Publications by Vladimir Kopysov

Identification of Isomeric Metabolites Using Cold Ion Spectroscopy Add-on to Orbitrap-Based Mass Spectrometer

Oleg Boyarkine, Vladimir Kopysov, Andrei Zviagin

The identification of chemical structures of metabolites available in trace-level quantities remains a challenging task in analytical chemistry. Although cold ion spectroscopy (CIS) has considerable potential to assist in such identification, the widesprea ...

American Chemical Society (ACS)2025

Oligomers of diphenylalanine examined using cold ion spectroscopy and neural network-based conformational search

Oleg Boyarkine, Vladimir Kopysov, Ruslan Yamaletdinov

Diphenylalanine (Phe2) is the primary building block of many self-assembling nanostructures that are important in biology and materials science. Understanding the detailed mechanism of their formation requires knowledge of the structural motives that the s ...

2024

Quantification of enantiomers and blind identification of erythro-sphingosine non-racemates by cold ion spectroscopy

Oleg Boyarkine, Vladimir Kopysov, Ruslan Yamaletdinov

Enantiomers of a lipid erythro-sphingosine have been quantified with ≈4% accuracy by UV cold ion spectroscopy of their non-covalent complexes with a chiral aromatic molecule. The diastereomeric configuration of such complexes enables the quantification usi ...

2024

Gentle nano-electrospray ion source for reliable and efficient generation of microsolvated ions

Oleg Boyarkine, Vladimir Kopysov, Andrei Zviagin

We present herein the design of a nano-electrospray ion source capable of reliable generation of large quantities of microsolvated ions. The source is based on a triple molecular skimmer scheme and can be quickly tuned to generate bare ions or their ionic ...

AIP Publishing2022

Tracking local and global structural changes in a protein by cold ion spectroscopy

Oleg Boyarkine, Natalia Nagornova, Vladimir Kopysov, Andrei Zviagin

Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated pro ...

ROYAL SOC CHEMISTRY2022

Spectroscopic Evidence for Peptide-Bond-Selective Ultraviolet Photodissociation

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev

We study the photodissociation induced by ultraviolet excitation of amide bonds in gas-phase protonated peptides. Jointly, mass spectrometry and cold ion spectroscopy provide evidence for a selective non-statistical dissociation of specific peptide bonds i ...

2020

Identification and Quantification of Any Isoforms of Carbohydrates by 2D UV-MS Fingerprinting of Cold Ions

Oleg Boyarkine, Vladimir Kopysov, Viktoriia Aladinskaia

Biological functionality of isomeric carbohydrates may differ drastically, making their identifications indispensable in many applications of life science. Because of the large number of isoforms, structural assignment of saccharides is challenging and oft ...

2020

Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev, Elizaveta Solovyeva

Identification of isomeric amino acid residues in peptides and proteins is challenging but often highly desired in proteomics. One of the practically important cases that require isomeric assignments is that associated with single-nucleotide polymorphism s ...

AMER CHEMICAL SOC2019

Gas-phase structures reflect the pain-relief potency of enkephalin peptides

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev

We use cold ion spectroscopy and quantum-chemical computations to solve the structures of opioid peptides enkephalins in the gas phase. The derived structural parameters clearly correlate with the known pharmacological efficiency of the studied drugs, sugg ...

2019

Interplay of H-Bonds with Aromatics in Isolated Complexes Identifies Isomeric Carbohydrates

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev, Ruslan Yamaletdinov

The tremendous isomeric diversity of carbohydrates enables a wide range of their biological functions but makes the identification and study of these molecules difficult. We investigated the ability of intermolecular interactions to communicate structural ...

Wiley-VCH Verlag GmbH2019

Peptide Bond Ultraviolet Absorption Enables Vibrational Cold-Ion Spectroscopy of Nonaromatic Peptides

Vladimir Kopysov, Aleksandr Pereverzev

Peptide-bond VUV absorption is inherent to all proteins and peptides. Although widely exploited in top-down proteomics for photodissociation, this absorption has never been spectroscopically characterized in the gas phase. We have measured VUV/UV photofrag ...

2018

Identification of isoforms of aspartic acid residues in peptides by 2D UV-MS fingerprinting of cold ions

Vladimir Kopysov

2018

Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy

Oleg Boyarkine, Natalia Nagornova, Vladimir Kopysov

The early stages of fibril formation are difficult to capture in solution. We use cold-ion spectroscopy to examine an 11-residue peptide derived from the protein transthyretin and clusters of this fibre-forming peptide containing up to five units in the ga ...

Wiley-Blackwell2018

Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev, Robert Benny Gerber

The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed th ...

2018

Identification of Isomeric Ephedrines by Cold Ion UV Spectroscopy: Toward Practical Implementation

Oleg Boyarkine, Vladimir Kopysov

Ephedrine and pseudoephedrine are stimulant drugs whose use is prohibited in athletic competition by the World Anti Doping Agency (WADA) at very different threshold doping violation concentrations. We use a recently developed universal approach that integr ...

2017

High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy

Oleg Boyarkine, Vladimir Kopysov, Aleksandr Pereverzev

Histidine remained the last aromatic amino acid for which the intrinsic spectroscopic properties and structures were obscure. We measured the UV and IR spectra of protonated histidine, isolated in the gas phase, using photofragmentation cold ion spectrosco ...

Wiley-Blackwell2017

Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features

Oleg Boyarkine, Vladimir Kopysov

Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by ...

Amer Chemical Soc2016

Resonance Energy Transfer Relates the Gas-Phase Structure and Pharmacological Activity of Opioid Peptides

Oleg Boyarkine, Vladimir Kopysov

Enkephalins are efficient pain-relief drugs that bind to transmembrane opioid receptors. One key structural param- eter that governs the pharmacological activity of these opioid peptides and is typically determined from condensed-phase structures is the di ...

Wiley-Blackwell2016

Novel Approaches in Cold Ion Spectroscopy for Structural Characterization of Biomolecules in the Gas Phase

Vladimir Kopysov

Mass spectrometry is a powerful analytical technique, which has become invaluable across a wide range of scientific fields, such as "omics" sciences (e.g., proteomics), doping control and forensic sciences, drug development, environmental analysis, geologi ...

EPFL2016

Method and apparatus for the analysis of molecules using mass spectrometry and optical spectroscopy

Oleg Boyarkine, Vladimir Kopysov

A method of analyzing molecules enabling chemical, structural and isomeric or conformational identification of the molecules, particularly in a stream from a chromatographic separation, comprising: generating ions from a sample of molecules to be analyzed; ...

2016