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Kumar R, Zemaitis KJ, Fulcher JM, Paša-Tolić L. Advances in mass spectrometry-enabled multiomics at single-cell resolution. Curr Opin Biotechnol 2024; 87:103096. [PMID: 38432187 DOI: 10.1016/j.copbio.2024.103096] [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] [Received: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Biological organisms are multifaceted, intricate systems where slight perturbations can result in extensive changes in gene expression, protein abundance and/or activity, and metabolic flux. These changes occur at different timescales, spatially across cells of heterogeneous origins, and within single-cells. Hence, multimodal measurements at the smallest biological scales are necessary to capture dynamic changes in heterogeneous biological systems. Of the analytical techniques used to measure biomolecules, mass spectrometry (MS) has proven to be a powerful option due to its sensitivity, robustness, and flexibility with regard to the breadth of biomolecules that can be analyzed. Recently, many studies have coupled MS to other analytical techniques with the goal of measuring multiple modalities from the same single-cell. It is with these concepts in mind that we focus this review on MS-enabled multiomic measurements at single-cell or near-single- cell resolution.
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Affiliation(s)
- Rashmi Kumar
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kevin J Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - James M Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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2
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Zhang X, Wei X, Wu CX, Men X, Wang J, Bai JJ, Sun XY, Wang Y, Yang T, Lim CT, Chen ML, Wang JH. Multiplex Profiling of Biomarker and Drug Uptake in Single Cells Using Microfluidic Flow Cytometry and Mass Spectrometry. ACS NANO 2024; 18:6612-6622. [PMID: 38359901 PMCID: PMC10906074 DOI: 10.1021/acsnano.3c12803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
To perform multiplex profiling of single cells and eliminate the risk of potential sample loss caused by centrifugation, we developed a microfluidic flow cytometry and mass spectrometry system (μCytoMS) to evaluate the drug uptake and induced protein expression at the single cell level. It involves a microfluidic chip for the alignment and purification of single cells followed by detection with laser-induced fluorescence (LIF) and inductively coupled plasma mass spectrometry (ICP-MS). Biofunctionalized nanoprobes (BioNPs), conjugating ∼3000 6-FAM-Sgc8 aptamers on a single gold nanoparticle (AuNP) (Kd = 0.23 nM), were engineered to selectively bind with protein tyrosine kinase 7 (PTK7) on target cells. PTK7 expression induced by oxaliplatin (OXA) uptake was assayed with LIF, while ICP-MS measurement of 195Pt revealed OXA uptake of the drug in individual cells, which provided further in-depth information about the drug in relation to PTK7 expression. At an ultralow flow of ∼0.043 dyn/cm2 (20 μL/min), the chip facilitates the extremely fast focusing of BioNPs labeled single cells without the need for centrifugal purification. It ensures multiplex profiling of single cells at a throughput speed of 500 cells/min as compared to 40 cells/min in previous studies. Using a machine learning algorithm to initially profile drug uptake and marker expression in tumor cell lines, μCytoMS was able to perform in situ profiling of the PTK7 response to the OXA at single-cell resolution for tests done on clinical samples from 10 breast cancer patients. It offers great potential for multiplex single-cell phenotypic analysis and clinical diagnosis.
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Affiliation(s)
- Xuan Zhang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
- Institute
for Health Innovation and Technology, National
University of Singapore, 117599, Singapore
- Academy
of Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Xing Wei
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Cheng-Xin Wu
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xue Men
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jiao Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jun-Jie Bai
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xiao-Yan Sun
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yu Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ting Yang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Chwee Teck Lim
- Institute
for Health Innovation and Technology, National
University of Singapore, 117599, Singapore
- Department
of Biomedical Engineering, National University
of Singapore, 117576, Singapore
| | - Ming-Li Chen
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
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3
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Cao J, Yao QJ, Wu J, Chen X, Huang L, Liu W, Qian K, Wan JJ, Zhou BO. Deciphering the metabolic heterogeneity of hematopoietic stem cells with single-cell resolution. Cell Metab 2024; 36:209-221.e6. [PMID: 38171334 DOI: 10.1016/j.cmet.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/14/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Metabolic status is crucial for stem cell functions; however, the metabolic heterogeneity of endogenous stem cells has never been directly assessed. Here, we develop a platform for high-throughput single-cell metabolomics (hi-scMet) of hematopoietic stem cells (HSCs). By combining flow cytometric isolation and nanoparticle-enhanced laser desorption/ionization mass spectrometry, we routinely detected >100 features from single cells. We mapped the single-cell metabolomes of all hematopoietic cell populations and HSC subpopulations with different division times, detecting 33 features whose levels exhibited trending changes during HSC proliferation. We found progressive activation of the oxidative pentose phosphate pathway (OxiPPP) from dormant to active HSCs. Genetic or pharmacological interference with OxiPPP increased reactive oxygen species level in HSCs, reducing HSC self-renewal upon oxidative stress. Together, our work uncovers the metabolic dynamics during HSC proliferation, reveals a role of OxiPPP for HSC activation, and illustrates the utility of hi-scMet in dissecting metabolic heterogeneity of immunophenotypically defined cell populations.
