Informed-Proteomics, a software suite for top-down proteomics analysis, consists of a high-accuracy liquid chromatography–mass spectrometry feature-finding algorithm, an efficient database search tool, and an interactive results viewer. Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography–tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.

Secondary organic aerosol (SOA), formed in the photooxidation of diesel fuel, biodiesel fuel, and 20% biodiesel fuel/80% diesel fuel mixture, are prepared under high-NO_x conditions in the presence and absence of sulfur dioxide (SO₂), ammonia (NH₃), and relative humidity (RH). The composition of condensed-phase organic compounds in SOA is measured using several complementary techniques including aerosol mass spectrometry (AMS), high-resolution nanospray desorption electrospray ionization mass spectrometry (nano-DESI/HRMS), and ultrahigh resolution and mass accuracy 21T Fourier transform ion cyclotron resonance mass spectrometry (21T FT-ICR MS). Results demonstrate that sulfuric acid and condensed organosulfur species formed in photooxidation experiments with SO₂ are present in the SOA particles. Fewer organosulfur species are formed in the high humidity experiments, performed at RH 90%, in comparison with experiments done under dry conditions. There is a strong overlap of organosulfur species observed in this study with previous field and chamber studies of SOA. Many MS peaks of organosulfates (R–OS(O)₂OH) previously designated as biogenic or of unknown origin in field studies might have originated from anthropogenic sources, such as photooxidation of hydrocarbons present in diesel and biodiesel fuel.

The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated. Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles. The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community.