AI Article Synopsis
Article Abstract
Cross-linking mass spectrometry is an emerging structural biology technique. Almost exclusively, the analyzer of choice for such an experiment has been the Orbitrap. We present an optimized protocol for the use of a Synapt G2-Si for the analysis of cross-linked peptides. We first tested six different energy ramps and analyzed the fragmentation behavior of cross-linked peptides identified by xQuest. By combining the most successful energy ramps, cross-link yield can be increased by up to 40%. When compared to previously published Orbitrap data, the Synapt G2-Si also offers improved fragmentation of the β peptide. In order to improve cross-link quality control we have also developed ValidateXL, a programmatic solution that works with existing cross-linking software to improve cross-link quality control.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383985 | PMC |
| http://dx.doi.org/10.1021/acs.analchem.8b02319 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Locating Polyubiquitin Receptors on the 19S Regulatory Proteasome of by Cross-Linking Mass Spectrometry.
J Am Soc Mass Spectrom
January 2025
Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, United States.
The effectiveness of state-of-the-art cross-linking strategies and mass spectrometry (MS) detection was explored in an important biological context, namely, the ubiquitin-proteasome system, which is responsible for most of the regulated protein degradation in eukaryotic cells. The locations of possible binding sites on the 19S proteasome regulatory particle for Lys linked polyubiquitin chains were examined using cross-linking strategies and MS based detection by comparing two types of cross-linkers: a (bis)-sulfosuccinimidyl suberate (BS) and diethyl suberothioimidate (DEST). The well-established BS-based strategy produced 328 cross-linked peptides; however, no ubiquitin-19S cross-links were observed.
View Article and Find Full Text PDFClick chemistry-driven asymmetrically modified superhydrophobic/superhydrophilic gelatin sponge for improved dry socket prophylaxis.
Int J Biol Macromol
January 2025
Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Ji'nan 250012, China. Electronic address:
Dry socket, a common painful complication after tooth extraction, is typically caused by improper blood clot formation or its premature dislodgement, often exacerbated by bacterial infections. Traditional gelatin sponges, widely used as clinical fillers, provide favorable biocompatibility and hemostatic support but suffer from suboptimal hemostatic efficiency, lack of antimicrobial properties, and insufficient anticoagulant factors, which increase the risk of dry socket. Addressing these limitations, a novel tannic acid cross-linked gelatin sponge has been developed using directional lyophilization.
View Article and Find Full Text PDFThe serum level of sclerostin decreases in radiographic axial spondyloarthritis patients with fatty lesions.
Arthritis Res Ther
January 2025
Department of Rheumatology, the Fifth Affiliated Hospital of Sun Yat-sen University, 52 Meihua East Road, Zhuhai, People's Republic of China.
Background: Currently, the pathophysiology of new bone formation in radiographic axial spondyloarthritis (r-axSpA) remains unclear. Cellular elements and their secreted bone turnover markers might be one of the underlying mechanisms that drive the new bone formation. Our study aimed to investigate the role of bone turnover markers in r-axSpA patients with fatty lesions.
View Article and Find Full Text PDFCharacterization by LC-MS/MS analysis of KLH vaccine conjugated with a tick antigen peptide.
Analyst
January 2025
Department of Proteomics, Mass Spectrometry Laboratory, Center for Genetic Engineering and Biotechnology, 31 Avenue, Cubanacan, Playa, Havana, Cuba.
Keyhole limpet haemocyanins (KLH1 and KLH2) from , are multi-subunit oxygen-carrying metalloproteins of approximately 3900 amino acids, that are widely used as carrier proteins in conjugate vaccines and in immunotherapy. KLHs and their derived conjugate vaccines are poorly characterized by LC-MS/MS due to their very stable supramolecular structures with megadalton molecular mass, and their resistance to efficient digestion with standard protocols. KLH1 and KLH2 proteins were conjugated to the conserved P0 peptide (pP0), derived from the P0 acidic ribosomal protein of sp.
View Article and Find Full Text PDFAssociation between fibrinogen-to-albumin ratio and bone metabolism markers (β-CTX and P1NP) in Chinese individuals with osteoporotic fracture: a cross-sectional investigation.
BMC Musculoskelet Disord
January 2025
Department of Orthopedics, Affiliated Kunshan Hospital of Jiangsu University, No. 566 East of Qianjin Road, Suzhou, Jiangsu, 215300, China.
Objective: Research on the link between inflammatory indicators and markers of bone metabolism is currently lacking, especially the interaction between Procollagen type 1 N-terminal propeptide (P1NP), the β-C-terminal telopeptide of type 1 collagen (β-CTX), and the fibrinogen-to-albumin ratio (FAR). This study intends to fill that knowledge gap by investigating the possible link between inflammatory indicators and bone metabolism.
Methods: This observational study included 718 individuals diagnosed with osteoporotic fractures from Kunshan Hospital Affiliated to Jiangsu University between January 2017 and July 2022.
Want 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!