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Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at

Transformative technologies are enabling the construction of threedimensional (3D) maps of tissues with unprecedented spatial and molecularresolution. Over the next seven years, the NIH Common Fund Human BiomolecularAtlas Program (HuBMAP) intends to develop a widely accessible framework forcomprehensively mapping the human body at single-cell resolution by supportingtechnology development, data acquisition, and detailed spatial mapping. HuBMAPwill integrate its efforts with other funding agencies, programs, consortia,and the biomedical research community at large towards the shared vision of acomprehensive, accessible 3D molecular and cellular atlas of the human body, inhealth and various disease settings.

Abstract. Information on liquid–liquid phase separation (LLPS) and viscosity (ordiffusion) within secondary organic aerosol (SOA) is needed to improvepredictions of particle size, mass, reactivity, and cloud nucleatingproperties in the atmosphere. Here we report on LLPS and viscosities withinSOA generated by the photooxidation of diesel fuel vapors. Diesel fuelcontains a wide range of volatile organic compounds, and SOA generated bythe photooxidation of diesel fuel vapors may be a good proxy for SOA fromanthropogenic emissions. In our experiments, LLPS occurred over the relativehumidity (RH) range of ∼70 % to ∼100 %,resulting in an organic-rich outer phase and a water-rich inner phase. Theseresults may have implications for predicting the cloud nucleating propertiesof anthropogenic SOA since the presence of an organic-rich outer phase athigh-RH values can lower the supersaturation with respect to water requiredfor cloud droplet formation. At ≤10 % RH, the viscosity was ≥1×108 Pa s, which corresponds to roughly the viscosity of tarpitch. At 38 %–50 % RH, the viscosity was in the range of 1×108 to 3×105 Pa s. These measured viscosities areconsistent with predictions based on oxygen to carbon elemental ratio (O:C)and molar mass as well as predictions based on the number of carbon,hydrogen, and oxygen atoms. Based on the measured viscosities and theStokes–Einstein relation, at ≤10 % RH diffusion coefficients oforganics within diesel fuel SOA is ≤5.4×10-17 cm2 s−1 and the mixing time of organics within 200 nm diesel fuel SOAparticles (τmixing) is 50 h. These small diffusion coefficientsand large mixing times may be important in laboratory experiments, where SOAis often generated and studied using low-RH conditions and on timescales ofminutes to hours. At 38 %–50 % RH, the calculated organic diffusioncoefficients are in the range of 5.4×10-17 to 1.8×10-13 cm2 s−1 and calculated τmixing values arein the range of ∼0.01 h to ∼50 h. These valuesprovide important constraints for the physicochemical properties ofanthropogenic SOA.

Nanospray desorption electrospray ionization (nano‐DESI) is an ambient ionization mass spectrometry imaging (MSI) approach that enables spatial mapping of biological and environmental samples with high spatial resolution and throughput. Because nano‐DESI has not yet been commercialized, researchers develop their own sources and interface them with different commercial mass spectrometers. Previously, several protocols focusing on the fabrication of nano‐DESI probes have been reported. In this tutorial, we discuss different hardware requirements for coupling the nano‐DESI source to commercial mass spectrometers, such as the safety interlock, inlet extension, and contact closure. In addition, we describe the structure of our custom software for controlling the nano‐DESI MSI platform and provide detailed instructions for its usage. With this tutorial, interested researchers should be able to implement nano‐DESI experiments in their labs. [ABSTRACT FROM AUTHOR]

Secondary organic aerosol (SOA) accounts for a large fraction of submicron particles in the atmosphere. SOA can occur in amorphous solid or semi-solid phase states depending on chemical composition, relative humidity (RH), and temperature. The phase transition between amorphous solid and semi-solid states occurs at the glass transition temperature (Tg). We have recently developed a method to estimate Tg of pure compounds containing carbon, hydrogen, and oxygen atoms (CHO compounds) with molar mass less than 450 g mol-1 based on their molar mass and atomic O: C ratio. In this study, we refine and extend this method for CH and CHO compounds with molar mass up to ∼ 1100 g mol-1 using the number of carbon, hydrogen, and oxygen atoms. We predict viscosity from the Tg-scaled Arrhenius plot of fragility (viscosity vs. Tg •T) as a function of the fragility parameter D. We compiled D values of organic compounds from the literature and found that D approaches a lower limit of ∼ 10 (±1.7) as the molar mass increases. We estimated the viscosity of α-pinene and isoprene SOA as a function of RH by accounting for the hygroscopic growth of SOA and applying the Gordon-Taylor mixing rule, reproducing previously published experimental measurements very well. Sensitivity studies were conducted to evaluate impacts of Tg, D, the hygroscopicity parameter (κ), and the Gordon-Taylor constant on viscosity predictions. The viscosity of toluene SOA was predicted using the elemental composition obtained by high-resolution mass spectrometry (HRMS), resulting in a good agreement with the measured viscosity. We also estimated the viscosity of biomass burning particles using the chemical composition measured by HRMS with two different ionization techniques: electrospray ionization (ESI) and atmospheric pressure photoionization (APPI). Due to differences in detected organic compounds and signal intensity, predicted viscosities at low RH based on ESI and APPI measurements differ by 2-5 orders of magnitude. Complementary measurements of viscosity and chemical composition are desired to further constrain RH-dependent viscosity in future studies.

