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We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

©2018 IUPAC & De Gruyter. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. For more information, please visit: http://creativecommons.org/licenses/by-nc-nd/4.0/ 2018. Novel functional polymeric microcapsules, based on modified azobenzene moieties, are exhaustively investigated, both from a theoretical and experimental points of view. Theoretical calculations and several measurements demonstrate that visible light can act as a trigger for release of encapsulated material, as a consequence of trans-cis isomerization which modifies microcapsule surface topography and can induce a squeezing release mechanism. Interfacial polymerization of an oil-in-water emulsion is performed and leads to core-shell microcapsules which are characterized by means of atomic force microscopy (AFM), optical microscopy (OM), scanning electron microscopy (SEM) and light scattering. These analyses put into evidence that microcapsules' size and surface morphology are strongly affected by irradiation under visible light: moreover, these changes can be reverted by sample exposure to temperatures around 50°C. This last evidence is also confirmed by NMR kinetic analyses on modified azobenzene moiety. Finally, it is shown that these smart microcapsules can be successfully used to get a controlled release of actives such as fragrancies, as a consequence of visible light irradiation, as confirmed by an olfactive panel.

© 2019, The Author(s). The production of hydrogen through water splitting using earth-abundant metal catalysts is a promising pathway for converting solar energy into chemical fuels. However, existing approaches for fine stoichiometric control, structural and catalytic modification of materials by appropriate choice of earth abundant elements are either limited or challenging. Here we explore the tuning of redox active immobilised molecular metal-chalcoxide electrocatalysts by controlling the chalcogen or metal stoichiometry and explore critical aspects of the hydrogen evolution reaction (HER). Linear sweep voltammetry (LSV) shows that stoichiometric and structural control leads to the evolution of hydrogen at low overpotential with no catalyst degradation over 1000 cycles. Density functional calculations reveal the effect of the electronic and structural features and confer plausibility to the existence of a unimolecular mechanism in the HER process based on the tested hypotheses. We anticipate these findings to be a starting point for further exploration of molecular catalytic systems.

The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.

By means of density functional calculations, we perform a mechanistic analysis of the Huisgen cycloaddition reaction taking place with the chemical involvement of the {Mo132} nanocapsule, initially reported by Besson and others [Dalton Trans. 2012, 41, 9852-9854], whereby a 2:1 regioselectivity is obtained by chemically grafting the reactants onto the cavity walls of this metal‐oxide catalyst. We explore the mechanistic pathways quantitatively and explore the basis of this regioselectivity. When propiolate is coordinated to the nanocapsule, the selectivity of the catalytic system is both kinetically and thermodynamically in favour of the formation of 1,4‐triazole, whereas in the alternative pathway, which begins with the triazidoacetate coordination, the selectivity is kinetic alone. The former and latter pathways have activation barrier differences between each isomer of 29.9 kJ/mol and 39.2 kJ/mol, respectively.

Photosensitive microcapsules are important targets for medical, pharmaceutical, agriculture, consumer goods and chemical companies. In this study, we report the development of UV-sensitive capsules containing vanillin as a model encapsulated active material. Polyamide microcapsule shells containing azobenzene moieties in the main chain of the polymer were fabricated by oil-in-water interfacial polymerization method. Triggered perfume release and morphological variations of the microcapsule shell during UV light irradiation were observed by means of high-performance liquid chromatography (HPLC) and optical microscopy.

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The Proteome Informatics Research Group (iPRG) this year performed a study to evaluate the benefits of using databases derived from RNA-Seq data for peptide identification. The proteomic dataset provided consisted of high mass accuracy tandem mass spectra acquired when analyzing human peripheral blood mononuclear cells. A variety of different types of sequence databases were supplied. These included a standard protein sequence database; a database containing only sequences of proteins expressed in the sample based on RNA-Seq data; a database that included sequence and splice variants; a database of sequences that could not be reconciled to known expressed gene sequences. Participants were asked to report spectral identifications in the form of an Excel spreadsheet, highlighting those identifications that were only identified using one of the RNA-Seq derived specialized sequence databases. Participants were also required to complete a web-based questionnaire summarizing the tools and methods they used. Additional peptide identifications were achieved by the use of each of the different RNA-Seq derived databases, although the number of additional identifications was modest. Nevertheless, these new identifications could have potential biological significance, so this type of analysis may still be worthwhile.

Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097–1100]. The antifungal effect of strain SH-C52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is a monochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities