Mass spectrometry‐based high‐throughput proteomics and its role in biomedical studies and systems biology

CB Messner, V Demichev, Z Wang, J Hartl… - …, 2023 - Wiley Online Library
There are multiple reasons why the next generation of biological and medical studies
require increasing numbers of samples. Biological systems are dynamic, and the effect of a …

The dynamic fungal genome: polyploidy, aneuploidy and copy number variation in response to stress

P Vande Zande, X Zhou… - Annual review of …, 2023 - annualreviews.org
Fungal species have dynamic genomes and often exhibit genomic plasticity in response to
stress. This genome plasticity often comes with phenotypic consequences that affect fitness …

Cancer aneuploidies are shaped primarily by effects on tumour fitness

J Shih, S Sarmashghi, N Zhakula-Kostadinova… - Nature, 2023 - nature.com
Aneuploidies—whole-chromosome or whole-arm imbalances—are the most prevalent
alteration in cancer genomes,. However, it is still debated whether their prevalence is due to …

The proteomic landscape of genome-wide genetic perturbations

CB Messner, V Demichev, J Muenzner, SK Aulakh… - Cell, 2023 - cell.com
Functional genomic strategies have become fundamental for annotating gene function and
regulatory networks. Here, we combined functional genomics with proteomics by quantifying …

Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage

J Zerbib, MR Ippolito, Y Eliezer, G De Feudis… - Nature …, 2024 - nature.com
Aneuploidy is a hallmark of human cancer, yet the molecular mechanisms to cope with
aneuploidy-induced cellular stresses remain largely unknown. Here, we induce …

[HTML][HTML] Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan

C Correia-Melo, S Kamrad, R Tengölics, CB Messner… - Cell, 2023 - cell.com
Metabolism is deeply intertwined with aging. Effects of metabolic interventions on aging
have been explained with intracellular metabolism, growth control, and signaling. Studying …

Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics

L Szyrwiel, L Sinn, M Ralser, V Demichev - BioRxiv, 2022 - biorxiv.org
We present Slice-PASEF, a novel mass spectrometry technology based on trapped ion
mobility separation of ions. Slice-PASEF allows to achieve the theoretical maximum of …

Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics

MEH White, LR Sinn, DM Jones, J de Folter… - Nature Biomedical …, 2024 - nature.com
Protein glycosylation, a complex and heterogeneous post-translational modification that is
frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a …

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

J Rojas, J Hose, HA Dutcher, M Place, JF Wolters… - Cell Genomics, 2024 - cell.com
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid
phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs …

Cellular control of protein levels: A systems biology perspective

V Munro, V Kelly, CB Messner, G Kustatscher - Proteomics, 2024 - Wiley Online Library
How cells regulate protein levels is a central question of biology. Over the past decades,
molecular biology research has provided profound insights into the mechanisms and the …