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FractionOptimizer: a method for optimal peptide fractionation in bottom-up proteomics

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Abstract

Recent advances in mass spectrometry and separation technologies created the opportunities for deep proteome characterization using shotgun proteomics approaches. The “real world” sample complexity and high concentration range limit the sensitivity of this characterization. The common strategy for increasing the sensitivity is sample fractionation prior to analysis either at the protein or the peptide level. Typically, fractionation at the peptide level is performed using linear gradient high-performance liquid chromatography followed by uniform fraction collection. However, this way of peptide fractionation results in significantly suboptimal operation of the mass spectrometer due to the non-uniform distribution of peptides between the fractions. In this work, we propose an approach based on peptide retention time prediction allowing optimization of chromatographic conditions and fraction collection procedures. An open-source software implementing the approach called FractionOptimizer was developed and is available at http://hg.theorchromo.ru/FractionOptimizer. The performance of the developed tool was demonstrated for human embryonic kidney (HEK293) cell line lysate. In these experiments, we improved the uniformity of the peptides distribution between fractions. Moreover, in addition to 13,492 peptides, we found 6787 new peptides not identified in the experiments without fractionation and up to 800 new proteins (or 25%).

The analysis workflow employing FractionOptimizer software.

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Acknowledgments

This work was supported by the Russian Science Foundation, project no. 14-14-00971. The authors thank Dr. Irina A. Tarasova and Mark V. Ivanov for helpful discussions.

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Authors and Affiliations

  1. Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141701, Russia

    Elizaveta M. Solovyeva

  2. V.L. Talrose Institute for Energy Problems of Chemical Physics, RAS, Moscow, 119334, Russia

    Elizaveta M. Solovyeva, Anna A. Lobas, Lev I. Levitsky & Mikhail V. Gorshkov

  3. Institute of Biomedical Chemistry, Moscow, 119121, Russia

    Arthur T. Kopylov, Irina Y. Ilina & Sergei A. Moshkovskii

  4. Pirogov Russian National Research Medical University, Moscow, 117997, Russia

    Sergei A. Moshkovskii

Authors
  1. Elizaveta M. Solovyeva
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  2. Anna A. Lobas
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  3. Arthur T. Kopylov
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  4. Irina Y. Ilina
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  5. Lev I. Levitsky
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  7. Mikhail V. Gorshkov
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Correspondence to Mikhail V. Gorshkov.

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Solovyeva, E.M., Lobas, A.A., Kopylov, A.T. et al. FractionOptimizer: a method for optimal peptide fractionation in bottom-up proteomics. Anal Bioanal Chem 410, 3827–3833 (2018). https://doi.org/10.1007/s00216-018-1054-2

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  • DOI: https://doi.org/10.1007/s00216-018-1054-2

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