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Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms

Authors

  • Ivan Terterov,

    Corresponding author
    1. St. Petersburg Academic University Nanotechnology Research and Education Center RAS, St. Petersburg, Russia
    • Correspondence to: I. Terterov, St. Petersburg Academic University – Nanotechnology Research and Educational Center of Russian Academy of Sciences, 8/3 Khlopina Street, St. Petersburg 194021, Russia.

      E-mail: ivan.terterov@gmail.com

      Correspondence to: E. Nikolaev, Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow 119334, Russia.

      E-mail: ivan.terterov@gmail.com

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  • Kira Vyatkina,

    1. St. Petersburg Academic University Nanotechnology Research and Education Center RAS, St. Petersburg, Russia
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  • Alexey S. Kononikhin,

    1. Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow Region, Russia
    2. Institute of Biochemical Physics, RAS, Moscow, Russia
    3. Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
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  • Vitali Boitsov,

    1. St. Petersburg Academic University Nanotechnology Research and Education Center RAS, St. Petersburg, Russia
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  • Sergey Vyazmin,

    1. St. Petersburg Academic University Nanotechnology Research and Education Center RAS, St. Petersburg, Russia
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  • Igor A. Popov,

    1. Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow Region, Russia
    2. Institute of Biochemical Physics, RAS, Moscow, Russia
    3. Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
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  • Eugene N. Nikolaev,

    Corresponding author
    1. Moscow Institute of Physics and Technology (State University), Dolgoprudnyi, Moscow Region, Russia
    2. Institute of Biochemical Physics, RAS, Moscow, Russia
    3. Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
    • Correspondence to: I. Terterov, St. Petersburg Academic University – Nanotechnology Research and Educational Center of Russian Academy of Sciences, 8/3 Khlopina Street, St. Petersburg 194021, Russia.

      E-mail: ivan.terterov@gmail.com

      Correspondence to: E. Nikolaev, Institute for Energy Problems of Chemical Physics Russian Academy of Sciences, Leninskij pr. 38 k.2, Moscow 119334, Russia.

      E-mail: ivan.terterov@gmail.com

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  • Pavel Pevzner,

    1. St. Petersburg Academic University Nanotechnology Research and Education Center RAS, St. Petersburg, Russia
    2. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
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  • Michael Dubina

    1. St. Petersburg Academic University Nanotechnology Research and Education Center RAS, St. Petersburg, Russia
    2. St. Petersburg State Polytechnical University, St.Petersburg, Russia
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Abstract

RATIONALE

Peptides and proteins are among the most important components of living systems. Different attempts have been made to experimentally model the formation of peptides from amino acid monomers in investigation of the origin of life. Detailed characterization of peptides formed under various conditions in such reactions is very important for understanding processes of abiogenic peptide formation.

METHODS

We used liquid chromatography coupled with tandem mass spectrometry (MS/MS) for an accurate study of homo-peptides formed in a model reaction: glutamic acid oligomerization catalyzed by 1,1'-carbonyldiimidazole in aqueous solution with 1 M of sodium or potassium chloride and without any salts. We used de novo sequencing software for peptide identification. In addition we propose an approach that uses more spectral information for de novo sequencing then standard methods.

RESULTS

Peptides up to 9 amino acids long were found in the experiments with KCl, while in experiments with NaCl and without salts only peptides of up to 7 amino acids were detected. Due to high salt concentrations in samples a high number of singly charged peptide ions with up to 4 substitutions of hydrogen atoms by sodium or potassium atoms were observed. De novo sequencing software provided correct identifications even for peptide ions with substitutions.

CONCLUSIONS

Multiple substitutions of hydrogen by alkali metal atoms in peptide ions strongly change their fragmentation patterns. Proposed approach for de novo sequencing was found very effective, even for ions with substitutions. So, it may be useful in more complicated cases like sequencing abiogenic peptides consisting of different amino acids. Copyright © 2013 John Wiley & Sons, Ltd.

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