo
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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Sobre autores
E. Solovyeva
Moscow Institute of Physics and Technology (State University); Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences
Email: mike.gorshkov@gmail.com
Rússia, Dolgoprudny, Moscow oblast, 141700; Moscow, 119334
A. Lobas
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences
Email: mike.gorshkov@gmail.com
Rússia, Moscow, 119334
A. Surin
Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; Microbiology & Biotechnology
Email: mike.gorshkov@gmail.com
Rússia, Pushchino, Moscow oblast, 142290; Obolensk, Moscow oblast, 142279
L. Levitsky
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences
Email: mike.gorshkov@gmail.com
Rússia, Moscow, 119334
V. Gorshkov
University of Southern Denmark
Email: mike.gorshkov@gmail.com
Dinamarca, Odense, 5230
M. Gorshkov
Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences
Autor responsável pela correspondência
Email: mike.gorshkov@gmail.com
Rússia, Moscow, 119334