Protein sequencing

Applied sciences
Biological engineering
Biotechnology
Bioinformatics

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Combining multi-stage ion mobility spectrometry with cryogenic infrared spectroscopy for glycan analysis

Priyanka Bansal

Structural analysis of biomolecules is essential to understanding biological processes. Among the various classes of biomolecules, glycans have gained significant attention recently due to their ubiquitous roles in biological systems. However, study of gly ...

EPFL2022

Ultraviolet Photodissociation of Peptides: New Insight on the Mobile Proton Model

Oleg Boyarkine, Aleksandr Pereverzev, Elizaveta Solovyeva

In this work, we study the mechanism of peptide photodissociation by ultraviolet irradiation at 193 nm wavelength and discuss the role of ionization proton in this process. We found that substituting the ionization proton for the alkali metal cations (sodi ...

PLEIADES PUBLISHING INC2020

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

A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage

Beat Fierz, Sinan Kilic, Iuliia Boichenko, Carolin Christine Lechner

The cellular response to DNA damage results in a signaling cascade that primes chromatin for repair. Combinatorial post-translational modifications (PTMs) play a key role in this process by altering the physical properties of chromatin and recruiting downs ...

2018

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Duccio Malinverni

Recent advances in DNA sequencing technologies led to the accumulation of enormous quantities of genetic information available in public databases. This rapid growth of available biological datasets calls for quantitative analysis tools and concomitantly o ...

EPFL2018

Scanning tunneling microscopy on large bio-molecular systems on surfaces

Sebastian Koslowski

The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of int ...

EPFL2017

Thermodynamic bounds on the ultra- and infra-affinity of Hsp70 for its substrates

Paolo De Los Rios, Basile Nguyen

The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting proteins against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into organelles. These f ...

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

Middle-down approaches for mass spectrometry-based protein identification and characterization

Kristina Srzentic

Mass spectrometry (MS) has emerged over the last two decades as the analytical technique of choice in systems-level protein studies, known as proteomics. Two are the MS-based approaches generally applied to proteomics: bottom-up (BU), which relies on the p ...

EPFL2016

A mammalian transcription factor-specific peptide repository for targeted proteomics

Bart Deplancke, Jovan Simicevic, Romain Hamelin, Marc Moniatte

Site-specific transcription factors (TFs) play an essential role in mammalian development and function as they are vital for the majority of cellular processes. Despite their biological importance, TF proteomic data is scarce in the literature, likely due ...

Wiley-Blackwell2015

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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

Elsevier Science Bv2017