Cross-linking mass spectrometry for investigating protein conformations and protein–protein interactions─ a method for all seasons

L Piersimoni, PL Kastritis, C Arlt, A Sinz - Chemical Reviews, 2021 - ACS Publications
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …

Deciphering molecular interactions by proximity labeling

W Qin, KF Cho, PE Cavanagh, AY Ting - Nature methods, 2021 - nature.com
Many biological processes are executed and regulated through the molecular interactions of
proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the …

Mitochondrial proteins: from biogenesis to functional networks

N Pfanner, B Warscheid, N Wiedemann - Nature reviews Molecular cell …, 2019 - nature.com
Mitochondria are essential for the viability of eukaryotic cells as they perform crucial
functions in bioenergetics, metabolism and signalling and have been associated with …

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

ZL Chen, JM Meng, Y Cao, JL Yin, RQ Fang… - Nature …, 2019 - nature.com
We describe pLink 2, a search engine with higher speed and reliability for proteome-scale
identification of cross-linked peptides. With a two-stage open search strategy facilitated by …

Proteome discoverer—a community enhanced data processing suite for protein informatics

BC Orsburn - Proteomes, 2021 - mdpi.com
Proteomics researchers today face an interesting challenge: how to choose among the
dozens of data processing and analysis pipelines available for converting tandem mass …

Mass-spectrometric exploration of proteome structure and function

R Aebersold, M Mann - Nature, 2016 - nature.com
Numerous biological processes are concurrently and coordinately active in every living cell.
Each of them encompasses synthetic, catalytic and regulatory functions that are, almost …

Complement is activated by elevated IgG3 hexameric platforms and deposits C4b onto distinct antibody domains

L Abendstein, DJ Dijkstra, RTN Tjokrodirijo… - Nature …, 2023 - nature.com
IgG3 is unique among the IgG subclasses due to its extended hinge, allotypic diversity and
enhanced effector functions, including highly efficient pathogen neutralisation and …

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology

FJ O'Reilly, J Rappsilber - Nature structural & molecular biology, 2018 - nature.com
Over the past decade, cross-linking mass spectrometry (CLMS) has developed into a robust
and flexible tool that provides medium-resolution structural information. CLMS data provide …

Mass spectrometry‐based protein–protein interaction networks for the study of human diseases

AL Richards, M Eckhardt, NJ Krogan - Molecular systems biology, 2021 - embopress.org
A better understanding of the molecular mechanisms underlying disease is key for
expediting the development of novel therapeutic interventions. Disease mechanisms are …

Understanding the extracellular vesicle surface for clinical molecular biology

S Hallal, Á Tűzesi, GE Grau… - Journal of …, 2022 - Wiley Online Library
Extracellular vesicles (EVs) are lipid‐membrane enclosed nanoparticles that play significant
roles in health and disease. EVs are abundant in body fluids and carry an array of molecules …