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Item 3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development(Wolters Kluwer, 2021) Lipp, Sarah N.; Jacobson, Kathryn R.; Hains, David S.; Schwarderer, Andrew L.; Calve, Sarah; Pediatrics, School of MedicineESKD is increasing in incidence and a limited number of organs are available for transplantation. Therefore, researchers have focused on understanding how cellular signaling influences kidney development to expand strategies to rebuild a kidney. However, the extracellular matrix (ECM), another critical component that biomechanically regulates nephrogenesis, has been largely neglected. Proteomics and 3D imaging of the murine kidney resolved previously undescribed dynamics of the interstitial matrix in the cortex and corticomedullary junction during development. Combined with cells and growth factors, scaffolds modeled after the composition and organization of the developmental ECM have the potential to improve engineered models of the kidney.Item Analysis of Histone Lysine Methylation Using Mass Spectrometry(2012-12-11) True, Jason Donald; Goebl, Mark G.; Mosley, Amber L.; Witzmann, F. A. (Frank A.)Histones are highly basic proteins which when digested by trypsin are hard to analyze using mass spectrometry. Because histones are basic nuclear proteins, a nuclei prep followed by acid extraction is the best purification strategy to increase overall abundance of purified histones. Blocking the lysine residues and cleaving with trypsin is a useful technique to increase detection of histone peptides using MudPIT. In particular, carbamylation and propionylation are the best two methods to block lysine residues. Using both propionylation and carbamylation along with no treatment has been shown to increase the identification of unmodified and modified histone peptides when coupled with MudPIT analysis.Item Analysis of human gliomas by swab touch spray-mass spectrometry: applications to intraoperative assessment of surgical margins and presence of oncometabolites(Royal Society of Chemistry, 2017-10-23) Pirro, Valentina; Llor, Raquel Sero; Jarmusch, Alan K.; Alfaro, Clint M.; Cohen-Gadol, Aaron A.; Hattab, Eyas M.; Cooks, R. Graham; Neurological Surgery, School of MedicineTouch spray mass spectrometry using medical swabs is an ambient ionization technique (ionization of unprocessed sample in the open air) that has potential intraoperative application in quickly identifying the disease state of tissue and in better characterizing the resection margin. To explore this potential, we studied 29 human brain tumor specimens and obtained evidence that this technique can provide diagnostic molecular information that is relevant to brain cancer. Touch spray using medical swabs involves the physical sampling of tissue using a medical swab on a spatial scale of a few mm2 with subsequent ionization occurring directly from the swab tip upon addition of solvent and application of a high voltage. Using a tertiary mixture of acetonitrile, N,N-dimethylformamide, and ethanol, membrane-derived phospholipids and oncometabolites are extracted from the tissue, incorporated into the sprayed microdroplets, vacuumed into the mass spectrometer, and characterized in the resulting mass spectra. The tumor cell load was assessed from the complex phospholipid pattern in the mass spectra and also separately by measurement of N-acetylaspartate. Mutation status of the isocitrate dehydrogenase gene was determined via detection of the oncometabolite 2-hydroxyglutarate. The lack of sample pretreatment makes touch spray mass spectrometry using medical swabs a feasible intraoperative strategy for rapid surgical assessment.Item Analysis of Keratinocytic Exosomes from Diabetic and Nondiabetic Mice by Charge Detection Mass Spectrometry(American Chemical Society, 2022) Brown, Brooke A.; Guda, Poornachander R.; Zeng, Xuyao; Anthony, Adam; Couse, Andrew; Barnes, Lauren F.; Sharon, Edie M.; Trinidad, Jonathan C.; Sen, Chandan K.; Jarrold, Martin F.; Ghatak, Subhadip; Clemmer, David E.; Surgery, School of MedicineUnresolved inflammation compromises diabetic wound healing. Recently, we reported that inadequate RNA packaging in murine wound-edge keratinocyte-originated exosomes (Exoκ) leads to persistent inflammation [Zhou, X. ACS Nano 2020, 14(10), 12732-12748]. Herein, we use charge detection mass spectrometry (CDMS) to analyze intact Exoκ isolated from a 5 day old wound-edge tissue of diabetic mice and a heterozygous nondiabetic littermate control group. In CDMS, the charge (z) and mass-to-charge ratio (m/z) of individual exosome particles are measured simultaneously, enabling the direct analysis of masses in the 1-200 MDa range anticipated for exosomes. These measurements reveal a broad mass range for Exoκ from ∼10 to >100 MDa. The m and z values for these exosomes appear to fall into families (subpopulations); a statistical modeling analysis partially resolves ∼10-20 Exoκ subpopulations. Complementary proteomics, immunofluorescence, and electron microscopy studies support the CDMS results that Exoκ from diabetic and nondiabetic mice vary substantially. Subpopulations having high z (>650) and high m (>44 MDa) are more abundant in nondiabetic animals. We propose that these high m and