The effect of relative humidity (RH) on the chemical composition of secondary organic aerosol (SOA) formed from low-NOx toluene oxidation in the absence of seed particles was investigated. SOA samples were prepared in an aerosol smog chamber at >2%RH and 75%RH, collected on Teflon filters, and analyzed with nanospray desorption electrospray ionization high-resolution mass spectrometry (nano-DESI-HRMS). Measurements revealed a significant reduction in the fraction of oligomers present in the SOA generated at 75%RH compared to SOA generated under dry conditions. In a separate set of experiments, the particle mass concentrations were measured with a scanning mobility particle sizer (SMPS) at RHs ranging from >2 to 90 %. It was found that the particle mass loading decreased by nearly an order of magnitude when RH increased from >2 to 75-90% for low-NOx toluene SOA. The volatility distributions of the SOA compounds, estimated from the distribution of molecular formulas using the "molecular corridor" approach, confirmed that low-NOx toluene SOA became more volatile on average under high-RH conditions. In contrast, the effect of RH on SOA mass loading was found to be much smaller for high-NOx toluene SOA. The observed increase in the oligomer fraction and particle mass loading under dry conditions were attributed to the enhancement of condensation reactions, which produce water and oligomers from smaller compounds in low-NOx toluene SOA. The reduction in the fraction of oligomeric compounds under humid conditions is predicted to partly counteract the previously observed enhancement in the toluene SOA yield driven by the aerosol liquid water chemistry in deliquesced inorganic seed particles.

Emissions of airborne particles from biomass burning are a significant source of black carbon (BC) and brown carbon (BrC) in rural areas of developing countries where biomass is the predominant energy source for cooking and heating. This study explores the molecular composition of organic aerosols from household cooking emissions with a focus on identifying fuel-specific compounds and BrC chromophores. Traditional meals were prepared by a local cook with dung and brushwood-fueled cookstoves in a village in Palwal district, Haryana, India. Cooking was done in a village kitchen while controlling for variables including stove type, fuel moisture, and meal. Fine particulate matter (PM2.5) emissions were collected on filters, and then analyzed via nanospray desorption electrospray ionization-high-resolution mass spectrometry (nano-DESI-HRMS) and high-performance liquid chromatography-photodiode array-high-resolution mass spectrometry (HPLC-PDA-HRMS) techniques. The nano-DESI-HRMS analysis provided an inventory of numerous compounds present in the particle phase. Although several compounds observed in this study have been previously characterized using gas chromatography methods a majority of the species in the nano-DESI spectra were newly observed biomass burning compounds. Both the stove (chulha or angithi) and the fuel (brushwood or dung) affected the composition of organic aerosols. The geometric mean of the PM2.5 emission factor and the observed molecular complexity increased in the following order: brushwood-chulha (7.3±1.8 g kg-1 dry fuel, 93 compounds), dung-chulha (21.1±4.2 g kg-1 dry fuel, 212 compounds), and dung-angithi (29.8±11.5 g kg-1 dry fuel, 262 compounds). The mass-normalized absorption coefficient (MACbulk) for the organic-solvent extractable material for brushwood PM2.5 was 3.7±1.5 and 1.9±0.8m2 g-1 at 360 and 405 nm, respectively, which was approximately a factor of two higher than that for dung PM2.5. The HPLC-PDA-HRMS analysis showed that, regardless of fuel type, the main chromophores were CxHyOz lignin fragments. The main chromophores accounting for the higher MACbulk values of brushwood PM2.5 were C8H10O3 (tentatively assigned to syringol), nitrophenols C8H9NO4, and C10H10O3 (tentatively assigned to methoxycinnamic acid).

The impact of sea spray aerosol (SSA) on climate depends on the size and chemical composition of individual particles that make up the total SSA ensemble. There remains a lack of understanding as to the composition of individual particles within the SSA ensemble and how it changes in response to dynamic ocean biology. Here, we characterize the classes of organic compounds as well as specific molecules within individual SSA particles. The diversity of molecules within the organic fraction was observed to vary between submicrometer- and supermicrometer-sized particles and included contributions from fatty acids, monosaccharides, polysaccharides, and siliceous material. Significant changes in this molecular diversity were observed to coincide with the rise and fall of phytoplankton and heterotrophic bacteria populations within the seawater. Furthermore, the water uptake of individual particles was affected, as learned from studying the hygroscopicity of model systems composed of representative mixtures of salts and organic compounds.

