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Frontiers in Immunology 2022Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with... (Review)
Review
Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.
Topics: Antigen-Antibody Complex; Deuterium; Deuterium Exchange Measurement; Epitopes; Hydrogen Deuterium Exchange-Mass Spectrometry; Mass Spectrometry; Proteins
PubMed: 35720345
DOI: 10.3389/fimmu.2022.859964 -
British Journal of Pharmacology Jul 2015In pharmaceutical research, understanding the biodistribution, accumulation and metabolism of drugs in tissue plays a key role during drug discovery and development. In... (Review)
Review
In pharmaceutical research, understanding the biodistribution, accumulation and metabolism of drugs in tissue plays a key role during drug discovery and development. In particular, information regarding pharmacokinetics, pharmacodynamics and transport properties of compounds in tissues is crucial during early screening. Historically, the abundance and distribution of drugs have been assessed by well-established techniques such as quantitative whole-body autoradiography (WBA) or tissue homogenization with LC/MS analysis. However, WBA does not distinguish active drug from its metabolites and LC/MS, while highly sensitive, does not report spatial distribution. Mass spectrometry imaging (MSI) can discriminate drug and its metabolites and endogenous compounds, while simultaneously reporting their distribution. MSI data are influencing drug development and currently used in investigational studies in areas such as compound toxicity. In in vivo studies MSI results may soon be used to support new drug regulatory applications, although clinical trial MSI data will take longer to be validated for incorporation into submissions. We review the current and future applications of MSI, focussing on applications for drug discovery and development, with examples to highlight the impact of this promising technique in early drug screening. Recent sample preparation and analysis methods that enable effective MSI, including quantitative analysis of drugs from tissue sections will be summarized and key aspects of methodological protocols to increase the effectiveness of MSI analysis for previously undetectable targets addressed. These examples highlight how MSI has become a powerful tool in drug research and development and offers great potential in streamlining the drug discovery process.
Topics: Animals; Diagnostic Imaging; Drug Discovery; Humans; Mass Spectrometry; Research
PubMed: 25766375
DOI: 10.1111/bph.13135 -
Journal of Biomedicine & Biotechnology 2010
Topics: Mass Spectrometry; Proteomics
PubMed: 21541239
DOI: 10.1155/2010/453045 -
BioTechniques Apr 2016Mass spectrometry is often seen as a complicated, highly technical technique requiring years of experience to master. Jeffrey Perkel talks to users about the best ways...
Mass spectrometry is often seen as a complicated, highly technical technique requiring years of experience to master. Jeffrey Perkel talks to users about the best ways for novices to approach mass spectrometry experiments.
Topics: Mass Spectrometry; Peptides; Proteins; Proteomics
PubMed: 27071604
DOI: 10.2144/000114399 -
Mass Spectrometry Reviews Mar 2020Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as... (Review)
Review
Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry-based techniques are also routinely used to assess glycosylation and other post-translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted.
Topics: Animals; Glycopeptides; Glycoproteins; Glycosylation; Humans; Mass Spectrometry; Protein Processing, Post-Translational; Proteins; Vaccines
PubMed: 29852530
DOI: 10.1002/mas.21571 -
Journal of Chromatography. A Jan 2023Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest...
Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest possible, the so-called quench conditions of low pH and low temperature. To retain maximum deuterium, separation must also be done as quickly as possible. The low temperature (0 °C) of quench conditions complicates the separation and leads primarily to a reduction in separation quality and an increase in chromatographic backpressure. To improve the separation in HDX MS, one could use a longer gradient, smaller particles, a different separation mechanism (for example, capillary electrophoresis), or multi-dimensional separations such as combining ion mobility separation with reversed-phase separation. Another way to improve separations under HDX MS quench conditions is to use a higher flow rate where separation efficiency at 0 °C is more ideal. Higher flow rates, however, require chromatographic systems (both pumps and fittings) with higher backpressure limits. We tested what improvements could be realized with a commercial UPLC/UHPLC system capable of ∼20,000 psi backpressure. We found that a maximum flow rate of 225 µL/min (using a 1 × 50 mm column packed with 1.8 µm particles) was possible and that higher flow rate clearly led to higher peak capacity. HDX MS analysis of both simple and particularly complex samples improved, permitting both shorter separation time, if desired, and providing more deuterium recovery.
