University of North Texas, Huazhong Agricultural University, Heinrich Heine University, University of Goettingen, Leibniz Institute of Plant Genetics & Crop Plant Research, USDA-ARS
Abstract
Seeds of the desert shrub, jojoba (Simmondsia chinensis), are an abundant, renewable source of liquid wax esters, which are valued additives in cosmetic products and industrial lubricants. Jojoba is relegated to its own taxonomic family, and there is little genetic information available to elucidate its phylogeny. Here, we report the high-quality, 887-Mb genome of jojoba assembled into 26 chromosomes with 23,490 protein-coding genes. The jojoba genome has only the whole-genome triplication (γ) shared among eudicots and no recent duplications. These genomic resources coupled with extensive transcriptome, proteome, and lipidome data helped to define heterogeneous pathways and machinery for lipid synthesis and storage, provided missing evolutionary history information for this taxonomically segregated dioecious plant species, and will support efforts to improve the agronomic properties of jojoba.
NanoESI-MS/MS and UPLC-nanoESI-MS/MS methods using the Advion TriVersa NanoMate were used to analyze triacylglycerols from jojoba.
Authors: Cecilie Rosting, Jinglei Yu, and Helen J. Cooper*
Abstract
Despite the great potential of dried blood spots (DBS) as a source of endogenous proteins for biomarker discovery, the literature relating to nontargeted bottom-up proteomics of DBS is sparse, primarily due to the inherent complexity and very high dynamic range associated with these samples. Here, we present proof-of-concept results in which we have coupled high field asymmetric waveform ion mobility spectrometry (FAIMS) with liquid chromatography–tandem mass spectrometry (LC–MS/MS) for nontargeted bottom-up proteomics of DBS with the aim of addressing these challenges.
We, and others, have previously demonstrated the benefits of FAIMS more generally in proteomics including improved signal-to-noise and extended proteome coverage, and the aim of the current work was to extend those benefits specifically to DBS. The DBS samples were either extracted by the more traditional manual “punch and elute” approach or by an automated liquid surface extraction (LESA) approach prior to trypsin digestion. The resulting samples were analyzed by LC–MS/MS and LC–FAIMS–MS/MS analysis. The results show that the total number of proteins identified increased by ∼50% for the punch and elute samples and ∼45% for the LESA samples in the LC–FAIMS–MS/MS analysis. For both the punch and elute samples and the LESA samples, ∼30% of the total proteins identified were observed in both the LC–MS/MS and the LC–FAIMS–MS/MS data sets, illustrating the complementarity of the approaches.
Overall, this work demonstrates the benefits of inclusion of FAIMS for nontargeted proteomics of DBS.
Liquid extraction surface analysis (LESA) is an ambient surface sampling technique that allows the analysis of intact proteins directly from tissue samples via mass spectrometry. Integration of ion mobility separation to LESA mass spectrometry workflows has shown significant improvements in the signal-to-noise ratios of the resulting protein mass spectra and hence the number of proteins detected. Here, we report the use of a quadrupole–cyclic ion mobility–time-of-flight mass spectrometer (Q-cIM-ToF) for the analysis of proteins from mouse brain and rat kidney tissues sampled via LESA. Among other features, the instrument allows multiple pass cyclic ion mobility separation, with concomitant increase in resolving power. Single-pass experiments enabled the detection of 30 proteins from mouse brain tissue, rising to 44 when quadrupole isolation was employed. In the absence of ion mobility separation, 21 proteins were detected in rat kidney tissue including the abundant α- and β-globin chains from hemoglobin. Single-pass cyclic ion mobility mass spectrometry enabled the detection of 60 additional proteins. Multipass experiments of a narrow m/z range (m/z 870–920) resulted in the detection of 24 proteins (one pass), 37 proteins (two passes) and 54 proteins (three passes), thus demonstrating the benefits of improved mobility resolving power.
Helen J. Cooper, Emma K. Sisley, Jakub Ujma, Martin Palmer, Kevin Giles, Francisco A. Fernandez-Lima
Shanghai University of Traditional Chinese Medicine
Objective
To establish a simple, rapid and non‐destructive technique for identifying the authenticity of agarwood.
Methods
Liquid extraction surface analysis mass spectrometry (LESA‐MS) was firstly proposed to identify the authenticity of 62 agarwood samples without sample preparation. In addition, multivariate statistical models and thin‐layer chromatography (TLC) method were used to analyse and verify the results of LESA‐MS.
Conclusion
The proposed LESA‐MS method was successfully applied in the direct qualitative analysis of agarwood from different sources. This study indicated great feasibility and practicality of LESA‐MS in the rapid identification of agarwood, and provided a non‐destructive and meaningful preliminary screening tool for the agarwood industry.
The brain is a remarkably complex organ and cholesterol homeostasis underpins brain function. It is known that cholesterol is not evenly distributed across different brain regions; however, the precise map of cholesterol metabolism in the brain remains unclear. If cholesterol metabolism is to be correlated with brain function it is essential to generate such a map. Here we describe an advanced mass spectrometry platform to reveal spatial cholesterol metabolism in situ at 400-µm spot diameter on 10-µm tissue slices from mouse brain. We mapped, not only cholesterol, but also other biologically active sterols arising from cholesterol turnover in both wild type and mice lacking cholesterol 24S-hydroxylase (CYP46A1), the major cholesterol metabolizing enzyme.
