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 …

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

M Matzinger, K Mechtler - Journal of proteome research, 2020 - ACS Publications
Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein–
protein interactions or to uncover protein structures in living cells, tissues, or organelles. The …

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 …

Dynamic interactomics by cross-linking mass spectrometry: map** the daily cell life in postgenomic era

L Santorelli, M Caterino, M Costanzo - OMICS: A Journal of …, 2022 - liebertpub.com
The majority of processes that occur in daily cell life are modulated by hundreds to
thousands of dynamic protein–protein interactions (PPI). The resulting protein complexes …

Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross‐Linking

H Lu, Z Zhu, L Fields, H Zhang… - Mass Spectrometry …, 2024 - Wiley Online Library
The exploration of protein structure and function stands at the forefront of life science and
represents an ever‐expanding focus in the development of proteomics. As mass …

High-sensitivity proteome-scale searches for crosslinked peptides using CRIMP 2.0

DA Crowder, V Sarpe, BC Amaral, NI Brodie… - Analytical …, 2023 - ACS Publications
Crosslinking mass spectrometry (XL-MS) is a valuable technique for generating point-to-
point distance measurements in protein space. However, cell-based XL-MS experiments …

Cross‐linking reactions in food proteins and proteomic approaches for their detection

G Renzone, S Arena, A Scaloni - Mass Spectrometry Reviews, 2022 - Wiley Online Library
Various protein cross‐linking reactions leading to molecular polymerization and covalent
aggregates have been described in processed foods. They are an undesired side effect of …

Exhaustive cross-linking search with protein feedback

C Zhou, S Dai, Y Lin, S Lian, X Fan, N Li… - Journal of Proteome …, 2022 - ACS Publications
Improving the sensitivity of protein–protein interaction detection and protein structure
probing is a principal challenge in cross-linking mass spectrometry (XL-MS) data analysis. In …

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex

MJ Birklbauer, F Müller, SS Geetha… - Communications …, 2024 - nature.com
The field of crosslinking mass spectrometry has seen substantial advancements over the
past decades, enabling the structural analysis of proteins and protein complexes and …

ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis

C Zhou, S Dai, S Lai, Y Lin, X Zhang, N Li, W Yu - BMC bioinformatics, 2023 - Springer
Background Cross-linking mass spectrometry (XL-MS) is a powerful technique for detecting
protein–protein interactions (PPIs) and modeling protein structures in a high-throughput …