Topics: Hydrogen Deuterium Exchange-Mass Spectrometry; Deuterium; Deuterium Exchange Measurement; Mass Spectrometry; Peptides; Hydrogen
PubMed: 36586285
DOI: 10.1016/j.chroma.2022.463742 -
Journal of the American Society For... Nov 2006Protein molecules naturally emit streams of information-rich signals in the language of hydrogen exchange concerning the intimate details of their stability, dynamics,... (Review)
Review
Protein molecules naturally emit streams of information-rich signals in the language of hydrogen exchange concerning the intimate details of their stability, dynamics, function, changes therein, and effects thereon, all resolved to the level of their individual amino acids. The effort to measure protein hydrogen exchange behavior, understand the underlying chemistry and structural physics of hydrogen exchange processes, and use this information to learn about protein properties and function has continued for 50 years. Recent work uses mass spectrometric analysis together with an earlier proteolytic fragmentation method to extend the hydrogen exchange capability to large biologically interesting proteins. This article briefly reviews the advances that have led us to this point and the understanding that has so far been achieved.
Topics: Deuterium Exchange Measurement; History, 20th Century; History, 21st Century; Hydrogen; Mass Spectrometry; Protein Conformation; Proteins
PubMed: 16876429
DOI: 10.1016/j.jasms.2006.06.006 -
Clinical Microbiology and Infection :... Nov 2010
Topics: Bacteria; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 20874750
DOI: 10.1111/j.1469-0691.2010.03380.x -
Journal of Neurochemistry Oct 2021Over the last 10 years, considerable technical advances in mass spectrometry (MS)-based bioanalysis have enabled the investigation of lipid signatures in... (Review)
Review
Over the last 10 years, considerable technical advances in mass spectrometry (MS)-based bioanalysis have enabled the investigation of lipid signatures in neuropathological structures. In Alzheimer´s Disease (AD) research, it is now well accepted that lipid dysregulation plays a key role in AD pathogenesis and progression. This review summarizes current MS-based strategies, notably MALDI and ToF-SIMS imaging as well as laser capture microdissection combined with LC-ESI-MS. It also presents recent advances to assess lipid alterations associated with Amyloid-β plaques, one of the hallmarks of AD. Collectively, these methodologies offer new opportunities for the study of lipids, thus pushing forward our understanding of their role in such a complex and still untreatable disease as AD.
Topics: Animals; Humans; Laser Capture Microdissection; Lipids; Mass Spectrometry; Microglia; Neuroimaging; Plaque, Amyloid; Spectrometry, Mass, Electrospray Ionization; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 33048341
DOI: 10.1111/jnc.15216 -
Insights of ion mobility spectrometry and its application on food safety and authenticity: A review.Analytica Chimica Acta Aug 2022Ion mobility spectrometry (IMS) is gaining importance in the field of food safety and authenticity in recent years due to its main potential to overcome the challenges... (Review)
Review
Ion mobility spectrometry (IMS) is gaining importance in the field of food safety and authenticity in recent years due to its main potential to overcome the challenges that arise from the complexity of food matrices. For many years, IMS has been used as a stand-alone analytical detector due to its quick response, high sensitivity, and portability, and stand-alone applications in food analysis have been explored in recent years. At the same time, IMS hyphenation to mass spectrometry (MS) techniques, usually combined with liquid or gas chromatography (LC/GC), provides an additional dimension to separate isobaric compounds and thus improves method selectivity. Besides, with such ion mobility - mass spectrometry (IM-MS) methods, background noise decreases, increasing method sensitivity, and it provides complementary information to mass spectra and retention time with the collision cross section (CCS). The development of CCS databases within the food safety field would even permit the identification of compounds in non-targeted approaches. Furthermore, it would increase the confidence of control laboratories when determining a sample as non-compliant. Therefore, the number of applications by IMS on food safety and authenticity has increased remarkably in recent years. This review provides the general insights of IMS with the current state and recent approaches for its performance improvement and a general outlook of its applicability in food safety and authenticity.
Topics: Food Analysis; Food Safety; Gas Chromatography-Mass Spectrometry; Ion Mobility Spectrometry; Mass Spectrometry
PubMed: 35934427
DOI: 10.1016/j.aca.2022.340039