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Wang Y, Wang Y, Wang X, Sun W, Yang F, Yao X, Pan T, Li B, Chu J. Label-free active single-cell encapsulation enabled by microvalve-based on-demand droplet generation and real-time image processing. Talanta 2024; 276:126299. [PMID: 38788384 DOI: 10.1016/j.talanta.2024.126299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/01/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Droplet microfluidics-based single-cell encapsulation is a critical technology that enables large-scale parallel single-cell analysis by capturing and processing thousands of individual cells. As the efficiency of passive single-cell encapsulation is limited by Poisson distribution, active single-cell encapsulation has been developed to theoretically ensure that each droplet contains one cell. However, existing active single-cell encapsulation technologies still face issues related to fluorescence labeling and low throughput. Here, we present an active single-cell encapsulation technique by using microvalve-based drop-on-demand technology and real-time image processing to encapsulate single cells with high throughput in a label-free manner. Our experiments demonstrated that the single-cell encapsulation system can encapsulate individual polystyrene beads with 96.3 % efficiency and HeLa cells with 94.9 % efficiency. The flow speed of cells in this system can reach 150 mm/s, resulting in a corresponding theoretical encapsulation throughput of 150 Hz. This technology has significant potential in various biomedical applications, including single-cell omics, secretion detection, and drug screening.
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Affiliation(s)
- Yiming Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Yousu Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaojie Wang
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Wei Sun
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
| | - Fengrui Yang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Tingrui Pan
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Baoqing Li
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China.
| | - Jiaru Chu
- Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei, 230027, China; Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, 230027, China
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Yao H, Yang J, Wang Z, Pan X, Pan J, Li H, Zhang S. High-Throughput Metabolite Analysis of Unicellular Microalgae by Orthogonal Hybrid Ionization Label-Free Mass Cytometry. Anal Chem 2024; 96:11404-11411. [PMID: 38960896 DOI: 10.1021/acs.analchem.4c01541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Microalgae metabolite analysis is fundamental for the rational design of metabolic engineering strategies for the biosynthesis of high-value products. Mass spectrometry (MS) has been utilized for single-cell microalgae analysis. However, limitations in the detection throughput and polarities of detectable substances make it difficult to realize high-throughput screening of high-performance microalgae. Herein, a plasma-assisted label-free mass cytometry, named as PACyESI-MS, was proposed combining the advantages of orthogonal hybrid ionization and high-throughput MS analysis, which realized rapid metabolite detection of single microalgae. The cell detection throughput of PACyESI-MS was up to 52 cells/min. Dozens of the critical primary and secondary metabolites within single microalgae were detected simultaneously, including pigments, lipids, and energy metabolites. Furthermore, metabolite changes of Chlamydomonas reinhardtii and Haematococcus pluvialis under nitrogen deficiency stress were studied. Discrimination of Chlamydomonas under different nutrient conditions was realized using single-cell metabolite profiles obtained by PACyESI-MS. The relationships between the accumulation of bioactive astaxanthin and changes in functional primary metabolites of Haematococcus were investigated. It was demonstrated that PACyESI-MS can detect the flexible change of metabolites in single microalgae cells under different nutritional conditions and during the synthesis of high-value products, which is expected to become an important tool for the design of metabolic engineering-based high-performance microalgae factories.
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Affiliation(s)
- Huan Yao
- National Institute of Metrology, Beijing 100029, China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing 100029, China
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Zhengmao Wang
- MOE Key Laboratory of Protein Sciences, School of Life Science, Tsinghua University, Beijing 100084, P.R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province 266000, China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, School of Life Science, Tsinghua University, Beijing 100084, P.R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province 266000, China
| | - Hongmei Li
- National Institute of Metrology, Beijing 100029, China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing 100029, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China
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3
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Kertesz V, Carper DL, Cahill JF. High-throughput mass spectrometry analysis using immediate drop-on-demand technology coupled with an open port sampling interface. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9687. [PMID: 38212650 DOI: 10.1002/rcm.9687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
RATIONALE The sampling throughput of immediate drop-on-demand technology (I.DOT) coupled with an open port sampling interface (OPSI) is limited by software communication. To enable much-needed high-throughput mass spectrometry (MS) analysis capabilities, a novel software was developed that allows for flexible sample selection from a 96-well plate and for maximized analysis throughput using I.DOT/OPSI-MS coupling. METHODS Wells of a 96-well I.DOT plate were filled with propranolol solution and were used to test maximum sampling throughput strategies to minimize analysis time. Demonstration of chemical reaction monitoring was done using acid-catalyzed ring closure of 2,3-diaminonaphthalene (DAN) with nitrite to form 2,3-naphthotriazole (NAT). Analytes were detected in positive electrospray ionization mode using selected reaction monitoring. RESULTS A maximum throughput of 1.54 s/sample (7.41 min/96-well plate with three technical replicates) was achieved, and it was limited by the peak width of the MS signal resulting in an occasional slight overlap between the peaks. Relative standard deviation was 10 ± 1% with all tested sampling strategies. Chemical reaction monitoring of DAN to NAT using nitrite was successfully accomplished with 2 s/sample throughout showing almost complete transformation in 10 min with no signal overlap. CONCLUSIONS This work illustrates the development of a noncontact, automated I.DOT/OPSI-MS system with improved throughput achieved through an optimized software interface. Its achievable analysis time and precision make it a viable approach for drug discovery and in situ reaction monitoring studies.