z particles may arise from differences in cargo packaging. The veracity of this idea is discussed in light of other recent CDMS results involving genome packaging in vaccines, as well as exosome imaging experiments. Characterization of intact exosome particles based on the physical properties of m and z provides a new means of investigating wound healing and suggests that CDMS may be useful for other pathologies.Item APOE ε2 resilience for Alzheimer's disease is mediated by plasma lipid species: Analysis of three independent cohort studies(Wiley, 2022) Wang, Tingting; Huynh, Kevin; Giles, Corey; Mellett, Natalie A.; Duong, Thy; Nguyen, Anh; Lim, Wei Ling Florence; Smith, Alex At; Olshansky, Gavriel; Cadby, Gemma; Hung, Joseph; Hui, Jennie; Beilby, John; Watts, Gerald F.; Chatterjee, Pratishtha; Martins, Ian; Laws, Simon M.; Bush, Ashley I.; Rowe, Christopher C.; Villemagne, Victor L.; Ames, David; Masters, Colin L.; Taddei, Kevin; Doré, Vincent; Fripp, Jürgen; Arnold, Matthias; Kastenmüller, Gabi; Nho, Kwangsik; Saykin, Andrew J.; Baillie, Rebecca; Han, Xianlin; Martins, Ralph N.; Moses, Eric K.; Kaddurah-Daouk, Rima; Meikle, Peter J.; Radiology and Imaging Sciences, School of MedicineIntroduction: The apolipoprotein E (APOE) genotype is the strongest genetic risk factor for late-onset Alzheimer's disease. However, its effect on lipid metabolic pathways, and their mediating effect on disease risk, is poorly understood. Methods: We performed lipidomic analysis on three independent cohorts (the Australian Imaging, Biomarkers and Lifestyle [AIBL] flagship study, n = 1087; the Alzheimer's Disease Neuroimaging Initiative [ADNI] 1 study, n = 819; and the Busselton Health Study [BHS], n = 4384), and we defined associations between APOE ε2 and ε4 and 569 plasma/serum lipid species. Mediation analysis defined the proportion of the treatment effect of the APOE genotype mediated by plasma/serum lipid species. Results: A total of 237 and 104 lipid species were associated with APOE ε2 and ε4, respectively. Of these 68 (ε2) and 24 (ε4) were associated with prevalent Alzheimer's disease. Individual lipid species or lipidomic models of APOE genotypes mediated up to 30% and 10% of APOE ε2 and ε4 treatment effect, respectively. Discussion: Plasma lipid species mediate the treatment effect of APOE genotypes on Alzheimer's disease and as such represent a potential therapeutic target.Item Association between plasma endocannabinoids and appetite in hemodialysis patients: A pilot study(Elsevier, 2016-07) Friedman, Allon N.; Kim, Jeffrey; Kaiser, Shaun; Pedersen, Theresa L.; Newman, John W.; Watkins, Bruce A.; Medicine, School of MedicineUremia-associated anorexia may be related to altered levels of long chain n-6 and n-3 polyunsaturated fatty acid (PUFA) derived circulating endocannabinoids (EC) and EC-like compounds that are known to mediate appetite. Our study's hypothesis was that such molecules are associated with appetite in patients with end-stage renal disease. A cross-sectional observational study was performed in 20 chronic hemodialysis patients (9 females, 11 males) and 10 healthy female controls in whom appetite was assessed using the Simplified Nutritional Appetite Questionnaire (SNAQ) and blood drawn in the fasting (and when applicable) pre-dialysis state. Blood levels of PUFA and EC were also measured. Higher blood levels of the long chain n-6 fatty acid 20:4n6 (arachidonic acid) and lower levels of the long chain n-3 fatty acid 20:5n3 (eicosapentaenoic acid) were observed in female hemodialysis patients compared to controls. No differences were observed between male and female patients. In female study participants strong correlations between specific EC-like compounds and total SNAQ scores were noted, including with the n-6 PUFA derived linoleoyl ethanolamide (L-EA; ρ=-0.60, P<.01) and the n-3 PUFA derived docosahexaenoyl ethanolamide (DH-EA; ρ=0.63, P<.01). The L-EA:DH-EA ratio was most strongly associated with the SNAQ score (ρ=-0.74, P≤.001), and its questions associated with appetite (ρ=-0.69, P≤.01) and satiety (ρ=-0.81, P≤.001). These findings support a link between circulating EC and appetite in hemodialysis patients.Item AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry(Oxford University Press, 2021) Lee, Joon-Yong; Bilbao, Aivett; Conant, Christopher R.; Bloodsworth, Kent J.; Orton, Daniel J.; Zhou, Mowei; Wilson, Jesse W.; Zheng, Xueyun; Webb, Ian K.; Li, Ailin; Hixson, Kim K.; Fjeldsted, John C.; Ibrahim, Yehia M.; Payne, Samuel H.; Jansson, Christer; Smith, Richard D.; Metz, Thomas O.; Chemistry and Chemical Biology, School of ScienceMotivation: Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion's collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results: We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation: https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information: Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).Item Automated Derivatization and Identification of Controlled Substances via Total Vaporization Solid Phase Microextraction (TV-SPME) and Gas Chromatography/Mass Spectrometry (GC/MS)(U.S. Department of Justice, Office of Justice Programs, 2018-11) Goodpaster, John V.The hypothesis tested was that Total Vaporization - Solid Phase