Optimization Strategies for Mass Spectrometry-Based Untargeted Metabolomics Analysis of Small Polar Molecules in Human Plasma

The untargeted approach to mass spectrometry-based metabolomics has a wide potential to investigate health and disease states, identify new biomarkers for diseases, and elucidate metabolic pathways. All this holds great promise for many applications in biological and chemical research. However, the complexity of instrumental parameters on advanced hybrid mass spectrometers can make the optimization of the analytical method immensely challenging. Here, we report a strategy to optimize the selected settings of a hydrophilic interaction liquid chromatography-tandem mass spectrometry method for untargeted metabolomics studies of human plasma, as a sample matrix. Specifically, we evaluated the effects of the reconstitution solvent in the sample preparation procedure, the injection volume employed, and different mass spectrometry-related operating parameters including mass range, the number of data-dependent fragmentation scans, collision energy mode, duration of dynamic exclusion time, and mass resolution settings on the metabolomics data quality and output. This study highlights key instrumental variables influencing the detection of metabolites along with suggested settings for the IQ-X tribrid system and proposes a new methodological framework to ensure increased metabolome coverage

Magnetically responsive carboxylated magnetite-polydipyrrole/polydicarbazole nanocomposites of core-shell morphology. Preparation, characterization, and use in DNA hybridization

Novel bis-heterocyclic mono- and dicarboxylated dipyrrole and dicarbazole monomers have been synthesized in a modular manner. Their oxidative polymerization around magnetite nanosized particles has been investigated and optimized toward new magnetic magnetite-polydipyrrole/polydicarbazole nanocomposites (NCs) of a core-shell morphology. These NCs were thoroughly characterized by FT-IR, TGA (Thermal Gravimetric Analysis), low- and high-resolution TEM/HR-TEM microscopies, and Mossbauer spectroscopy along with magnetization studies. Exploiting the versatile COOH chemistry (activation by water-soluble diimides) introduced by the polymeric shell, DNA hybridization experiments have been conducted onto NC surfaces using an efficient blue-colored HRP-based enzymatic screening biological system. Highly parallel NC-supported DNA hybridization experimentations revealed that these NCs presented an interesting potential for DNA-based diagnostic applications

New magnetically responsive polydicarbazole-magnetite nanoparticles.

Magnetically responsive COOH-polydicarbazole-magnetite nanocomposites have been prepared by chemical oxidation of three COOH-dicarbazole monomers and - in the presence of magnetite nanoparticles. These functionalized nanoparticles have been tested for DNA hybridization experiments

The influence of chemical chaperones on enzymatic activity under thermal and chemical stresses: common features and variation among diverse chemical families.

Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups

Molecular Engineering of Self-Assembling Diphenylalanine Analogues Results in the Formation of Distinctive Microstructures

Diphenylalanine is one of the most studied building blocks in organic supramolecular chemistry, forming ordered assemblies with unique mechanical, optical, piezoelectric, and semiconductive properties. These structures are being used for diverse applications, including energy storage, biosensing, light emission, drug delivery, artificial photosynthesis, and chemical propulsion. To increase the structural diversity of this dipeptide building block, three previously unreported analogues in which the aliphatic chain between the peptide backbone and the phenyl ring was gradually lengthened were synthesized. Each dipeptide self-assembled into unique microstructures, differing in morphology, which ranged from flat plates to long microrods to flattened microplanks. The structures were also found to possess distinctive optical properties. Furthermore, X-ray crystallography of each of the three diphenylalanine analogues presented distinctive molecular arrangements. The remarkable differences between each dipeptide in the intermolecular interactions they formed provide insight into the physicochemical mechanisms of self-assembly and, in addition, indicate the biological significance of the single methylene bridge of phenylalanine

Molecular Engineering of Self-Assembling Diphenylalanine Analogues Results in the Formation of Distinctive Microstructures

Diphenylalanine is one of the most studied building blocks in organic supramolecular chemistry, forming ordered assemblies with unique mechanical, optical, piezoelectric, and semiconductive properties. These structures are being used for diverse applications, including energy storage, biosensing, light emission, drug delivery, artificial photosynthesis, and chemical propulsion. To increase the structural diversity of this dipeptide building block, three previously unreported analogues in which the aliphatic chain between the peptide backbone and the phenyl ring was gradually lengthened were synthesized. Each dipeptide self-assembled into unique microstructures, differing in morphology, which ranged from flat plates to long microrods to flattened microplanks. The structures were also found to possess distinctive optical properties. Furthermore, X-ray crystallography of each of the three diphenylalanine analogues presented distinctive molecular arrangements. The remarkable differences between each dipeptide in the intermolecular interactions they formed provide insight into the physicochemical mechanisms of self-assembly and, in addition, indicate the biological significance of the single methylene bridge of phenylalanine

Trypsin structure under denaturating conditions.

<p>0.06/ml trypsin was dissolved in buffer alone (solid black line) and in the presence of 30% TFE (gray line) or at 60°C (dashed line). In the presence of TFE, the CD spectrum showed misfolding while under heating an unfolded state was observed.</p

Trypsin secondary structure in the process of heat denaturation in the presence and absence of choline chloride.

<p>0.0625/ml trypsin was heated from 20°C to 60°C in (A) buffer solution alone or in the presence of choline chloride (B) 1 M, (C) 2 M, (D) 3 M and (E) 4 M and cooled down back to 20°C. CD spectra were taken at 20°C, 40°C and 60°C during the heating process and again at 20°C and 40°C during the cooling process.</p