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Affiliation(s)
- Vilmos Kertesz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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4
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Prophet AM, Polley K, Van Berkel GJ, Limmer DT, Wilson KR. Iodide oxidation by ozone at the surface of aqueous microdroplets. Chem Sci 2024; 15:736-756. [PMID: 38179528 PMCID: PMC10762724 DOI: 10.1039/d3sc04254e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/03/2023] [Indexed: 01/06/2024] Open
Abstract
The oxidation of iodide by ozone occurs at the sea-surface and within sea spray aerosol, influencing the overall ozone budget in the marine boundary layer and leading to the emission of reactive halogen gases. A detailed account of the surface mechanism has proven elusive, however, due to the difficulty in quantifying multiphase kinetics. To obtain a clearer understanding of this reaction mechanism at the air-water interface, we report pH-dependent oxidation kinetics of I- in single levitated microdroplets as a function of [O3] using a quadrupole electrodynamic trap and an open port sampling interface for mass spectrometry. A kinetic model, constrained by molecular simulations of O3 dynamics at the air-water interface, is used to understand the coupled diffusive, reactive, and evaporative pathways at the microdroplet surface, which exhibit a strong dependence on bulk solution pH. Under acidic conditions, the surface reaction is limited by O3 diffusion in the gas phase, whereas under basic conditions the reaction becomes rate limited on the surface. The pH dependence also suggests the existence of a reactive intermediate IOOO- as has previously been observed in the Br- + O3 reaction. Expressions for steady-state surface concentrations of reactants are derived and utilized to directly compute uptake coefficients for this system, allowing for an exploration of uptake dependence on reactant concentration. In the present experiments, reactive uptake coefficients of O3 scale weakly with bulk solution pH, increasing from 4 × 10-4 to 2 × 10-3 with decreasing solution pH from pH 13 to pH 3.
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Affiliation(s)
- Alexander M Prophet
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Kritanjan Polley
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | | | - David T Limmer
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Department of Chemistry, University of California Berkeley CA 94720 USA
- Materials Science Division, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
- Kavli Energy NanoScience Institute Berkeley California 94720 USA
| | - Kevin R Wilson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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6
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Dolatmoradi M, Stopka SA, Corning C, Stacey G, Vertes A. High-Throughput f-LAESI-IMS-MS for Mapping Biological Nitrogen Fixation One Cell at a Time. Anal Chem 2023; 95:17741-17749. [PMID: 37989253 DOI: 10.1021/acs.analchem.3c03651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
For the characterization of the metabolic heterogeneity of cell populations, high-throughput single-cell analysis platforms are needed. In this study, we utilized mass spectrometry (MS) enhanced with ion mobility separation (IMS) and coupled with an automated sampling platform, fiber-based laser ablation electrospray ionization (f-LAESI), for in situ high-throughput single-cell metabolomics in soybean (Glycine max) root nodules. By fully automating the in situ sampling platform, an overall sampling rate of 804 cells/h was achieved for high numbers (>500) of tissue-embedded plant cells. This is an improvement by a factor of 13 compared to the previous f-LAESI-MS configuration. By introducing IMS, the molecular coverage improved, and structural isomers were separated on a millisecond time scale. The enhanced f-LAESI-IMS-MS platform produced 259 sample-related peaks/cell, almost twice as much as the 131 sample-related peaks/cell produced by f-LAESI-MS without IMS. Using the upgraded system, two types of metabolic heterogeneity characterization methods became possible. For unimodal metabolite abundance distributions, the metabolic noise reported on the metabolite level variations within the cell population. For bimodal distributions, the presence of metabolically distinct subpopulations was established. Discovering these latent cellular phenotypes could be linked to the presence of different cell states, e.g., proliferating bacteria in partially occupied plant cells and quiescent bacteroids in fully occupied cells in biological nitrogen fixation, or spatial heterogeneity due to altered local environments.
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Affiliation(s)
- Marjan Dolatmoradi
- Department of Chemistry, The George Washington University, Washington, District of Columbia 20052, United States
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, District of Columbia 20052, United States
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chloe Corning
- Department of Chemistry, The George Washington University, Washington, District of Columbia 20052, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, District of Columbia 20052, United States
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7
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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8
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Cahill JF, Kertesz V. Rapid Droplet Sampling Interface for Low-Volume, High-Throughput Mass Spectrometry Analysis. Anal Chem 2023; 95:16418-16425. [PMID: 37888790 DOI: 10.1021/acs.analchem.3c04015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Here, we present a rapid droplet sampling interface (RDSI) electrospray ionization mass spectrometry (ESI-MS) system as a high-throughput, low-volume, noncontact, and minimal-carryover approach for characterization of liquids. Liquid characterization was achieved by combining droplet ejection with an open-face microflow capillary with a 2.5 μL/min continuous flow of carrier solvent. Through this implementation, single 0.3 nL droplets containing the analyte effectively mix with 4-8 nL of carrier solvent and create a combined electrospray plume. The carrier solvent continuously cleaned the system, eliminating carryover. A sampling rate of 5 Hz was achieved for droplets containing 1 μM propranolol or 5 μM leu-enkephalin with each droplet fully baseline-resolved (138 ± 32 ms baseline-to-baseline). Using a SCIEX API4000 mass spectrometer, a lower limit of quantification (LLOQ) of propranolol was 15 nM, corresponding to 1.16 fg of propranolol in the droplet, and was linear across 3 orders of magnitude. Quantitation could be achieved by adding an isotopically labeled internal standard, as done in conventional ESI. Signal transients were faster than the acquisition speed of the mass spectrometer, resulting in artificially high reproducibility of 15-30% RSD droplet-to-droplet. Analyte-solvent mixing ratios could be controlled by adjusting droplet positioning along the open-face capillary with an optimal position about 0.4 mm from the tip end. The range of analyte coverage was exemplified by measures of peptides and drugs in methanol, water, and buffer solutions. In a comparison to the Open Port Sampling Interface (OPSI) implemented on the same system, the RDSI had 78× greater sensitivity, 6× greater throughput and used significantly less carrier solvent.
