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

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A recipe for cracking the quantum scaling limit with machine learned electron densities

Mario Geiger

A long-standing goal of science is to accurately simulate large molecular systems using quantum mechanics. The poor scaling of current quantum chemistry algorithms on classical computers, however, imposes an effective limit of about a few dozen atoms on tr ...

IOP Publishing Ltd2023

Combining ion mobility spectrometry and cryogenic ion spectroscopy with enzymatic digestion/synthesis for the study of N-linked glycans

Irina Märki

Glycans play an essential role in numerous physiological and pathological processes of living organisms. Despite their significant biological relevance, glycobiology remains one of the least explored fields of biochemistry. The intrinsic isomeric complexit ...

EPFL2023

Electron spectrometer calibration method

Tobias Kippenberg, Fabrizio Carbone, Arslan Sajid Raja, Thomas La Grange, Yujia Yang, Alexey Sapozhnik, Bruce Michael Raleigh Weaver, Paolo Cattaneo

The present invention concerns an energy dispersion calibration method for calibrating an electron spectrometer of an electron spectrometer system including at least one electron emission source, electron optics and the electron spectrometer. The method co ...

2023

Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints

Pablo Rivera Fuentes, Salome Riccarda Püntener

The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but the ...

AMER CHEMICAL SOC2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

Implementing Multi-Electron Transfer Strategies in Uranium Chemistry

Dieuwertje Katelijn Modder

In the last decades, the activation of small molecules has attracted increasing attention for their use as cheap and abundant feedstock. Low-oxidation state uranium complexes have displayed high reactivity towards small molecules thanks to their unique pro ...

EPFL2023

De novo protein design by inversion of the AlphaFold structure prediction network

Benedict Dieter Gregor Wolf, Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Hamed Khakzad

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

Identification of human milk oligosaccharide positional isomers by combining IMS-CID-IMS and cryogenic IR spectroscopy

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Vasyl Yatsyna, Ali H Abikhodr

High-resolution ion mobility spectrometry (IMS) coupled with cryogenic infrared spectroscopy has proven to be a powerful technique for the identification of oligosaccharides. However, the need for an extensive database, combined with the scarcity of pure s ...

2023

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

David Daniel Girardier, Fabio Pietrucci, Sara Bonella

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

Aip Publishing2023

Spectroscopic characterisation of TCV divertor towards a detached regime

Lorenzo Martinelli

The challenge of power exhaust of the high heat and particle fluxes foreseen for ITER and the forthcoming nuclear fusion reactors can be mitigated by operating in a detached divertor regime. This regime has been the object of three decades of studies, as i ...

EPFL2023

Predicting Ion Diffusion from the Shape of Potential Energy Landscapes

Berend Smit, Senja Dominique Barthel

We present an efficient method to compute diffusion coefficients of multiparticle systems with strong interactions directly from the geometry and topology of the potential energy field of the migrating particles. The approach is tested on Li-ion diffusion ...

Amer Chemical Soc2023