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-NOx 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.

Emissions from biomass burning are a significant source of brown carbon (BrC) in the atmosphere. In this study, we investigate the molecular composition of freshly emitted biomass burning organic aerosol (BBOA) samples collected during test burns of sawgrass, peat, ponderosa pine, and black spruce. We demonstrate that both the BrC absorption and the chemical composition of light-absorbing compounds depend significantly on the type of biomass fuels. Common BrC chromophores in the selected BBOA samples include nitro-aromatics, polycyclic aromatic hydrocarbon derivatives, and polyphenols spanning a wide range of molecular weights, structures, and light absorption properties. A number of biofuel-specific BrC chromophores are observed, indicating that some of them may be used as source-specific markers of BrC. On average, ∼50% of the light absorption in the solvent-extractable fraction of BBOA can be attributed to a limited number of strong BrC chromophores. The absorption coefficients of BBOA are affected by solar photolysis. Specifically, under typical atmospheric conditions, the 300 nm absorbance decays with a half-life of ∼16 h. A "molecular corridor" analysis of the BBOA volatility distribution suggests that many BrC compounds in the fresh BBOA have low saturation mass concentration (

Recently, solution‐processable n‐doped poly(benzodifurandione) (n‐PBDF) has been made through in‐situ oxidative polymerization and reductive doping, which exhibited exceptionally high electrical conductivities and optical transparency. The discovery of n‐PBDF is considered a breakthrough in the field of organic semiconductors. In the initial report, the possibility of structural defect formation in n‐PBDF was proposed, based on the observation of structural isomerization from (E)‐2H,2′H‐[3,3′‐bibenzofuranylidene]‐2,2′‐dione (isoxindigo) to chromeno[4,3‐c]chromene‐5,11‐dione (dibenzonaphthyrone) in the dimer model reactions. In this study, we present clear evidence that structural isomerization is inhibited during polymerization. We reveal that the dimer (BFD1) and the trimer (BFD2) can be reductively doped by several mechanisms, including hydride transfer, forming charge transfer complexes (CTC) or undergoing an integer charge transfer (ICT) with reactants available during polymerization. Once the hydride transfer adducts, the CTC, or the ICT product forms, structural isomerization can be effectively prevented even at elevated temperatures. Our findings provide a mechanistic understanding of why isomerization‐derived structural defects are absent in n‐PBDF backbone. It lays a solid foundation for the future development of n‐PBDF as a benchmark polymer for organic electronics and beyond. [ABSTRACT FROM AUTHOR]

This work presents a systematic investigation of the molecular level composition and the extent of aqueous photochemical processing in different types of secondary organic aerosol (SOA) from biogenic and anthropogenic precursors including α-pinene, β-pinene, β-myrcene, d-limonene, α-humulene, 1,3,5-trimethylbenzene, and guaiacol, oxidized by ozone (to simulate a remote atmosphere) or by OH in the presence of NOx (to simulate an urban atmosphere). Chamber- and flow-tube-generated SOA samples were collected, extracted in a methanol/water solution, and photolyzed for 1 h under identical irradiation conditions. In these experiments, the irradiation was equivalent to about 3-8 h of exposure to the sun in its zenith. The molecular level composition of the dissolved SOA was probed before and after photolysis with direct-infusion electrospray ionization high-resolution mass spectrometry (ESI-HR-MS). The mass spectra of unphotolyzed SOA generated by ozone oxidation of monoterpenes showed qualitatively similar features and contained largely overlapping subsets of identified compounds. The mass spectra of OH/NOx-generated SOA had more unique visual appearance and indicated a lower extent of product overlap. Furthermore, the fraction of nitrogen-containing species (organonitrates and nitroaromatics) was highly sensitive to the SOA precursor. These observations suggest that attribution of high-resolution mass spectra in field SOA samples to specific SOA precursors should be more straightforward under OH/NOx oxidation conditions compared to the ozone-driven oxidation. Comparison of the SOA constituents before and after photolysis showed the tendency to reduce the average number of atoms in the SOA compounds without a significant effect on the overall O/C and H/C ratios. SOA prepared by OH/NOx photooxidation of 1,3,5-trimethylbenzene and guaiacol were more resilient to photolysis despite being the most light-absorbing. The composition of SOA prepared by ozonolysis of monoterpenes changed more significantly as a result of the photolysis. The results indicate that aqueous photolysis of dissolved SOA compounds in cloud/fog water can occur in various types of SOA, and on atmospherically relevant time scales. However, the extent of the photolysis-driven change in molecular composition depends on the specific type of SOA.