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Affiliation(s)
- John F Cahill
- Bioanalytical Mass Spectrometry Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Vilmos Kertesz
- Bioanalytical Mass Spectrometry Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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9
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Han J, Wang X, Wang W, Chen J, Xu B, Wei Z. Direct Analysis of Micro-biopsy Samples by Polarity Gradient Focusing Dip-and-Go Mass Spectrometry. Anal Chem 2023; 95:13266-13272. [PMID: 37610922 DOI: 10.1021/acs.analchem.3c02425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Direct analysis of micro-biopsy samples by mass spectrometry at single-cell level still faces major challenges. In this work, we developed a polarity gradient focusing dip-and-go strategy (PGF-Dip&Go) during induced electrospray ionization mass spectrometry (iESI-MS) analysis for real-time enrichment and spatial separation of compounds such as lipids, alkaloids, fatty amines, and drugs. Compared with direct iESI-MS analysis, enrichment of analytes (enrichment factor of 5.0-100.0) and spatial separation between different analytes were achieved. Owing to the enrichment effect and salt cleanup effect, the sensitivity of PGF-Dip&Go has been improved by 25-10,000 times compared with direct iESI-MS. PGF-Dip&Go has been successfully applied for the analysis of lipids in a 200 pL micro-biopsy section from an individual fish egg. Lysophosphatidylcholine (LPC), phosphatidylcholine (PC), and triglyceride (TG) were significantly enriched and separated according to their polarity differences, proving the potential of PGF-Dip&Go to be a noninvasive and powerful analytical tool for in situ analysis of complex small volumes in the future.
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Affiliation(s)
- Jin Han
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiangyu Wang
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
- School of Public Health, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Wenxin Wang
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Jianxiong Chen
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Bin Xu
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zhenwei Wei
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
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10
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Abstract
Lipids are essential cellular components forming membranes, serving as energy reserves, and acting as chemical messengers. Dysfunction in lipid metabolism and signaling is associated with a wide range of diseases including cancer and autoimmunity. Heterogeneity in cell behavior including lipid signaling is increasingly recognized as a driver of disease and drug resistance. This diversity in cellular responses as well as the roles of lipids in health and disease drive the need to quantify lipids within single cells. Single-cell lipid assays are challenging due to the small size of cells (∼1 pL) and the large numbers of lipid species present at concentrations spanning orders of magnitude. A growing number of methodologies enable assay of large numbers of lipid analytes, perform high-resolution spatial measurements, or permit highly sensitive lipid assays in single cells. Covered in this review are mass spectrometry, Raman imaging, and fluorescence-based assays including microscopy and microseparations.
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Affiliation(s)
- Ming Yao
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
| | | | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
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11
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Cahill JF, Kertesz V, Saint-Vincent P, Valentino H, Drufva E, Thiele N, Michener JK. High-Throughput Characterization and Optimization of Polyamide Hydrolase Activity Using Open Port Sampling Interface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37262418 DOI: 10.1021/jasms.3c00097] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Enzymatic biodegradation of polymers, such as polyamides (PA), has the potential to cost-effectively reduce plastic waste, but enhancements in degradation efficiency are needed. Engineering enzymes through directed evolution is one pathway toward identification of critical domains needed for improving activity. However, screening such enzymatic libraries (100s-to-1000s of samples) is time-consuming. Here we demonstrate the use of robotic autosampler (PAL) and immediate drop on demand technology (I.DOT) liquid handling systems coupled with open-port sampling interface-mass spectrometry (OPSI-MS) to screen for PA6 and PA66 hydrolysis by 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC) in a high-throughput (8-20 s/sample) manner. The OPSI-MS technique required minimal sample preparation and was amenable to 96-well plate formats for automated processing. Enzymatic hydrolysis of PA characteristically produced soluble linear oligomer products that could be identified by OPSI-MS. Incubation temperatures and times were optimized for PA6 (65 °C, 24 h) and PA66 (75 °C, 24 h) over 108 experiments. In addition, the I.DOT/OPSI-MS quantified production of PA6 linear dimer (8.3 ± 1.6 μg/mL) and PA66 linear monomer (13.5 ± 1.5 μg/mL) by NylC with a lower limit of detection of 0.029 and 0.032 μg/mL, respectively. For PA6 and PA66, linear oligomer production corresponded to 0.096 ± 0.018% and 0.204 ± 0.028% conversion of dry pellet mass, respectively. The developed methodology is expected to be utilized to assess enzymatic hydrolysis of engineered enzyme libraries, comprising hundreds to thousands of individual samples.
