Cross-linking mass spectrometry (XL-MS): An emerging technology for interactomics and structural biology

C Yu, L Huang - Analytical chemistry, 2017 - pmc.ncbi.nlm.nih.gov
Protein-protein interactions are fundamental to the formation of intricate interaction networks
and the assembly of multisubunit protein complexes that represent the functional …

Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies

C Schmidt, H Urlaub - Current opinion in structural biology, 2017 - Elsevier
Highlights•CX-MS identifies protein–protein interactions.•Cross-linking strategies targeting
different amino acids are available.•Combining CX-MS and cryo-EM delivers high-resolution …

Identification and characterization of protein cross-links induced by oxidative reactions

P Hägglund, M Mariotti, MJ Davies - Expert review of proteomics, 2018 - Taylor & Francis
Introduction: Protein cross-links are common in biological systems and are generated both
deliberately as a part of normal metabolism and also accidently as a result of exposure to …

Identification of MS-cleavable and noncleavable chemically cross-linked peptides with MetaMorpheus

L Lu, RJ Millikin, SK Solntsev, Z Rolfs… - Journal of proteome …, 2018 - ACS Publications
Protein chemical cross-linking combined with mass spectrometry has become an important
technique for the analysis of protein structure and protein–protein interactions. A variety of …

Mass-Spectrometry-Based Identification of Cross-Links in Proteins Exposed to Photo-Oxidation and Peroxyl Radicals Using 18O Labeling and Optimized Tandem …

M Mariotti, F Leinisch, DJ Leeming… - Journal of proteome …, 2018 - ACS Publications
Protein cross-links are formed in regulated biochemical processes in many biological
systems, but they are also generated inadvertently via the reactions of exogenous or …

The Vaccinia virion: Filling the gap between atomic and ultrastructure

Y Mirzakhanyan, P Gershon - PLoS Pathogens, 2019 - journals.plos.org
We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-
protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective …

Cross‐linked peptide identification: A computational forest of algorithms

Ş Yılmaz, GA Shiferaw, J Rayo… - Mass spectrometry …, 2018 - Wiley Online Library
Chemical cross‐linking analyzed by mass spectrometry (XL‐MS) has become an important
tool in unravelling protein structure, dynamics, and complex formation. Because the analysis …

Structural investigation of proteins and protein complexes by chemical cross-linking/mass spectrometry

C Piotrowski, A Sinz - Integrative Structural Biology with Hybrid Methods, 2018 - Springer
During the last two decades, cross-linking combined with mass spectrometry (MS) has
evolved as a valuable tool to gain structural insights into proteins and protein assemblies …

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 …

Exhaustively identifying cross-linked peptides with a linear computational complexity

F Yu, N Li, W Yu - Journal of proteome research, 2017 - ACS Publications
Chemical cross-linking coupled to mass spectrometry is a powerful tool to study protein–
protein interactions and protein conformations. Two linked peptides are ionized and …