Shanghai University of Traditional Chinese Medicine
Abstract
The 5α-reductase converts testosterone to dihydrotestosterone (DHT), and excess DHT could cause androgen-related diseases such as androgenetic alopecia and benign prostatic hyperplasia (BPH). To discover new 5α-reductase inhibitors, effective drug screening method with high throughput is thus essential. In this study, fully automated chip-based nanoelectrospray ionization-mass spectrometry (nano-ESI-MS) was innovatively utilized as a screening tool for 5α-reductase inhibitory assay in direct infusion mode, which simplified sample pretreatment and greatly improved experimental efficiency. The preliminary data indicated that curcumin, a natural anti-inflammatory compound, exhibited notably 5α-reductase inhibition activity. Moreover, the obtained results of the chip-based nano-ESI-MS were well consistent with those of HPLC-MS, which suggested that the chip-based nano-ESI-MS could be treated as a rapid and high-throughput drugs screening strategy in pharmaceutical development.
The Advion TriVersa NanoMate nanoelectrospray ionization technology was selected as the ion source for its long, stable spray capabilities ideal for lipid analysis.
Abstract
Cold atmospheric plasma (CAP) is an emerging source for the locally defined delivery of reactive species, and its clinical potential has been identified in the control of inflammatory processes, such as acute and chronic wounds, or cancerous lesions. Lipids, due to their localization and chemical structure as ideal targets for oxidative species, are relevant modifiers of physiological processes. Human forehead lipids collected on a target were treated by an argon plasma jet and immediately analyzed by direct-infusion high-resolution tandem mass spectrometry (DI-MS2) or liquid chromatography-tandem MS (RP-LC/MS2). Subsequent data analysis was performed by LipidHunter (University of Leipzig), LipidXplorer (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden), and LipidSearch (TS). With either MS method, all major lipid classes of sebum lipids were detected. Significant differences regarding triacylglycerols (predominantly identified in RP-LC/MS2) and ceramides (predominantly identified in DI-MS2) indicate experimental- or approach-inherent distinctions. A CAP-driven oxidation of triacyclglycerols, ceramides, and cholesteryl esters was detected such as truncations and hydroperoxylations, but at a significantly lower extent than expected. Scavenging of reactive species due to naturally present antioxidants in the samples and the absence of a liquid interphase to allow reactive species deposition by the CAP will have contributed to the limited amount of oxidation products observed. In addition, limitations of the software’s capability of identifying unexpected oxidized lipids potentially led to an underestimation of the CAP impact on skin lipids, indicating a need for further software development. With respect to the clinical application of CAP, the result indicates that intact skin with its sebum/epidermal lipid overlay is well protected and that moderate treatment will yield limited (if any) functional consequences in the dermal tissue.
Almost exclusively high throughput lipid profiling of samples from large epidemiological studies, where we study gene-lifestyle interactions. The method works with plasma samples as well as dried blood spots. The method is also applied to small-scale studies of specific disease groups, dietary interventions and model systems such as yeast. The TriVersa NanoMate® is also used to study the lipid composition of tissues analyzed by LESA®.
Why did you incorporate the TriVersa NanoMate® into your laboratory?
The TriVersa NanoMate® is essential to efficiently analyze large-scale studies. It offers a really robust method for high throughput studies with minimal carryover.
Who would you recommend to purchase the TriVersa NanoMate®?
I recommend the TriVersa NanoMate® to laboratories with a large number of samples requiring a robust and reliable delivery system. The TriVersa NanoMate® eliminates typical nanoelectrospray ionization challenges.
Do you have any publications or presentations using the TriVersa NanoMate®?
Publication Highlight: Development and Application of High-Throughput Single Cell Lipid Profiling: A Study of SNCA-A53T Human Dopamine Neurons Snowden, et al. iScience, 2020, 23(10), 101703
Combining FACS and LESA-MS to establish high-throughput single cell lipid profiling. Research identifies lipid differences found within and between populations of human dopamine neurons.
Other Publications:
Snowden et al. Combining lipidomics and machine learning to measure clinical lipids in dried blood spots. Metabolomics. DOI: 10.1007/s11306-020-01703-0
Koulman et al. The development and validation of a fast and robust dried blood spot based lipid profiling method to study infant metabolism. Metabolomics. DOI: 10.1007/s11306-014-0628-z
Furse et al. A high-throughput platform for detailed lipidomic analysis of a range of mouse and human tissues. Analytical and Bioanalytical Chemistry. DOI: 10.1007/s00216-020-02511-0
Harshfield et al. An unbiased lipid phenotyping approach to study the genetic determinants of lipids and their associations with coronary heart disease risk factors. J Proteom Res. DOI: 10.1021/acs.jproteome.8b00786
Mann et al. Insights into genetic variants associated with NASH-fibrosis from metabolite profiling. Hum Mol Genet. DOI: 10.1093/hmg/ddaa162