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Affiliation(s)
- John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Vilmos Kertesz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Patricia Saint-Vincent
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Hannah Valentino
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Erin Drufva
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Nikki Thiele
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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12
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Ebenezer TE, Low RS, O'Neill EC, Huang I, DeSimone A, Farrow SC, Field RA, Ginger ML, Guerrero SA, Hammond M, Hampl V, Horst G, Ishikawa T, Karnkowska A, Linton EW, Myler P, Nakazawa M, Cardol P, Sánchez-Thomas R, Saville BJ, Shah MR, Simpson AGB, Sur A, Suzuki K, Tyler KM, Zimba PV, Hall N, Field MC. Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world. Biol Open 2022; 11:bio059561. [PMID: 36412269 PMCID: PMC9836076 DOI: 10.1242/bio.059561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.
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Affiliation(s)
- ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ross S. Low
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ishuo Huang
- Office of Regulatory Science, United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Antonio DeSimone
- The BioRobotics Institute, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Scott C. Farrow
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Robert A. Field
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Sergio Adrián Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral. CCT CONICET Santa Fe, Santa Fe 3000, Argentina
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 25250, Czech Republic
| | - Geoff Horst
- Kemin Industries, Research and Development, Plymouth, MI 48170, USA
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue 690-8504, Japan
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Warsaw 02-089, Poland
| | - Eric W. Linton
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Peter Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Masami Nakazawa
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Sakai, Osaka, 599-8531, Japan
| | - Pierre Cardol
- Department of Life Sciences, Institut de Botanique, Université de Liège, Liège 4000, Belgium
| | | | - Barry J. Saville
- Forensic Science, Environmental and Life Sciences Graduate Program, Trent University, Peterborough K9L 0G2, Canada
| | - Mahfuzur R. Shah
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
| | - Alastair G. B. Simpson
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Aakash Sur
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Kengo Suzuki
- R&D Company, Euglena Co., Ltd., 2F Yokohama Bio Industry Center (YBIC), 1-6 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kevin M. Tyler
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Center of Excellence for Bionanoscience Research, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Paul V. Zimba
- PVZimba, LLC, 12241 Percival St, Chester, VA 23831, USA
- Rice Rivers Center, VA Commonwealth University, Richmond, VA 23284, USA
| | - Neil Hall
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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13
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Portero EP, Pade L, Li J, Choi SB, Nemes P. Single-Cell Mass Spectrometry of Metabolites and Proteins for Systems and Functional Biology. NEUROMETHODS 2022; 184:87-114. [PMID: 36699808 PMCID: PMC9872963 DOI: 10.1007/978-1-0716-2525-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Molecular composition is intricately intertwined with cellular function, and elucidation of this relationship is essential for understanding life processes and developing next-generational therapeutics. Technological innovations in capillary electrophoresis (CE) and liquid chromatography (LC) mass spectrometry (MS) provide previously unavailable insights into cellular biochemistry by allowing for the unbiased detection and quantification of molecules with high specificity. This chapter presents our validated protocols integrating ultrasensitive MS with classical tools of cell, developmental, and neurobiology to assess the biological function of important biomolecules. We use CE and LC MS to measure hundreds of metabolites and thousands of proteins in single cells or limited populations of tissues in chordate embryos and mammalian neurons, revealing molecular heterogeneity between identified cells. By pairing microinjection and optical microscopy, we demonstrate cell lineage tracing and testing the roles the dysregulated molecules play in the formation and maintenance of cell heterogeneity and tissue specification in frog embryos (Xenopus laevis). Electrophysiology extends our workflows to characterizing neuronal activity in sections of mammalian brain tissues. The information obtained from these studies mutually strengthen chemistry and biology and highlight the importance of interdisciplinary research to advance basic knowledge and translational applications forward.
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Affiliation(s)
| | | | - Jie Li
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Sam B. Choi
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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14
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Lanekoff I, Sharma VV, Marques C. Single-cell metabolomics: where are we and where are we going? Curr Opin Biotechnol 2022; 75:102693. [DOI: 10.1016/j.copbio.2022.102693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 12/11/2022]
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15
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Kaur Kohli R, Van Berkel GJ, Davies JF. An Open Port Sampling Interface for the Chemical Characterization of Levitated Microparticles. Anal Chem 2022; 94:3441-3445. [PMID: 35167275 DOI: 10.1021/acs.analchem.1c05550] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several studies have reported ionization methods to classify the chemical composition of levitated particles held in an electrodynamic balance using mass spectrometry (MS). These methods include electrospray-based paper spray (PS) ionization, plasma discharge ionization, and direct analysis in real-time (DART) ionization, with each showing advantages and disadvantages. Our recent work demonstrated that PS ionization could yield accurate data for the chemical evolution of mixed component particles undergoing evaporation. However, measurements were performed using an internal standard to account for and correct the inherent variability in the PS ionization source. Here, we explore a new electrospray-based method coupled to particle levitation-the Open Port Sampling Interface (OPSI), which provides many advantages over the PS method, with few disadvantages. In this application note we report experiments in which micron-sized particles, containing analytes such as citric acid, maleic acid, and tetraethylene glycol, were levitated and optically probed to determine their size and mass. Subsequent transfer of individual levitated particles into the OPSI allowed for the ionization and mass spectrometry analysis of these particles. We discuss the stability and reproducibility of MS measurements, demonstrate effective quantitation in both positive and negative mode, and determine the sensitivity of the OPSI to a range of analyte mass present in levitated particles. Importantly, we show stability of the OPSI over >6 h without the need for normalizing signal variations with an internal standard in the sample, demonstrating robust application of the OPSI to measurements over extended periods of time.
