Experimental and data analysis advances in thermal proteome profiling.

Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.

Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling.

Repeated measures experimental designs, which quantify proteins in biological subjects repeatedly over multiple experimental conditions or times, are commonly used in mass spectrometry-based proteomics. Such designs distinguish the biological variation within and between the subjects and increase the statistical power of detecting within-subject changes in protein abundance. Meanwhile, proteomics experiments increasingly incorporate tandem mass tag (TMT) labeling, a multiplexing strategy that gains both relative protein quantification accuracy and sample throughput. However, combining repeated measures and TMT multiplexing in a large-scale investigation presents statistical challenges due to unique interplays of between-mixture, within-mixture, between-subject, and within-subject variation. This manuscript proposes a family of linear mixed-effects models for differential analysis of proteomics experiments with repeated measures and TMT multiplexing. These models decompose the variation in the data into the contributions from its sources as appropriate for the specifics of each experiment, enable statistical inference of differential protein abundance, and recognize a difference in the uncertainty of between-subject versus within-subject comparisons. The proposed family of models is implemented in the R/Bioconductor package MSstatsTMT v2.2.0. Evaluations of four simulated datasets and four investigations answering diverse biological questions demonstrated the value of this approach as compared to the existing general-purpose approaches and implementations.

Xanthommatin-Based Electrochromic Displays Inspired by Nature.

Color is a signature visual feature in nature; however, the ability to trigger color change in the presence of different environmental stimuli is unique to only a handful of species in the animal kingdom. We exploit the natural color-changing properties of the predominant pigment in arthropods and cephalopods-xanthommatin (Xa)-and describe its utility as a new broad-spectrum electrochromic material. To accomplish this goal, we explored the spectroelectrochemical properties of Xa adsorbed to an indium-doped tin oxide-coated substrate chemically modified with poly(3,4-ethylene dioxythiophene) doped with poly(styrenesulfonate) (PEDOT:PSS). We identified a synergistic role between PEDOT:PSS and Xa that contributed to its absorption profile, which could be modulated across multiple cycles. By varying the ratio of the two electroactive components, we also altered the perceived visible color of Xa-based devices, which cycled from different shades of red to yellow under reducing and oxidizing potentials, respectively. Together, our data illustrate the utility of Xa-based devices as new broad-spectrum electrochromic materials.

Optical Properties of ß-RDX Thin Films Deposited on Gold and Stainless Steel Substrates Calculated from Reflection-Absorption Infrared Spectra.

The optical properties for crystalline films of the highly energetic material (HEM) hexahydro-1,3,5-trinitro-s-triazine, which is also known as RDX, deposited on gold (Au) and stainless steel (SS) substrates are presented. RDX has two important stable conformational polymorphs at room temperature: α-RDX and ß-RDX. The optical properties obtained in the present work correspond to thin film samples of predominantly ß-RDX polymorph. The infrared spectroscopic intensities measured showed significant differences in the ß-RDX crystalline films deposited on the two substrates with respect to the calculated real part of refractive index. The ß-RDX/Au crystalline films have a high dynamic response, which is characterized by the asymmetric stretching mode of the axial nitro groups, whereas for the ß-RDX/SS crystalline films, the dynamic response was mediated by the -N-NO2 symmetric stretch mode. This result provides an idea of how the electric field vector propagates through the ß-RDX crystalline films deposited on the two substrates.

Standoff detection of highly energetic materials using laser-induced thermal excitation of infrared emission.

A laser-mediated methodology for standoff infrared detection of threat chemicals is described in this article. Laser-induced thermal emissions (LITE) from vibrationally excited residue of highly energetic material (HEM) deposited on substrates were detected remotely. Telescope-based Fourier transform infrared (FT-IR) spectroscopy measurements were carried out on substrates containing small amounts of HEM at surface concentrations of 5-200 µg/cm(2). Target substrates of various thicknesses were heated remotely using a carbon dioxide laser, and their mid-infrared (mid-IR), thermally stimulated emission spectra were recorded after heating. The telescope was configured from reflective optical elements to minimize emission losses in the mid-IR frequencies. Spectral replicas were acquired at distances from 4 to 64 m using an FT-IR interferometer at 4 cm(-1) resolution. The laser power, laser exposure times, and acquisition time of the FT-IR interferometer were adjusted to improve the detection and identification of samples. The advantages of increasing the thermal emission were easily observed in the results. The signal intensities were proportional to the thickness of the coated surface (a function of the surface concentration) as well as the laser power and laser exposure time. The limits of detection obtained for the HEM studied were 140-21 µg/cm(2) at 4 m. Detection was achieved at 64 m for a surface concentration of 200 µg/cm(2).