Publications by Yury Tsybin | EPFL Graph Search

Related publications (75)

Tissue Transglutaminase-mediated Glutamine Deamidation of beta-Amyloid Peptide Increases Peptide Solubility, Whereas Enzymatic Cross-linking and Peptide Fragmentation May Serve as Molecular Triggers for Rapid Peptide Aggregation

Horst Arthur Vogel, Yury Tsybin, Marc Moniatte, Adrian Schmid, Diego Chiappe, Enrico Condemi

Tissue transglutaminase (TGase) has been implicated in a number of cellular processes and disease states, where the enzymatic actions of TGase may serve in both, cell survival and apoptosis. To date, the precise functional properties of TGase in cell survi ...

American Society for Biochemistry and Molecular Biology2011

UV radiation induces genome-mediated, site-specific cleavage in viral protein

Tamar Kohn, Yury Tsybin, Laure Menin, Krista Rule Wigginton, Michele Cascella, Anne Thérèse Sigstam, Hisham Ben Hamidane

Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome-mediated mechanism that causes sitespecific virus protein clea ...

2012

Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments

Yury Tsybin, Kristina Srzentic, Unige Anna Laskay

Mass spectrometry (MS)-based bottom-up proteomics (BUP) is currently the method of choice for large-scale identification and characterization of proteins present in complex samples, such as cell lysates, body fluids, or tissues. Technically, BUP relies on ...

Amer Chemical Soc2013

High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Increased Throughput for Biomolecular Analysis

Yury Tsybin, Anton Kozhinov, Konstantin Nagornov

A multielectrode ion cyclotron resonance (ICR) cell, herein referred to as the 4X cell, for signal detection at the quadruple frequency multiple was implemented and characterized on a commercial 10 T Fourier transform ICR mass spectrometer (FT-ICR MS). Not ...

Amer Chemical Soc2014

Electron Capture and Transfer Dissociation: Peptide Structure Analysis at Different Ion Internal Energy Levels

Yury Tsybin, Marc Moniatte, Aleksey Vorobyev, Diego Chiappe, Hisham Ben Hamidane

We decoupled electron-transfer dissociation (ETD) and collision-induced dissociation of charge-reduced species (CRCID) events to probe the lifetimes of intermediate radical species in ETD-based ion trap tandem mass spectrometry of peptides. Short-lived int ...

Springer-Verlag2009

Reaction of C60 with Hydrogen Gas: In Situ Monitoring and Pathways

Yury Tsybin

Kinetics and pathways of C60 reaction with hydrogen gas were studied in a broad temperature interval and over extended periods of time. Specifically, hydrogenation was monitored in situ at high temperature and high hydrogen pressure conditions using the gr ...

American Chemical Society2011

On the Viability of Heterolytic Peptide N-Calpha Bond Cleavage in Electron Capture and Transfer Dissociation Mass Spectrometry

Anne-Clémence Corminboeuf, Yury Tsybin, Matthew Wodrich, Konstantin Zhurov

While frequently employed as an experimental technique, the mechanistic picture surrounding the gas-phase dissociation of peptides carrying multiple positive charges during electron capture and electron transfer dissociation tandem mass spectrometry remain ...

Amer Chemical Soc2014

Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics

Yury Tsybin, Aleksey Vorobyev

The conformation of model Arg(Ala)(4)X(Ala)(4)Lys+2H and Arg(Gly)(4)X(Gly)(4)Lys+2H peptides has been systematically investigated as a function of the central amino acid X through a combined experimental and theoretical approach. Mass spectrome ...

American Chemical Society2010

Structural Preferences of Gas-Phase M2TMP Monomers upon Sequence Variations

Yury Tsybin, Hisham Ben Hamidane

The conformations of a number of M2TMP-(22-46) sequence variants have been investigated using ion mobility spectrometry (IMS). Substantial conformational changes were evidenced by IMS upon the variation of a single amino acid in the peptide sequence, with ...

2011

A Functional Group Approach for Prediction of APPI Response of Organic Synthetic Targets

Yury Tsybin, Laure Menin, Konstantin Zhurov, Thomas Clément Di Franco

Atmospheric pressure photoionization (APPI) is a technique of choice for ionization of non-polar molecules in mass spectrometry (MS). Reported APPI-based studies tend to focus on a selected compound class, which may contain a variety of functional groups. ...

