scholarly journals Towards structure-focused glycoproteomics

2021 ◽  
Author(s):  
Anastasia Chernykh ◽  
Rebeca Kawahara ◽  
Morten Thaysen-Andersen
Keyword(s):  
Mass Spectrometry ◽  
Detection Methods ◽  
Technological Innovations ◽  
Specific Information ◽  
Quantitative Accuracy ◽  
Structural Details ◽  
Biological Mixtures ◽  
Linkage Information ◽  
Fine Structures ◽  
New Strategies

Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.

Untangling the Metabolic Reprogramming in Brain Cancer: Discovering Key Molecular Players Using Mass Spectrometry

2019 ◽  
Vol 19 (17) ◽  
pp. 1521-1534 ◽  
Author(s):  
Anatoly Sorokin ◽  
Vsevolod Shurkhay ◽  
Stanislav Pekov ◽  
Evgeny Zhvansky ◽  
Daniil Ivanov ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Brain Cancer ◽  
De Novo ◽  
Aerobic Glycolysis ◽  
Lipid Production ◽  
Dietary Fatty Acids ◽  
Metabolic Reprogramming ◽  
Detection Methods ◽  
Malignant Cells ◽  
Proliferating Cells

Cells metabolism alteration is the new hallmark of cancer, as well as an important method for carcinogenesis investigation. It is well known that the malignant cells switch to aerobic glycolysis pathway occurring also in healthy proliferating cells. Recently, it was shown that in malignant cells de novo synthesis of the intracellular fatty acid replaces dietary fatty acids which change the lipid composition of cancer cells noticeably. These alterations in energy metabolism and structural lipid production explain the high proliferation rate of malignant tissues. However, metabolic reprogramming affects not only lipid metabolism but many of the metabolic pathways in the cell. 2-hydroxyglutarate was considered as cancer cell biomarker and its presence is associated with oxidative stress influencing the mitochondria functions. Among the variety of metabolite detection methods, mass spectrometry stands out as the most effective method for simultaneous identification and quantification of the metabolites. As the metabolic reprogramming is tightly connected with epigenetics and signaling modifications, the evaluation of metabolite alterations in cells is a promising approach to investigate the carcinogenesis which is necessary for improving current diagnostic capabilities and therapeutic capabilities. In this paper, we overview recent studies on metabolic alteration and oncometabolites, especially concerning brain cancer and mass spectrometry approaches which are now in use for the investigation of the metabolic pathway.

scholarly journals N-Terminomics Strategies for Protease Substrates Profiling

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4699
Author(s):  
Mubashir Mintoo ◽  
Amritangshu Chakravarty ◽  
Ronak Tilvawala
Keyword(s):  
Mass Spectrometry ◽  
Protease Activity ◽  
Viral Infections ◽  
Mass Spectrometry Analysis ◽  
Post Translational Modification ◽  
Spectrometry Analysis ◽  
Physiological Conditions ◽  
Inflammatory Conditions ◽  
Biological Mixtures

Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.

scholarly journals Spatiotemporal Visualization of Insecticides and Fungicides within Fruits and Vegetables Using Gold Nanoparticle-Immersed Paper Imprinting Mass Spectrometry Imaging

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1327
Author(s):  
Run Qin ◽  
Ping Li ◽  
Mingyi Du ◽  
Lianlian Ma ◽  
Yudi Huang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Food Safety ◽  
Gold Nanoparticle ◽  
Pesticide Residue ◽  
Rational Design ◽  
Mass Spectrometry Imaging ◽  
Fruits And Vegetables ◽  
Detection Methods ◽  
Safety Issues ◽  
Spatiotemporal Visualization

Food safety issues caused by pesticide residue have exerted far-reaching impacts on human daily life, yet the available detection methods normally focus on surface residue rather than pesticide penetration to the internal area of foods. Herein, we demonstrated gold nanoparticle (AuNP)-immersed paper imprinting mass spectrometry imaging (MSI) for monitoring pesticide migration behaviors in various fruits and vegetables (i.e., apple, cucumber, pepper, plum, carrot, and strawberry). By manually stamping food tissues onto AuNP-immersed paper, this method affords the spatiotemporal visualization of insecticides and fungicides within fruits and vegetables, avoiding tedious and time-consuming sample preparation. Using the established MSI platform, we can track the migration of insecticides and fungicides into the inner region of foods. The results revealed that both the octanol-water partition coefficient of pesticides and water content of garden stuffs could influence the discrepancy in the migration speed of pesticides into food kernels. Taken together, this nanopaper imprinting MSI is poised to be a powerful tool because of its simplicity, rapidity, and easy operation, offering the potential to facilitate further applications in food analysis. Moreover, new perspectives are given to provide guidelines for the rational design of novel pesticide candidates, reducing the risk of food safety issues caused by pesticide residue.

Comparison of Water and Gas Tracers Field Breakthrough

2021 ◽  
Author(s):  
Hsieh Chen ◽  
Sehoon Chang ◽  
Gawain Thomas ◽  
Wei Wang ◽  
Afnan Mashat ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Detection Method ◽  
Tracer Tests ◽  
Field Tests ◽  
Field Trials ◽  
Breakthrough Curves ◽  
Detection Methods ◽  
Reservoir Conditions ◽  
Gas Tracer

