title: Threonine versus isothreonine in synthetic peptides analyzed by high-resolution liquid chromatography/tandem mass spectrometry.
abstract: One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of Met to isoThr is not encoded genetically and should be unambiguously distinguished from, e.g., point mutations in proteins that result in Met conversion to Thr.
  
  
  
  In this work we compared tandem mass (MS/MS) spectra produced by an Orbitrap mass spectrometer of Thr- and isoThr-containing tryptic peptides and found a distinctive feature in their collisionally activated fragmentation patterns.
  
  
  
  Up to 84% of MS/MS spectra for peptides containing isoThr residues have been positively specified. We also studied the differences in retention times for peptides containing Thr isoforms that can be further used for their distinction.
  
  
  
  Threonine can be distinguished from isothreonine by its retention time and HCD fragmentation pattern, specifically relative intensity of the bn - product ion, which can be further used in proteomic research. Copyright © 2016 John Wiley & Sons, Ltd.
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: Ksenia G
authors.initials: KG
authors.lastname: Kuznetsova
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.|Moscow State University, Biological Faculty, Moscow, Russia.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Trufanov
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Moysa
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: Mikhail A
authors.initials: MA
authors.lastname: Pyatnitskiy
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.
authors.forename: Viktor G
authors.initials: VG
authors.lastname: Zgoda
authors.affiliation: Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.|Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia.
authors.forename: Mikhail V
authors.initials: MV
authors.lastname: Gorshkov
authors.affiliation: Institute of Biomedical Chemistry, Moscow, Russia.|Pirogov Russian National Medical University, Moscow, Russia.
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Moshkovskii
mesh_terms: D000595:Amino Acid Sequence; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D006801:Humans; D007536:Isomerism; D010455:Peptides / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D013912:Threonine / Q000032:analysis*
chemical_list: D010455:Peptides; D013912:Threonine