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Affiliation(s)
- Ravleen Kaur Kohli
- Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
| | | | - James F Davies
- Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
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16
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Zhou X, Wu H, Wen H, Zheng B. Advances in Single-Cell Printing. MICROMACHINES 2022; 13:80. [PMID: 35056245 PMCID: PMC8778191 DOI: 10.3390/mi13010080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/20/2022]
Abstract
Single-cell analysis is becoming an indispensable tool in modern biological and medical research. Single-cell isolation is the key step for single-cell analysis. Single-cell printing shows several distinct advantages among the single-cell isolation techniques, such as precise deposition, high encapsulation efficiency, and easy recovery. Therefore, recent developments in single-cell printing have attracted extensive attention. We review herein the recently developed bioprinting strategies with single-cell resolution, with a special focus on inkjet-like single-cell printing. First, we discuss the common cell printing strategies and introduce several typical and advanced printing strategies. Then, we introduce several typical applications based on single-cell printing, from single-cell array screening and mass spectrometry-based single-cell analysis to three-dimensional tissue formation. In the last part, we discuss the pros and cons of the single-cell strategies and provide a brief outlook for single-cell printing.
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Affiliation(s)
| | | | | | - Bo Zheng
- Shenzhen Bay Laboratory, Institute of Cell Analysis, Shenzhen 518132, China; (X.Z.); (H.W.); (H.W.)
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17
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Shao Y, Zhou Y, Liu Y, Zhang W, Zhu G, Zhao Y, Zhang Q, Yao H, Zhao H, Guo G, Zhang S, Zhang X, Wang X. Intact living-cell electrolaunching ionization mass spectrometry for single-cell metabolomics. Chem Sci 2022; 13:8065-8073. [PMID: 35919431 PMCID: PMC9278508 DOI: 10.1039/d2sc02569h] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
A novel living-cell mass spectrometry method allows a whole cell to enter entirely into the MS inlet and ionize with almost no sample dilution and matrix interference, which greatly improves the sensitivity of single-cell metabolite detection.
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Affiliation(s)
- Yunlong Shao
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yingyan Zhou
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yuanxing Liu
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Wenmei Zhang
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Guizhen Zhu
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yaoyao Zhao
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Qi Zhang
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Huan Yao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Guangsheng Guo
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
- Minzu University of China, Beijing 100081, P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xiayan Wang
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
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18
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Xu ST, Yang C, Yan XP. Nanothorn Filter-Facilitated Online Cell Lysis for Rapid and Deep Intracellular Profiling by Single-Cell Mass Spectrometry. Anal Chem 2021; 93:15677-15686. [PMID: 34784185 DOI: 10.1021/acs.analchem.1c03529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry combined with flow cytometry is emerging for high-throughput single-cell metabolite analysis but still has problems with limited intracellular information coverage. Here, we show a simple and efficient all-in-one system integrating cell injection, cell extraction, online cell lysis, analyte ionization, and mass spectrometric detection for rapid single-HeLa-cell screening with in-depth profiling of cellular metabolites and drugs. Zinc oxide nanothorn-decorated filters with three bore sizes (5.22, 8.36, and 16.75 μm) were fabricated for efficient online lysis of the cell membrane (even nuclear membrane) to facilitate intracellular analyte release and demonstrated to have a size effect for potential subcellular discrimination. The two smaller-bore filters gave 2-11-fold improvements in signal response for representative intracellular metabolites, such as adenosine, glutamine, and leucine/isoleucine. Especially, the smallest-bore filter enabled successful detection of the metabolites in the nucleus, including tetrahydrobiopterin and cyclic guanosine monophosphate. The developed all-in-one system was explored to monitor the uptake of four anticancer drugs, including 5-fluorouracil, doxorubicin, gambogic acid, and paclitaxel in single cells, and further to investigate the drug uptake trends at the subcellular level. The all-in-one system integrates the merits of high-throughput single-cell screening and in-depth intracellular information profiling and is promising for high-coverage single-cell metabolome analysis to serve cell biology research and cancer research.