Microextraction (TV-SPME) will offer greater sensitivity than traditional liquid injection for controlled substances. In addition, TV-SPME was easily adapted to include either a pre-extraction or a post-extraction on-fiber derivatization step for thermally labile species. Project results were promising for all drug classes that were analyzed successfully by on-fiber derivatization as solutions. This discovery greatly improves the utility of the technique, since controlled substances are most often encountered in their solid forms in forensic science laboratories. The application of this technique to beverage samples and solid drug powders is of most interest, since these applications involve a significant decrease in sample preparation. Although not ideal for all analytes, TV-SPME with on-fiber derivatization could be a powerful technique for amine and hydroxylamine controlled substances, as well as GHB. The technique could increase analyst efficiency by reducing sample preparation time for these types of analytes. Thus, the main results of this project are a set of optimized derivatization methods that can be used in liquid injection or TV-SPfsME. This approach offers the possibility of automated sampling and derivatization for a wide variety of thermally labile compounds and the analysis of compounds that require no derivatization. Project design and methods are described. 4 figures and 1 tableItem Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes(American Chemical Society, 2021-05-11) Peck Justice, Sarah A.; McCracken, Neil A.; Victorino, José F.; Qi, Guihong D.; Wijeratne, Aruna B.; Mosley, Amber L.; Biochemistry and Molecular Biology, School of MedicineThe study of low-abundance proteins is a challenge to discovery-based proteomics. Mass spectrometry (MS) applications, such as thermal proteome profiling (TPP), face specific challenges in the detection of the whole proteome as a consequence of the use of nondenaturing extraction buffers. TPP is a powerful method for the study of protein thermal stability, but quantitative accuracy is highly dependent on consistent detection. Therefore, TPP can be limited in its amenability to study low-abundance proteins that tend to have stochastic or poor detection by MS. To address this challenge, we incorporated an affinity-purified protein complex sample at submolar concentrations as an isobaric trigger channel into a mutant TPP (mTPP) workflow to provide reproducible detection and quantitation of the low-abundance subunits of the cleavage and polyadenylation factor (CPF) complex. The inclusion of an isobaric protein complex trigger channel increased detection an average of 40× for previously detected subunits and facilitated detection of CPF subunits that were previously below the limit of detection. Importantly, these gains in CPF detection did not cause large changes in melt temperature (Tm) calculations for other unrelated proteins in the samples, with a high positive correlation between Tm estimates in samples with and without isobaric trigger channel addition. Overall, the incorporation of an affinity-purified protein complex as an isobaric trigger channel within a tandem mass tag (TMT) multiplex for mTPP experiments is an effective and reproducible way to gather thermal profiling data on proteins that are not readily detected using the original TPP or mTPP protocols.Item CDMS Analysis of Intact 19S, 20S, 26S, and 30S Proteasomes: Evidence for Higher-Order 20S Assemblies at a Low pH†(American Chemical Society, 2023) Anthony, Adam J.; Gautam, Amit K. S.; Miller, Lohra M.; Ma, Yiran; Hardwick, Anya G.; Sharma, Anu; Ghatak, Subhadip; Matouschek, Andreas; Jarrold, Martin F.; Clemmer, David E.; Surgery, School of MedicineCharge detection mass spectrometry (CDMS) was examined as a means of studying proteasomes. To this end, the following masses of the 20S, 19S, 26S, and 30S proteasomes from Saccharomyces cerevisiae (budding yeast) were measured: m(20S) = 738.8 ± 2.9 kDa, m(19S) = 926.2 ± 4.8 kDa, m(26S) = 1,637.0 ± 7.6 kDa, and m(30S) = 2,534.2 ± 10.8 kDa. Under some conditions, larger (20S)x (where x = 1 to ∼13) assemblies are observed; the 19S regulatory particle also oligomerizes, but to a lesser extent, forming (19S)x complexes (where x = 1 to 4, favoring the x = 3 trimer). The (20S)x oligomers are favored in vitro, as the pH of the solution is lowered (from 7.0 to 5.4, in a 20 mM ammonium acetate solution) and may be related to in vivo proteasome storage granules that are observed under carbon starvation. From measurements of m(20S)x (x = 1 to ∼13) species, it appears that each multimer retains all 28 proteins of the 20S complex subunit. Several types of structures that might explain the formation of (20S)x assemblies are considered. We stress that each structural type [hypothetical planar, raft-like geometries (where individual proteasomes associate through side-by-side interactions); elongated, rodlike geometries (where subunits are bound end-to-end); and geometries that are roughly spherical (arising from aggregation through nonspecific subunit interactions)] is highly speculative but still interesting to consider, and a short discussion is provided. The utility of CDMS for characterizing proteasomes and related oligomers is discussed.