Abstract We are developing new classes of barcoded advanced tracers, which, compared to present commercial offerings, can be optically detected in an automated fashion. The eventual goal for the advanced tracers is to deploy cost-effective, ubiquitous, long-term, and full-field tracer tests in supporting large-scale waterflooding optimization for improved oil recovery. In this paper, we compare model predictions to breakthrough data from two field tests of advanced tracers in a pilot during water alternating gas (WAG) cycles, where gas tracer tests have recently been performed as well. Two advanced tracer injections were performed at the test site. For the first injection, only a dipicolinic acid based advanced tracer (DPA) was injected. For the second injection, DPA and a phenanthroline- based advanced tracer, 4,7-bis(sulfonatophenyl)-1,10-phenanthroline-2,9-dicarboxylic acid (BSPPDA), was injected in conjunction with a commercially available fluorobenzoic acid-based tracer (FBA) to benchmark their performance. Produced water samples were collected weekly for tracer analysis. Both newly developed 2D-high performance liquid chromatography/time-resolved fluorescence optical detection method (2D-HPLC/TRF) and liquid chromatography-mass spectrometry (LC-MS) were used to construct the breakthrough curves for the advanced tracers. In parallel, gas chromatography-mass spectrometry (GC-MS) was used to detect FBA tracer. Gas tracer tests have been performed on the same field. Since DPA, BSPPDA and FBA tracers were water tracers as designed, they were expected to appear in between gas tracer breakthroughs, and we observed exactly that for BSPPDA and FBA. Unexpectedly, the DPA predominantly appeared along with gas tracer breakthroughs, suggesting its favorable compatibility with the gas phase. We suspect the presence of some gas components rendered the medium more acidic, which likely protonates DPA molecules, thereby alters its hydrophilicity. A wealth of information could be gathered from the field tests. First, all tracers survived not only the harsh reservoir conditions but also the irregular WAG injections. Their successful detection from the producers suggested robustness of these materials for reservoir applications. Second, the breakthrough curves of the BSPPDA tracers using optical detection method were very similar to those of FBA tracers detected by GC-MS, substantiating the competency of our in-house materials and detection methods to the present commercial offerings. Finally, even though DPA has passed prior lab tests as a good water tracer, its high solubility to gas phase warrants further investigation. This paper summarizes key results from two field trials of the novel barcoded advanced tracers, of which both the tracer materials and detection methods are new to the industry. Importantly, the two co- injected advanced tracers showed opposite correlations to the gas tracers, highlighting the complex physicochemical interactions in reservoir conditions. Nevertheless, the information collected from the field trials is invaluable in enabling further design and utilization of the advanced tracers in fulfilling their wonderful promises.

scholarly journals Comparison of Methodologies used to Determine Aromatic Lignin Unit Ratios in Lignocellulosic Biomass

2021 ◽  
Author(s):  
Renee M. Happs ◽  
Bennett Addison ◽  
Crissa Doeppke ◽  
Bryon S. Donohoe ◽  
Mark F. Davis ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Plant Cell ◽  
Cell Walls ◽  
Careful Consideration ◽  
Chemical Degradation ◽  
Plant Cell Walls ◽  
Linkage Information ◽  
Lignin Composition ◽  
Nmr Methods ◽  
G Ratio

Abstract Background Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. Results The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. Conclusions This work demonstrates that different methods using chemical, thermal, and nondestructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.

Proanthocyanidin Structural Details Revealed by Ultrahigh Resolution FT-ICR MALDI-Mass Spectrometry, 1H–13C HSQC NMR, and Thiolysis-HPLC–DAD

2020 ◽  
Vol 68 (47) ◽  
pp. 14038-14048
Author(s):  
Savanah G. Reeves ◽  
Arpad Somogyi ◽  
Wayne E. Zeller ◽  
Theresa A. Ramelot ◽  
Kelly C. Wrighton ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Maldi Mass Spectrometry ◽  
Ultrahigh Resolution ◽  
Structural Details ◽  
Ft Icr

scholarly journals It’s the Little Things (in Viral RNA)

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Jiří František Potužník ◽  
Hana Cahová
Keyword(s):  
Mass Spectrometry ◽  
Viral Rna ◽  
Detection Methods ◽  
Scientific Methodology ◽  
Rna Modifications ◽  
Chemical Modifications ◽  
Viral Protein Synthesis ◽  
Antibody Assays ◽  
Rna Export ◽  
Generation Sequencing

ABSTRACT Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.

Occupational Contamination with Cyclophosphamide in Manipulators

2020 ◽  
Vol 30 (Supplement_2) ◽  
Author(s):  
S Martins ◽  
Z Moreira
Keyword(s):  
Health Professionals ◽  
Biological Samples ◽  
Urine Samples ◽  
Detection Methods ◽  
Technological Innovations ◽  
Inclusion Criteria ◽  
New Techniques ◽  
Main Route ◽  
Scientific Papers

Abstract Introduction Cyclophosphamide is a cytotoxic widely used in the treatment of various cancers. It has been observed, for many years, that those responsible for its handling and administration are exposed and levels of contamination have been detected in biological samples collected from these professionals, in surfaces and in the air. Objectives To review the literature on occupational contamination by cyclophosphamide. Methodology The following inclusion criteria were selected: articles published until the present year, articles in English, scientific papers on cyclophosphamide contamination in hospital health professionals, scientific articles on contamination detection methods and articles on the effects that can outcome from cyclophosphamide contamination. Results The cyclophosphamide levels have been decreasing with the implementation of preparation and cleaning guidelines as well as with the emergence of new techniques of manipulation and technological innovations. However, the dermal route remains the main route of contamination and those responsible for cytotoxic manipulation are not the only ones exposed. It was verified that hospital professionals, who in their profession would not be in contact with cyclophosphamide, also presented levels of contamination in the collected urine samples. Conclusion It is necessary to continue to alert hospital professionals to the importance of always complying with the handling and cleaning protocols, since one of the main causes of contamination is precisely the performance of incorrect procedures during both tasks. This is a topic that should be further studied in order to minimize the exposure and consequently the associated risks.

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