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Affiliation(s)
- Shu-Ting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
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19
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Cahill JF, Kertesz V. Quantitation of amiodarone and N-desethylamiodarone in single HepG2 cells by single-cell printing-liquid vortex capture-mass spectrometry. Anal Bioanal Chem 2021; 413:6917-6927. [PMID: 34595558 DOI: 10.1007/s00216-021-03652-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Quantitative measure of a drug and its associated metabolite(s) with single-cell resolution is often limited by sampling throughput or other compromises that limit broad use. Here, we demonstrate the use of single-cell printing-liquid vortex capture-mass spectrometry (SCP-LVC-MS) to quantitatively measure the intracellular concentrations of amiodarone (AMIO) and its metabolite, N-desethylamiodarone (NDEA), from thousands of single cells across several AMIO incubation concentrations ranging from 0 to 10 μM. Concentrations obtained by SCP-LVC-MS were validated through comparison with average assays and traditional measurement of cells in bulk. Average of SCP-LVC-MS measurements and aggregate vial collection assay the concentrations differed by < 5%. Both AMIO and NDEA had clear log-normal distributions with similar standard deviation of concentrations in the cell population. The mean of both AMIO and NDEA intracellular concentrations were positively correlated with AMIO incubation concentration, increasing from 0.026 to 0.520 and 0.0055 to 0.048 mM for AMIO and NDEA, respectively. The standard deviation of AMIO and NDEA log-normal distribution fits were relatively similar in value across incubation concentrations, 0.15-0.19 log10 (mM), and exhibited a linear trend with respect to each other. The single cell-resolved conversion ratio of AMIO to NDEA increased with decreasing incubation concentration, 7 ± 2%, 18 ± 3%, and 20 ± 7% for 10.0, 1.0, and 0.1 μM AMIO incubation concentrations, respectively. Association with simultaneously measured lipids had several ions with statistically significant difference in intensity but no clear correlations with AMIO intracellular content was observed.
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Affiliation(s)
- John F Cahill
- Bioanalytical Mass Spectrometry Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA.
| | - Vilmos Kertesz
- Bioanalytical Mass Spectrometry Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA
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20
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Zhu G, Shao Y, Liu Y, Pei T, Li L, Zhang D, Guo G, Wang X. Single-cell metabolite analysis by electrospray ionization mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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21
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Xu S, Yang C, Yan X, Liu H. Towards high throughput and high information coverage: advanced single-cell mass spectrometric techniques. Anal Bioanal Chem 2021; 414:219-233. [PMID: 34435209 DOI: 10.1007/s00216-021-03624-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
Mass spectrometry (MS) is attractive for single-cell analysis because of its high sensitivity, rich information, and large dynamic ranges, especially for the single-cell metabolome and proteome analysis. Efforts have been made to deal with the throughput and information coverage problems in typical manual single-cell MS techniques. In this review, advanced techniques to improve the automation and throughput for single-cell sampling and single-cell metabolome and proteome MS detection have been discussed. Furthermore, representative MS-based strategies that can increase the in-depth cellular information coverage and achieve the more comprehensive single-cell multiomics information during high throughput detection have been highlighted, providing an ongoing perspective of the MS performance for the single-cell research.
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Affiliation(s)
- Shuting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xiuping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China. .,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Huwei Liu
- Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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22
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Yao H, Zhao H, Pan X, Zhao X, Feng J, Yang C, Zhang S, Zhang X. Discriminating Leukemia Cellular Heterogeneity and Screening Metabolite Biomarker Candidates using Label-Free Mass Cytometry. Anal Chem 2021; 93:10282-10291. [PMID: 34259005 DOI: 10.1021/acs.analchem.1c01746] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Discriminating various leukocyte subsets with specific functions is critical due to their important roles in the development of many diseases. Here, we proposed a general strategy to unravel leukocytes heterogeneity and screen differentiated metabolites as biomarker candidates for leukocyte subtypes using the label-free mass cytometry (CyESI-MS) combined with a homemade data processing workflow. Taking leukemia cells as an example, metabolic fingerprints of single leukemia cells were obtained from 472 HL-60, 416 THP-1, 313 U937, 356 Jurkat, and 366 Ramos cells, with throughput up to 40 cells/min. Five leukemia subtypes were clearly distinguished by unsupervised learning t-SNE analysis of the single-cell metabolic fingerprints. Cell discrimination in the mixed leukemia cell samples was also realized by supervised learning of the single-cell metabolic fingerprints with high recovery and good repetition (98.31 ± 0.24%, -102.35 ± 4.82%). Statistical analysis and metabolite assignment were carried out to screen characteristic metabolites for discrimination and 36 metabolites with significant differences were annotated. Then, differentiated metabolites for pairwise discrimination of five leukemia subtypes were further selected as biomarker candidates. Furthermore, discriminating cultured leukemia cells from human normal leukocytes, separated from fresh human peripheral blood, was performed based on single-cell metabolic fingerprints as well as the proposed biomarker candidates, unveiling the potential of this strategy in clinical research. This work makes efforts to realize high-throughput single-leukocyte metabolic analysis and metabolite-based discrimination of leukocytes. It is expected to be a powerful means for the clinical molecular diagnosis of hematological diseases.
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Affiliation(s)
- Huan Yao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xu Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Chengdui Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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23
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Abstract
A growing appreciation of the importance of cellular metabolism and revelations concerning the extent of cell-cell heterogeneity demand metabolic characterization of individual cells. We present SpaceM, an open-source method for in situ single-cell metabolomics that detects >100 metabolites from >1,000 individual cells per hour, together with a fluorescence-based readout and retention of morpho-spatial features. We validated SpaceM by predicting the cell types of cocultured human epithelial cells and mouse fibroblasts. We used SpaceM to show that stimulating human hepatocytes with fatty acids leads to the emergence of two coexisting subpopulations outlined by distinct cellular metabolic states. Inducing inflammation with the cytokine interleukin-17A perturbs the balance of these states in a process dependent on NF-κB signaling. The metabolic state markers were reproduced in a murine model of nonalcoholic steatohepatitis. We anticipate SpaceM to be broadly applicable for investigations of diverse cellular models and to democratize single-cell metabolomics.
