AI Article Synopsis
- Cross-linking mass spectrometry (XL-MS) is a crucial method for studying protein interactions, and this study improves its capabilities by using Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments.
- The research addresses challenges in XL-MS data interpretation, particularly for low abundant cross-linked peptides and complex spectra, by proposing a peptide-centric analysis method and integrating data-independent acquisition (DIA) into the XL-MS framework.
- A new workflow is developed for processing PASEF-derived data with Bruker Daltonics software, facilitating compatibility with MeroX and Skyline tools, ultimately enhancing the identification of cross-linked proteins in complex mixtures.
Article Abstract
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11099889 | PMC |
| http://dx.doi.org/10.1021/acs.analchem.4c00829 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Proteomics Reveals Mechanisms of Delayed Keratoconus Progression: A Study of Corneas Following Two Light-Activated Crosslinking Treatments.
Invest Ophthalmol Vis Sci
January 2025
University Eye Clinic Maastricht, Maastricht University Medical Center, Maastricht, the Netherlands.
Article Synopsis
- This study investigates the biological changes in rabbit corneas caused by two light-activated corneal stiffening methods: riboflavin with UVA and WST11 with NIR.
- Differentially expressed proteins were identified following treatments, showing RF-D/UVA affected cell metabolism and keratocyte differentiation, while WST-D/NIR influenced extracellular matrix regulation.
- The findings reveal a metabolic shift towards glycolysis in RF-D/UVA treated corneas compared to normal respiration in WST-D/NIR treated corneas, highlighting the distinct biological effects of each treatment.
Characterization of the N- and C-terminal domain interface of the three main apoE isoforms: A combined quantitative cross-linking mass spectrometry and molecular modeling study.
Biochim Biophys Acta Gen Subj
January 2025
Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Brussels, Belgium.
Apolipoprotein E (apoE) polymorphism is associated with different pathologies such as atherosclerosis and Alzheimer's disease. Knowledge of the three-dimensional structure of apoE and isoform-specific structural differences are prerequisites for the rational design of small molecule structure modulators that correct the detrimental effects of pathological isoforms. In this study, cross-linking mass spectrometry (XL-MS) targeting Asp, Glu and Lys residues was used to explore the intramolecular interactions in the E2, E3 and E4 isoforms of apoE.
View Article and Find Full Text PDFDeep eutectic solvent-mediated extraction of lignin: A novel strategy for producing high-quality biopolymers in controlled-release mulching applications.
Int J Biol Macromol
January 2025
Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, PR China. Electronic address:
Microplastic contamination of low-density polyethylene mulch and nutrient loss from fertilizers present significant challenges in the crop-growing. In this study, the focus was on creating a biodegradable film that combines the advantages of plastic film, thermal insulation and water retention, as well as the controlled release of fertilizer. A key innovation was the efficient introduction of low molecular weight and low dispersibility of poplar lignin into chitosan and polyvinyl alcohol matrices.
View Article and Find Full Text PDFSite-selective photo-crosslinking for the characterisation of transient ubiquitin-like protein-protein interactions.
PLoS One
January 2025
Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
Non-covalent protein-protein interactions are one of the most fundamental building blocks in cellular signalling pathways. Despite this, they have been historically hard to identify using conventional methods due to their often weak and transient nature. Using genetic code expansion and incorporation of commercially available unnatural amino acids, we have developed a highly accessible method whereby interactions between biotinylated ubiquitin-like protein (UBL) probes and their binding partners can be stabilised using ultraviolet (UV) light-induced crosslinks.
View Article and Find Full Text PDFVarious Options for Covalent Immobilization of Cysteine Proteases-Ficin, Papain, Bromelain.
Int J Mol Sci
January 2025
Biophysics and Biotechnology Department, Voronezh State University, 1 Universitetskaya Square, 394018 Voronezh, Russia.
This study explores various methods for the covalent immobilization of cysteine proteases (ficin, papain, and bromelain). Covalent immobilization involves the formation of covalent bonds between the enzyme and a carrier or between enzyme molecules themselves without a carrier using a crosslinking agent. This process enhances the stability of the enzyme and allows for the creation of preparations with specific and controlled properties.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!