Fine aerosol particles in the urban areas of Shanghai and Los Angeles were collected on days that were characterized by their stagnant air and high organic aerosol concentrations. They were analyzed by nanospray-desorption electrospray ionization mass spectrometry with high mass resolution (m/Δm = 100,000). Solvent mixtures of acetonitrile and water and acetonitrile and toluene were used to extract and ionize polar and nonpolar compounds, respectively. A diverse mixture of oxygenated hydrocarbons, organosulfates, organonitrates, and organics with reduced nitrogen were detected in the Los Angeles sample. A majority of the organics in the Shanghai sample were detected as organosulfates. The dominant organosulfates that were detected at two locations have distinctly different molecular characteristics. Specifically, the organosulfates in the Los Angeles sample were dominated by biogenic products, while the organosulfates of a yet unknown origin found in the Shanghai sample had distinctive characteristics of long aliphatic carbon chains and low degrees of oxidation and unsaturation. The use of the acetonitrile and toluene solvent facilitated the observation of this type of organosulfates, which suggests that they could have been missed in previous studies that relied on sample extraction using common polar solvents. The high molecular weight and low degree of unsaturation and oxidization of the uncommon organosulfates suggest that they may act as surfactants and plausibly affect the surface tension and hygroscopicity of atmospheric particles. We propose that direct esterification of carbonyl or hydroxyl compounds by sulfates or sulfuric acid in the liquid phase could be the formation pathway of these special organosulfates. Long-chain alkanes from vehicle emissions might be their precursors.

Ambient particles and droplets have a significant effect on climate, visibility, and human health. Once formed, they undergo continuous transformations through condensation and evaporation of water, uptake of low-volatility organic molecules, and photochemical reactions involving various gaseous and condensed-phase species in the atmosphere. These transformations determine the physical and chemical properties of airborne particles, such as their ability to absorb and scatter solar radiation and nucleate cloud droplets. The complexity, heterogeneity, and size of ambient particles make it challenging to understand the kinetics and mechanisms of their formation and chemical transformations. Mass spectrometry (MS) is a powerful analytical technique that enables detailed chemical characterization of both small and large molecules in complex matrices. This capability makes MS a promising tool for studying chemical transformations of particles and droplets in the atmosphere. This review is focused on new and emerging experimental MS-based approaches for understanding the kinetics and mechanisms of such transformations. Some of the techniques discussed herein are best suited for ambient samples, while the others work best in laboratory applications. However, in combination, they provide a comprehensive arsenal of methods for characterization of particles and droplets. In addition, we emphasize the role of fundamental physical chemistry studies in the development of new methods for chemical analysis of ambient particles and droplets.

Sources and chemical composition of brown carbon are poorly understood, and even less is known about the mechanisms of its atmospheric transformations. This work presents molecular-level investigations of the reactive compound ketolimononaldehyde (KLA, C9H14O3), a second-generation ozonolysis product of limonene (C10H16), as a potent brown carbon precursor in secondary organic aerosol (SOA) through its reactions with reduced nitrogen compounds, such as ammonium ion (NH4+), ammonia, and amino acids. The reactions of synthesized and purified KLA with NH4+ and glycine resulted in the formation of chromophores nearly identical in spectral properties and formation rates to those found in similarly-aged limonene/O3 SOA. Similar chemical reaction processes of limononaldehyde (LA, C10H16O2) and pinonaldehyde (PA, C10H16O2), the first-generation ozonolysis products of limonene and alpha-pinene, respectively, were also studied, but the resulting products did not exhibit the light absorption properties of brown carbon, suggesting that the unique molecular structure of KLA produces visible-light-absorbing compounds. The KLA/NH4+ and KLA/GLY reactions produce water-soluble, hydrolysis-resilient chromophores with high mass absorption coefficients (MAC = 2000-4000 cm2 g(-1)) at lambda - 500 nm, precisely at the maximum of the solar emission spectrum. Liquid chromatography was used to isolate the light-absorbing fraction, and UV-Vis, FTIR, NMR and high-resolution mass spectrometry (HR-MS) techniques were used to investigate the structures and chemical properties of the light-absorbing compounds. The KLA browning reaction generates a diverse mixture of light-absorbing compounds, with the majority of the observable products containing 1-4 units of KLA and 0-2 nitrogen atoms. Based on the HR-MS product distribution, conjugated aldol condensates, secondary imines (Schiff bases), and N-heterocycles like pyrroles may contribute in varying degree to the light-absorbing properties of the KLA brown carbon. The results of this study demonstrate the high degree of selectivity of organic compound structures on the light-absorbing properties of SOA.