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Angel PM, Rujchanarong D, Pippin S, Spruill L, Drake R. Mass Spectrometry Imaging of Fibroblasts: Promise and Challenge. Expert Rev Proteomics 2021; 18:423-436. [PMID: 34129411 PMCID: PMC8717608 DOI: 10.1080/14789450.2021.1941893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Fibroblasts maintain tissue and organ homeostasis through output of extracellular matrix that affects nearby cell signaling within the stroma. Altered fibroblast signaling contributes to many disease states and extracellular matrix secreted by fibroblasts has been used to stratify patient by outcome, recurrence, and therapeutic resistance. Recent advances in imaging mass spectrometry allow access to single cell fibroblasts and their ECM niche within clinically relevant tissue samples. AREAS COVERED We review biological and technical challenges as well as new solutions to proteomic access of fibroblast expression within the complex tissue microenvironment. Review topics cover conventional proteomic methods for single fibroblast analysis and current approaches to accessing single fibroblast proteomes by imaging mass spectrometry approaches. Strategies to target and evaluate the single cell stroma proteome on the basis of cell signaling are presented. EXPERT OPINION The promise of defining proteomic signatures from fibroblasts and their extracellular matrix niches is the discovery of new disease markers and the ability to refine therapeutic treatments. Several imaging mass spectrometry approaches exist to define the fibroblast in the setting of pathological changes from clinically acquired samples. Continued technology advances are needed to access and understand the stromal proteome and apply testing to the clinic.
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Affiliation(s)
- Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
| | - Denys Rujchanarong
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
| | - Sarah Pippin
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC
| | - Richard Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston SC USA
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Rankin‐Turner S, Heaney LM. Applications of ambient ionization mass spectrometry in 2020: An annual review. ANALYTICAL SCIENCE ADVANCES 2021; 2:193-212. [PMID: 38716454 PMCID: PMC10989608 DOI: 10.1002/ansa.202000135] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 06/26/2024]
Abstract
Recent developments in mass spectrometry (MS) analyses have seen a concerted effort to reduce the complexity of analytical workflows through the simplification (or removal) of sample preparation and the shortening of run-to-run analysis times. Ambient ionization mass spectrometry (AIMS) is an exemplar MS-based technology that has swiftly developed into a popular and powerful tool in analytical science. This increase in interest and demonstrable applications is down to its capacity to enable the rapid analysis of a diverse range of samples, typically in their native state or following a minimalistic sample preparation approach. The field of AIMS is constantly improving and expanding, with developments of powerful and novel techniques, improvements to existing instrumentation, and exciting new applications added with each year that passes. This annual review provides an overview of applications of AIMS techniques over the past year (2020), with a particular focus on the application of AIMS in a number of key fields of research including biomedical sciences, forensics and security, food sciences, the environment, and chemical synthesis. Novel ambient ionization techniques are introduced, including picolitre pressure-probe electrospray ionization and fiber spray ionization, in addition to modifications and improvements to existing techniques such as hand-held devices for ease of use, and USB-powered ion sources for on-site analysis. In all, the information provided in this review supports the view that AIMS has become a leading approach in MS-based analyses and that improvements to existing methods, alongside the development of novel approaches, will continue across the foreseeable future.
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Affiliation(s)
- Stephanie Rankin‐Turner
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Liam M. Heaney
- School of Sport, Exercise and Health SciencesLoughborough UniversityLoughboroughLeicestershireUK
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26
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Walton CL, Kertesz V, Cahill JF. Design and Evaluation of a Tethered, Open Port Sampling Interface for Liquid Extraction-Mass Spectrometry Chemical Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:198-205. [PMID: 33180483 DOI: 10.1021/jasms.0c00268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Presented is a tethered, liquid-extraction-sampling interface designed for the mass spectrometric surface sampling/analysis of 3D objects. The tethered, open port sampling interface (TOPSI) incorporates a vacuum line between the sampling probe and ionization source, which enables the ability for an extended, tethered sample transfer line. Herein, several designs of the hand-held TOPSI are presented and evaluated on the basis of the analytical metrics of analyte transport time, peak width, and analyte sensitivity. The best analytical metrics were obtained with capillary flow resistances arranged in a particular order and the vacuum region set at 6.2 kPa. This TOPSI design incorporated a transfer capillary 1 m in length, while retaining a fast analyte transport time (12 s), short signal peak width (5 s baseline-to-baseline), and high analyte signal at 90% of that obtained with a regular open port sampling interface (OPSI). The hand-held TOPSI was demonstrated for the characterization of extracted small molecules and metabolites from the surface of mint and rosemary leaves.
