Publications de Yury Tsybin | EPFL Graph Search

Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak

Yury Tsybin, Laure Menin, Anton Kozhinov, Natalia Gasilova, Konstantin Nagornov

Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus the ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for ...

Amer Chemical Soc2024

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

Drug-to-Antibody Ratio Estimation via Proteoform Peak Integration in the Analysis of Antibody-Oligonucleotide Conjugates with Orbitrap Fourier Transform Mass Spectrometry

Yury Tsybin, Laure Menin, Anton Kozhinov, Natalia Gasilova, Konstantin Nagornov

The therapeutic efficacy and pharmacokinetics of antibody-drug conjugates (ADCs) in general, and antibody-oligonucleotide conjugates (AOCs) in particular, depend on the drug-to-antibody ratio (DAR) distribution and average value. The DAR is considered a cr ...

AMER CHEMICAL SOC2021

Drosophila melanogaster cloak their eggs with pheromones, which prevents cannibalism

Yury Tsybin, Laure Menin, Konstantin Nagornov

Oviparous animals across many taxa have evolved diverse strategies that deter egg predation, providing valuable tests of how natural selection mitigates direct fitness loss. Communal egg laying in nonsocial species minimizes egg predation. However, in cann ...

2019

Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody

Yury Tsybin, Laure Menin, Luca Fornelli, Anton Kozhinov, Natalia Gasilova, Kristina Srzentic, Konstantin Nagornov, Daniel Ayoub

Pairing light and heavy chains in monoclonal antibodies (mAbs) using top-down (TD) or middle-down (MD) mass spectrometry (MS) may complement the sequence information on single chains provided by high-throughput genomic sequencing and bottom-up proteomics, ...

AMER CHEMICAL SOC2018

Device and Method for Ion Cyclotron Resonance Mass Spectrometry

Yury Tsybin, Anton Kozhinov, Konstantin Nagornov

The present invention relates to a method and device for measuring m/z ratios of ions in ion cyclotron resonance (ICR) mass spectrometry. The described ion traps for ICR mass spectrometry are distinct from the previous configurations by having one or many ...

2017

Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer

Yury Tsybin, Luca Fornelli, Daniel Ayoub

The increasing importance of immunoglobulins G (IgGs) as biotherapeutics calls for improved structural characterization methods designed for these large (similar to 150 kDa) macromolecules. Analysis workflows have to be rapid, robust, and require minimal s ...

Elsevier Science Bv2017

Monitoring Membrane Lipidome Turnover by Metabolic N-15 Labeling and Shotgun Ultra-High-Resolution Orbitrap Fourier Transform Mass Spectrometry

Yury Tsybin, Kristina Srzentic, Konstantin Nagornov

Lipidomes undergo permanent extensive remodeling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic N-15 labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) to quantify ...

Amer Chemical Soc2017

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

Ion Trap with Narrow Aperture Detection Electrodes for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Yury Tsybin, Anton Kozhinov, Konstantin Nagornov

The current paradigm in ion trap (cell) design for Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the ion detection with wide aperture detection electrodes. Specifically, excitation and detection electrodes are typically 90A deg ...

Springer2015

Gold finger formation studied by high-resolution mass spectrometry and in silico methods

Yury Tsybin, Angela Casini, Unige Anna Laskay

High-resolution mass spectrometry and quantum mechanics/molecular mechanics studies were employed for characterizing the formation of two gold finger (GF) domains from the reaction of zinc fingers (ZF) with gold complexes. The influence of both the gold ox ...

Royal Society of Chemistry2015

Identification of hemoglobin variants by top-down mass spectrometry using selected diagnostic product ions

Yury Tsybin

Hemoglobin disorder diagnosis is a complex procedure combining several analytical steps. Due to the lack of specificity of the currently used protein analysis methods, the identification of uncommon hemoglobin variants (proteoforms) can become a hard task ...

Springer Heidelberg2015

Producing absorption mode Fourier transform ion cyclotron resonance mass spectra with non-quadratic phase correction functions

Yury Tsybin, Konstantin Zhurov, Anton Kozhinov, Konstantin Nagornov

RATIONALE: Previously described methods for producing absorption mode Fourier transform ion cyclotron resonance (FTICR) mass spectra have all relied on the phase correction function being quadratic. This assumption has been found to be invalid for some ins ...

Wiley-Blackwell2015

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

Yury Tsybin, Konstantin Zhurov, Laure Menin, 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

On the use of electron capture rate constants to describe electron capture dissociation mass spectrometry of peptides

Yury Tsybin, Konstantin Zhurov, Aleksey Vorobyev, Unige Anna Laskay

Electron capture dissociation (ECD) tandem mass spectrometry (MS/MS) is a powerful analytical tool for peptide and protein structure analysis. The product ion abundance (PIA) distribution in ECD MS/MS is known to vary as a function of electron irradiation ...

Im Publications2015

Time-dependent frequency of ion motion in Fourier transform mass spectrometry

Yury Tsybin

Recent experimental and theoretical findings suggest that the concept of time-dependent instantaneous frequency(IF) is required to comprehensively describe ion motion and mass spectra generation in Fourier transform mass spectrometry (FTMS). Here, we deriv ...

Elsevier Science Bv2015

Distinguishing analyte from noise components in mass spectra of complex samples: where to cut the noise?

Yury Tsybin, Konstantin Zhurov, Luca Fornelli, Anton Kozhinov

Fourier transform mass spectrometry (FTMS) enables comprehensive analysis of complex molecular mixtures. Given the broad intensity ranges of components in the mass spectra, it is imperative to accurately determine a noise threshold level above which peak a ...

Amer Chemical Soc2014

Ping-Pong Protons: How Hydrogen Bonding Networks Facilitate Heterolytic Bond Cleavages in Peptide Radical Cations

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

Electron capture and electron transfer dissociation (ECD/ETD) tandem mass spectrometry (MS/MS) are commonly employed techniques for biomolecular analysis. The ECD/ETD process predominately cleaves N-C-alpha peptide backbone bonds, leading to primary sequen ...

Amer Chemical Soc2014

Extended Bottom-Up Proteomics with Secreted Aspartic Protease Sap9

Yury Tsybin, Unige Anna Laskay, Kristina Srzentic

We investigate the benefits and experimental feasibility of approaches enabling the shift from short (1.7 kDa on average) peptides in bottom-up proteomics to about twice longer (similar to 3.2 kDa on average) peptides in the so-called extended bottom-up pr ...

Elsevier Science Bv2014

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

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

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