Publications related to Practical Considerations for Improving the Productivity of Mass Spectrometry-based Proteomics

Related publications (34)

Top-Down and Middle-Down Mass Spectrometry of Antibodies

This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional c ...

Elsevier BV2025

Optimizing photon capture: advancements in amorphous silicon-based microchannel plates

Edoardo Charbon, Christophe Ballif, Claudio Bruschini, Nicolas Würsch, Luca Massimiliano Antognini, Emanuele Ripiccini, Jad Benserhir, Samira Alexandra Frey

Microchannel plates are electron multipliers widely used in applications such as particle detection, imaging, or mass spectrometry and are often paired with a photocathode to enable photon detection. Conventional microchannel plates, made of glass fibers, ...

2025

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

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

Nanostructure and Optical Property Tailoring of Zinc Tin Nitride Thin Films through Phenomenological Decoupling: A Pathway to Enhanced Control

Aïcha Hessler-Wyser, Johann Michler, Caroline Hain, Daniele Casari

This work addresses the need for precise control of thin film sputtering processes to enable thin film material tailoring on the example of zinc tin nitride (ZTN) thin films deposited via microwave plasma-assisted high power reactive magnetron sputtering ( ...

Amer Chemical Soc2024

Gradients of Deposition and In Situ Production Drive Global Glacier Organic Matter Composition

Tom Ian Battin, Hannes Markus Peter, Matteo Tolosano, Vincent Henri De Staercke, Michail Styllas, Martina Andrea Schön

Runoff from rapidly melting mountain glaciers is a dominant source of riverine organic carbon in many high-latitude and high-elevation regions. Glacier dissolved organic carbon is highly bioavailable, and its composition likely reflects internal (e.g., aut ...

2024

Innovative Biomarkers for Obesity and Type 1 Diabetes Based on Bifidobacterium and Metabolomic Profiling

Stephan Morgenthaler, Paul Refinetti

The role of Bifidobacterium species and microbial metabolites such as short-chain fatty acids (SCFAs) and human milk oligosaccharides in controlling intestinal inflammation and the pathogenesis of obesity and type 1 diabetes (T1D) has been largely studied ...

MDPI2024

Neurobiological and metabolic basis of motivation and effort-based decision-making - A human 1H-MRS, fMRI and machine learning study

Arthur Barakat

Motivation is a multifaceted phenomenon that we explore within the framework of decision-making. Through this cognitive process, actions are directed towards specific goals by performing a trade-off between the cost and benefit of an action. The dorsomedia ...

EPFL2024

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

Controlled Formation of Nanoribbons and Their Heterostructures via Assembly of Mass-Selected Inorganic Ions

Klaus Kern

Control of nanomaterial dimensions with atomic precision through synthetic methods is essential to understanding and engineering of nanomaterials. For single-layer inorganic materials, size and shape controls have been achieved by self-assembly and surface ...

Wiley-V C H Verlag Gmbh2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

Versatile Capillary Cells for Handling Concentrated Samples in Analytical Ultracentrifugation

Francesco Stellacci, Quy Ong Khac, Xufeng Xu

In concentrated macromolecular dispersions, far-from-ideal intermolecular interactions determine the dispersion behaviors including phase transition, crystallization, and liquid-liquid phase separation. Here, we present a novel versatile capillary-cell des ...

Amer Chemical Soc2024

Modulating Weak Protein-Protein Cross-Interactions by the Addition of Free Amino Acids at Millimolar Concentrations

Pamina Winkler, Francesco Stellacci, Cécilia Laetitia Carla Siri

In this paper, we quantify weak protein-protein interactions in solution using cross-interaction chromatography (CIC) and surface plasmon resonance (SPR) and demonstrate that they can be modulated by the addition of millimolar concentrations of free amino ...

2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Mixed ionic-electronic conduction in Ruddlesden-Popper and Dion-Jacobson layered hybrid perovskites with aromatic organic spacers

Michael Graetzel, Jovana Milic, Joachim Maier, Algirdas Ducinskas

The understanding of mixed ionic-electronic conductivity in hybrid perovskites has enabled major advances in the development of optoelectronic devices based on this class of materials. While recent investigations revealed the potential of using dimensional ...

Royal Society of Chemistry2024

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

Using Hadamard Transform Multiplexed IR Spectroscopy Together with a Segmented Ion Trap for the Identification of Mobility-Selected Isomers

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

The high isomeric complexity of glycans makes them particularly difficult to analyze. While ultra-high-resolution ion mobility spectrometry(IMS) can offer rapid baseline separation of many glycan isomers,their unambiguous identification remains a challengi ...

2023

Advancing Glycan Analysis: Cryogenic Ion Spectroscopy for Database-Driven Identification

Ali H Abikhodr

Glycans play a pivotal role in both physiological processes; however, the field of glycobiology remains relatively understudied within biochemistry. The intricate complexity of glycans, coupled with their abundance of isomeric forms, presents formidable ch ...

EPFL2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023