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Affiliation(s)
- Courtney L Walton
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Vilmos Kertesz
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - John F Cahill
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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Pedro L, Rudewicz PJ. Analysis of Live Single Cells by Confocal Microscopy and High-Resolution Mass Spectrometry to Study Drug Uptake, Metabolism, and Drug-Induced Phospholipidosis. Anal Chem 2020; 92:16005-16015. [PMID: 33280372 DOI: 10.1021/acs.analchem.0c03534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The analysis of large numbers of cells from a population results in information that does not reflect differences in cell phenotypes. Individual variations in cellular drug uptake, metabolism, and response to drug treatment may have profound effects on cellular survival and lead to the development of certain disease states, drug persistence, and resistance. Herein, we present a method that combines live cell confocal microscopy imaging with high-resolution mass spectrometry to achieve absolute cell quantification of the drug amiodarone (AMIO) and its major metabolite, N-desethylamiodarone (NDEA), in single liver cells (HepG2 and HepaRG cells). The method uses a prototype system that integrates a confocal microscope with an XYZ stage robot to image and automatically sample selected cells from a sample compartment, which is kept under growth conditions, with nanospray tips. Besides obtaining the distributions of AMIO and NDEA cell concentrations across a population of individual cells, as well as variabilities in drug metabolism, the effect of these on phospholipidosis and cell morphology was studied. The method was suited to identify subpopulations of cells that metabolized less drug and to correlate cell drug concentrations with cell phospholipid content, cell volume, sphericity, and other cell phenotypic features. Using principal component analysis (PCA), the treated cells could be clearly distinguished from vehicle control cells (0 μM AMIO) and HepaRG cells from HepG2 cells. The potential of using multidimensional and multimodal information collected from single cells to build predictive models for cell classification is demonstrated.
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Affiliation(s)
- Liliana Pedro
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Patrick J Rudewicz
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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28
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Domenick TM, Gill EL, Vedam-Mai V, Yost RA. Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions. Anal Chem 2020; 93:546-566. [PMID: 33146525 DOI: 10.1021/acs.analchem.0c04363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Taylor M Domenick
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Emily L Gill
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4283, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4283, United States
| | - Vinata Vedam-Mai
- Department of Neurology, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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29
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Recent Advances in Single Cell Analysis Methods Based on Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60038-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Wei X, Lu Y, Zhang X, Chen ML, Wang JH. Recent advances in single-cell ultra-trace analysis. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Bonzon D, Muller G, Bureau JB, Uffer N, Beuchat N, Barrandon Y, Renaud P. Impedance-Based Single-Cell Pipetting. SLAS Technol 2020; 25:222-233. [PMID: 32172665 DOI: 10.1177/2472630320911636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Many biological methods are based on single-cell isolation. In single-cell line development, the gold standard involves the dilution of cells by means of a pipet. This process is time-consuming as it is repeated over several weeks to ensure clonality. Here, we report the modeling, designing, and testing of a disposable pipet tip integrating a cell sensor based on the Coulter principle. We investigate, test, and discuss the effects of design parameters on the sensor performances with an analytical model. We also describe a system that enables the dispensing of single cells using an instrumented pipet coupled with the sensing tip. Most importantly, this system allows the recording of an impedance trace to be used as proof of single-cell isolation. We assess the performances of the system with beads and cells. Finally, we show that the electrical detection has no effect on cell viability.
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Affiliation(s)
- David Bonzon
- Laboratory of Microsystems 4, IMT, STI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland.,SEED Biosciences SA, Épalinges, Switzerland.,SEED Biosciences SA, Renens, Switzerland
| | - Georges Muller
- SEED Biosciences SA, Épalinges, Switzerland.,SEED Biosciences SA, Renens, Switzerland.,Laboratory of Stem Cell Dynamics, IBI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland
| | - Jean-Baptiste Bureau
- Laboratory of Stem Cell Dynamics, IBI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland
| | - Nicolas Uffer
- SEED Biosciences SA, Épalinges, Switzerland.,Laboratory of Stem Cell Dynamics, IBI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland
| | - Nicolas Beuchat
- Laboratory of Microsystems 4, IMT, STI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland
| | - Yann Barrandon
- Laboratory of Stem Cell Dynamics, IBI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland.,Institute of Medical Biology, A*STAR, Duke-NUS Graduate Medical School, Singapore.,Department of Plastic, Reconstructive and Aesthetic Surgery, Singapore General Hospital, Singapore
| | - Philippe Renaud
- Laboratory of Microsystems 4, IMT, STI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, VD, Switzerland
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Sosnowski P, Hopfgartner G. Application of 3D printed tools for customized open port probe-electrospray mass spectrometry. Talanta 2020; 215:120894. [PMID: 32312439 DOI: 10.1016/j.talanta.2020.120894] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 02/07/2023]
Abstract
Three dimensional printed open port probe (3DP-OPP) and air displacement based liquid handler, were designed and optimized using fused deposition modeling (FDM) and stereolitography (SLA) 3D printing. The performance of the devices were investigated for the analysis of solid and liquid samples with electrospray ionization mass spectrometry (ESI-MS). Direct analysis in less than 1 min and without any sample preparation, enabled detection of pesticides (azoxtystrobin/imazalil) on fruits peel surface and illegal substances (MDMA/MDEA) in home-made pills. Conjunction of OPP in the overspill mode with a customized autosampler, equipped with disposable pipette tips, enables direct quantitative analysis of drugs of abuse in urine and plasma, with minimized carry-over and reduced matrix effect compared to flow injection analysis.
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Affiliation(s)
- Piotr Sosnowski
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211, Geneva, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211, Geneva, Switzerland.
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