title: 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.
abstract: BACKGROUND
  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.
authors.affiliation: St. Petersburg Academic University Nanotechnology Research and Education Center RAS, 8/3 Khlopina st., St. Petersburg, 194021, Russia.
authors.forename: Ivan
authors.initials: I
authors.lastname: Terterov
authors.forename: Kira
authors.initials: K
authors.lastname: Vyatkina
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kononikhin
authors.forename: Vitali
authors.initials: V
authors.lastname: Boitsov
authors.forename: Sergey
authors.initials: S
authors.lastname: Vyazmin
authors.forename: Igor A
authors.initials: IA
authors.lastname: Popov
authors.forename: Eugene N
authors.initials: EN
authors.lastname: Nikolaev
authors.forename: Pavel
authors.initials: P
authors.lastname: Pevzner
authors.forename: Michael
authors.initials: M
authors.lastname: Dubina
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D016000:Cluster Analysis; D018698:Glutamic Acid / Q000737:chemistry*; D006859:Hydrogen / Q000737:chemistry; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011188:Potassium / Q000737:chemistry*; D011522:Protons; D012964:Sodium / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D009842:Oligopeptides; D011522:Protons; D018698:Glutamic Acid; D006859:Hydrogen; D012964:Sodium; D011188:Potassium