Springer2015

Least-Squares Fitting of Time-Domain Signals for Fourier Transform Mass Spectrometry

Yury Tsybin, Anton Kozhinov

To advance Fourier transform mass spectrometry (FTMS)-based molecular structure analysis, corresponding development of the FTMS signal processing methods and instrumentation is required. Here, we demonstrate utility of a least-squares fitting (LSF) method ...

Springer2014

Iterative Method for Mass Spectra Recalibration via Empirical Estimation of the Mass Calibration Function for Fourier Transform Mass Spectrometry-Based Petroleomics

Yury Tsybin, Anton Kozhinov, Konstantin Zhurov

We describe a mass spectra recalibration method, which enables analysis of petroleum samples with Orbitrap FTMS. In this method, the mass calibration function is estimated on the basis of mass-to-charge ratios and abundances of internal calibrants without ...

Amer Chemical Soc2013

Periodic Sequence Distribution of Product Ion Abundances in Electron Capture Dissociation of Amphipathic Peptides and Proteins

Yury Tsybin, Hisham Ben Hamidane

The rules for product ion formation in electron capture dissociation (ECD) mass spectrometry of peptides and proteins remain unclear. Random backbone cleavage probability and the nonspecific nature of ECD toward amino acid sequence have been reported, cont ...

Springer-Verlag2009

On-chip mesoporous functionalized magnetic microspheres for protein sequencing by extended bottom-up mass spectrometry

Hubert Girault, Yury Tsybin, Liang Qiao, Natalia Gasilova, Kristina Srzentic

Limited amount and extreme concentration variability of proteomic-related samples require efficient analyte preconcentration and purification prior to the mass spectrometry (MS)-based analysis. Preferably, these steps should be coupled on-line with chosen ...

American Chemical Society2016

Middle-down analysis of monoclonal antibodies with electron transfer dissociation Orbitrap FTMS

Yury Tsybin, Luca Fornelli, Daniel Ayoub

The rapid growth of approved biotherapeutics, e.g., monoclonal antibodies or immunoglobulins G (IgGs), demands improved techniques for their quality control. Traditionally, proteolysis-based bottom-up mass spectrometry (MS) has been employed. However, the ...

Amer Chemical Soc2014

Radical Stability Directs Electron Capture and Transfer Dissociation of Beta-Amino Acids in Peptides

Yury Tsybin, Aleksey Vorobyev, Hisham Ben Hamidane

We report on the characteristics of the radical-ion-driven dissociation of a diverse array of beta-amino acids incorporated into alpha-peptides, as probed by tandem electron-capture and electron-transfer dissociation (ECD/ETD) mass spectrometry. The report ...

2010

Statistical Analysis of Ion Mobility Spectrometry. I. Unbiased and Guided Replica-Exchange Molecular Dynamics

Yury Tsybin

Achieving (bio) macromolecular structural assignment from the interpretation of ion mobility spectrometry (IMS) experiments requires successful comparison with computer modeling. Replica-exchange molecular dynamics simulations with suitable force fields no ...

2012

Glycan variability on a recombinant IgG antibody transiently produced in HEK-293E cells

Florian Maria Wurm, Yury Tsybin, Lucia Baldi Unser, Luca Fornelli, Simone Schmitt

In this study, a recombinant monoclonal IgG antibody was produced by transient gene expression (TGE) in suspension-adapted HEK-293E cells. The objective of the study was to determine the variation in recombinant IgG yield and glycosylation in ten independe ...

Elsevier2012

Spatially-distributed cyclotron oscillators approach to FT-ICR MS at the true cyclotron frequency: Computational evaluation of sensitivity

Yury Tsybin, Anton Kozhinov, Konstantin Nagornov

Routine Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with ion detection at the unreduced (true) cyclotron frequency, instead of the reduced cyclotron frequency, has recently been demonstrated experimentally and supported computat ...

ELSEVIER2021

Deamidation and Transamidation of Substance P by Tissue Transglutaminase Revealed by Electron-Capture Dissociation Fourier Transform Mass Spectrometry (Chem. Eur. J. 2/2011)

Horst Arthur Vogel, Yury Tsybin, Adrian Schmid, Luca Fornelli, Luigino Grasso

Tissue transglutaminase (tTGase) catalyzes both deamidation and transamidation of peptides and proteins by using a peptidyl glutamine as primary substrate. A precise consensus sequence for the enzyme is unknown and the ratio between deamidated and transami ...

Wiley-Blackwell2011