Composition characterization of various viperidae snake venoms using MS-based proteomics N-glycoproteomics and N-glycomics

Categorization and Characterization of Snake Venom Variability through Intact Toxin Analysis by Mass Spectrometry

The variation in venom between and within snake species has significant implications for snakebite treatment. This highlights the critical importance of studying venom composition and its variations, not only for medical purposes but also from an evolutionary perspective. This study explores analytics for characterizing venom variability, focusing on venom toxin accurate masses, and emphasizes how the complexity of studying snake venom variability can be addressed by using liquid chromatography mass spectrometry (LC-MS) analysis with bioinformatics tools. This was demonstrated by investigating LC-MS data obtained from the venoms of 15 true cobras (Naja spp.), 5 mambas (Dendroaspis spp.) and 28 vipers (Crotalus and Bothrops spp.; total of 20 Elapidae and 28 Viperidae venoms), with newly developed bioinformatics tools. The measured LC-MS data was processed in an automated fashion and sorted based on the monoisotopic accurate masses of all toxins found, their peak intensities, and their retention times in LC. The data was then investigated using bioinformatic tools, before the toxin data available in open-source databases was used to predict the class of a toxin by means of its mass. This study highlights the importance of studying venom variability, which is performed by our combinatorial approach of intact-toxin analysis and toxin grouping by accurate mass.

Clinicopathological biomarker patterns, venom detection and venom proteomics in canine Vipera berus envenomation

Vipera berus (V. berus) bites are associated with high morbidity, including kidney injury, in dogs. Although antivenom is often used and perceived effective to treat this type of snakebite, it is costly and associated with adverse events and specific diagnostics for this type of snakebite are lacking. We sought to improve diagnostics in V. berus envenomation by using currently available tools, including evaluating urinary albumin as a biomarker for snakebite-associated kidney injury. Additionally, we planned to adapt a method from human medicine for venom detection in clinical samples from bitten dogs and describe the composition of Norwegian V. berus venom. Serum biochemical analytes and urine albumin (ELISA) were measured in samples collected at 24 hours and two weeks after bite in 29 envenomated dogs. An adapted ELISA was applied to detect venom in urine and plasma collected from 25 cases between presentation and 24 hours after bite, using a commercial antivenom as the capture and detection antibody. Proteomic analysis of venom collected from 11 V. berus was performed using liquid chromatography-tandem mass spectrometry. Elevated serum C-reactive protein, creatine kinase, and aspartate aminotransferase were common for the case group. Although no case dogs showed acute kidney injury with azotemia and/or reduced urine output, elevated urinary albumin concentrations may indicate early or mild kidney injury in some case dogs. The venom ELISA detected positive signals in both plasma and urine for up to 24 hours after bite. However, with false positives detected in plasma, urine seemed to be the most appropriate body fluid for this assay. The venom proteome identified L-amino acid oxidases as the dominant component. In conclusion, serum biochemical and urinary albumin analyses are useful tools for evaluating canine V. berus envenomation. The venom ELISA is proposed as a promising tool for studies of V. berus envenomation and future diagnostic test development. Venom from the studied Norwegian V. berus was shown to differ considerably from previous reports from other countries, implying geographical variation in composition.

Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions

Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.

Analysis of N- and O-linked site-specific glycosylation by ion mobility mass spectrometry: State of the art and future directions

Glycosylation, the major post-translational modification of proteins, significantly increases the diversity of proteoforms. Glycans are involved in a variety of pivotal structural and functional roles of proteins, and changes in glycosylation are profoundly connected to the progression of numerous diseases. Mass spectrometry (MS) has emerged as the gold standard for glycan and glycopeptide analysis because of its high sensitivity and the wealth of fragmentation information that can be obtained. Various separation techniques have been employed to resolve glycan and glycopeptide isomers at the front end of the MS. However, differentiating structures of isobaric and isomeric glycopeptides constitutes a challenge in MS-based characterization. Many reports described the use of various ion mobility-mass spectrometry (IM-MS) techniques for glycomic analyses. Nevertheless, very few studies have focused on N- and O-linked site-specific glycopeptidomic analysis. Unlike glycomics, glycoproteomics presents a multitude of inherent challenges in microheterogeneity, which are further exacerbated by the lack of dedicated bioinformatics tools. In this review, we cover recent advances made towards the growing field of site-specific glycosylation analysis using IM-MS with a specific emphasis on the MS techniques and capabilities in resolving isomeric peptidoglycan structures. Furthermore, we discuss commonly used software that supports IM-MS data analysis of glycopeptides.