A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor information have been developed to overcome the reproducibility challenges of data-dependent acquisition and the limited breadth of targeted proteomics strategies. Typical DIA implementations use wide MS/MS isolation windows to acquire comprehensive fragment ion data. However, wide isolation windows produce highly chimeric spectra, limiting the achievable sensitivity and accuracy of quantification and identification. Here, we present a DIA strategy in which spectra are collected with overlapping (rather than adjacent or random) windows and then computationally demultiplexed. This approach improves precursor selectivity by nearly a factor of 2, without incurring any loss in mass range, mass resolution, chromatographic resolution, scan speed, or other key acquisition parameters. We demonstrate a 64% improvement in sensitivity and a 17% improvement in peptides detected in a 6-protein bovine mix spiked into a yeast background. To confirm the method’s applicability to a realistic biological experiment, we also analyze the regulation of the proteasome in yeast grown in rapamycin and show that DIA experiments with overlapping windows can help elucidate its adaptation toward the degradation of oxidatively damaged proteins. Our integrated computational and experimental DIA strategy is compatible with any DIA-capable instrument. The computational demultiplexing algorithm required to analyze the data has been made available as part of the open-source proteomics software tools Skyline and msconvert (Proteowizard), making it easy to apply as part of standard proteomics workflows. Graphical Abstract Electronic supplementary material The online version of this article (10.1007/s13361-018-2122-8) contains supplementary material, which is available to authorized users.

Superparticles made from colloidal nanocrystals have recently shown great promise in bridging the nanoscale and mesoscale, building artificial materials with properties designed from the bottom-up. As these properties depend on the dimension of the superparticle, there is a need for a general method to produce monodisperse nanocrystal superparticles. Here, we demonstrate an approach that readily yields spherical nanocrystal superparticles with a polydispersity as low as 2%. This method relies on the controlled densification of the nanocrystal-containing “source” emulsion by the swelling of a secondary “sink” emulsion. We show that this strategy is general and rapid, yielding monodisperse superparticles with controllable sizes and morphologies, including core/shell structures, within a few minutes. The superparticles show a high optical quality that results in lasing through the whispering-gallery modes of the spherical structure, with an average quality factor of 1600. Assembling superparticles into small clusters selects the wavelength of the lasing modes, demonstrating an example of collective photonic behavior of these artificial solids.

We program the optical properties of colloidal Au nanocrystal (NC) assemblies via an unconventional ligand hybridization (LH) strategy to precisely engineer interparticle interactions and design materials with optical properties difficult or impossible to achieve in bulk form. Long-chain hydrocarbon ligands used in NC synthesis are partially exchanged, from 0% to 100%, with compact thiocyanate ligands by controlling the reaction time for exchange. The resulting NC assemblies show transmittance, reflectance, optical permittivity, and directcurrent (DC) resistivity that continuously traverse a dielectric-metal transition, providing analog tuning of their physical properties, unlike the digital control realized by complete exchange with ligands of varying length. Exploiting this LH strategy, we create Au NC assemblies that are strong, ultrathin film optical absorbers, as seen by a 6× increase in the extinction of infrared light compared to that in bulk Au thin films and by a temperature rise of 20 °C upon illumination with 808 nm light. Our LH strategy may be applied to the design of materials constructed from NCs of different size, shape, and composition for specific applications.

A recently developed emulsion-templated assembly method promises the scalable, low-cost, and reproducible fabrication of hierarchical nanocrystal (NC) superstructures. These superstructures derive properties from the unique combination of choices of NC building blocks and superstructure morphology and therefore realize the concept of “artificial solids”. To control the final properties of these superstructures, it is essential to control the assembly conditions that yield distinct architectural morphologies. Here, we explore the phase-space of experimental parameters describing the emulsion-templated assembly including temperature, interfacial tension, and NC polydispersity and demonstrate which conditions lead to the growth of the most crystalline NC superstructures or supercrystals. By using a combination of electron microscopy and small-angle X-ray scattering, we show that slower assembly kinetics, softer interfaces, and lower NC polydispersity contribute to the formation of supercrystals with grain sizes up to 600 nm, while reversing these trends yields glassy solids. These results provide a clear path to the realization of higher-quality supercrystals, necessary to many applications.

Wetting of polymer-grafted nanoparticles (NPs) in a polymer nanocomposite (PNC) film is driven by a difference in surface energy between components as well as bulk thermodynamics, namely, the value of the interaction parameter, χ. The interplay between these contributions is investigated in a PNC containing 25 wt % polymethyl methacrylate (PMMA)-grafted silica NPs (PMMA-NPs) in poly(styrene-ran-acrylonitrile) (SAN) upon annealing above the lower critical solution temperature (LCST, 160 °C). Atomic force microscopy (AFM) studies show that the areal density of particles increases rapidly and then approaches 80% of that expected for random close-packed hard spheres. A slightly greater areal density is observed at 190 °C compared to 170 °C. The PMMA-NPs are also shown to prevent dewetting of PNC films under conditions where the analogous polymer blend is unstable. Transmission electron microscopy (TEM) imaging shows that PMMANPs symmetrically wet both interfaces and form columns that span the free surface and substrate interface. Using grazingincidence Rutherford backscattering spectrometry (GI-RBS), the PMMA-NP surface excess (Z*) initially increases rapidly with time and then approaches a constant value at longer times. Consistent with the areal density, Z* is slightly greater at deeper quench depths, which is attributed to the more unfavorable interactions between the PMMA brush and SAN segments. The Z* values at early times are used to determine the PMMA-NP diffusion coefficients, which are significantly larger than theoretical predictions. These studies provide insights into the interplay between wetting and phase separation in PNCs and can be utilized in nanotechnology applications where surface-dependent properties, such as wettability, durability, and friction, are important.