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Affiliation(s)
- Jing Cao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Qi Jason Yao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiao Wu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Xiaonan Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Lin Huang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Wanshan Liu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Kun Qian
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC.
| | - Jing-Jing Wan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Bo O Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences, Tianjin 300020, China.
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4
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Madhuvilakku R, Hong Y, Nila IS, Villagra Moran VM, Subramanian P, Khan ZA, Jeong S, You SG. Quantification of Neuronal Cell-Released Hydrogen Peroxide Using 3D Mesoporous Copper-Enriched Prussian Blue Microcubes Nanozymes: A Colorimetric Approach in Real Time and Anticancer Effect. ACS APPLIED MATERIALS & INTERFACES 2023; 15:55466-55485. [PMID: 37991753 DOI: 10.1021/acsami.3c13594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Despite the effectiveness and selectivity of natural enzymes, their instability has paved the way for developing nanozymes with high peroxidase activity using a straightforward technique, thereby expanding their potential for multifunctional applications. Herein, meso-copper-Prussian blue microcubes (Meso-Cu-PBMCs) nanozymes were successfully prepared via a cost-effective hydrothermal route. It was found that the Cu-PBMCs nanozymes, with three-dimensional (3D) mesoporous cubic morphologies, exhibited an excellent peroxidase-like property. Based on the high affinity of Meso-Cu-PBMCs toward H2O2 (Km = 0.226 μM) and TMB (Km = 0.407 mM), a colorimetric sensor for in situ H2O2 detection was constructed. On account of the high catalytic activity, affinity, and cascade strategy, the Meso-Cu-PBMCs nanozyme generated rapid multicolor displays at varying H2O2 concentrations. Under optimized conditions, the proposed sensor exhibits a preferable sensitivity of 18.14 μA μM-1, a linear range of 10 nM-25 mM, and a detection limit of 6.36 nM (S/N = 10). The reliability of the sensor was verified by detecting H2O2 in spiked human blood serum and milk samples, as well as by detecting in situ H2O2 generated from the neuron cell SH-SY5Y. Besides, the Meso-Cu-PBMCs nanozyme facilitated the catalysis of H2O2 in cancer cells, generating •OH radicals that induce the death of cancer cells (HCT-116 colon cancer cells), which holds substantial potential for application in chemodynamic therapy (CDT). This proposed strategy holds promise for simple, rapid, inexpensive, and effective intracellular biosensing and offers a novel approach to improve CDT efficacy.
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Affiliation(s)
- Rajesh Madhuvilakku
- Department of Physical Therapy, College of Healthcare Medical Science & Engineering, Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Biohealth Products Research Center (BPRC), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Research Center for Aged-life Redesign (RCAR), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
| | - Yonggeun Hong
- Department of Physical Therapy, College of Healthcare Medical Science & Engineering, Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Biohealth Products Research Center (BPRC), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Research Center for Aged-life Redesign (RCAR), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Department of Digital Anti-Aging Healthcare, Graduate School of Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Department of Physical Therapy, Graduate School of Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Department of Rehabilitation Science, Graduate School of Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
| | - Irin Sultana Nila
- Biohealth Products Research Center (BPRC), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Research Center for Aged-life Redesign (RCAR), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Department of Digital Anti-Aging Healthcare, Graduate School of Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
| | - Vanina Myuriel Villagra Moran
- Biohealth Products Research Center (BPRC), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Research Center for Aged-life Redesign (RCAR), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Department of Physical Therapy, Graduate School of Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
| | - Palanisamy Subramanian
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Gangwon 25457, Republic of Korea
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangneung, Gangwon 25457, Republic of Korea
| | - Zeeshan Ahmad Khan
- Department of Physical Therapy, College of Healthcare Medical Science & Engineering, Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Biohealth Products Research Center (BPRC), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
- Research Center for Aged-life Redesign (RCAR), Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
| | - Sehoon Jeong
- Department of Medical Information Technology, College of Bio Nano Information Technology, Inje University, Gimhae, Gyeong-nam 50834, Republic of Korea
| | - Sang Guan You
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Gangwon 25457, Republic of Korea
- Department of Marine Food Science and Technology, Gangneung-Wonju National University, Gangneung, Gangwon 25457, Republic of Korea
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5
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Meng X, Xu P, Tao F. RespectM revealed metabolic heterogeneity powers deep learning for reshaping the DBTL cycle. iScience 2023; 26:107069. [PMID: 37426353 PMCID: PMC10329182 DOI: 10.1016/j.isci.2023.107069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/18/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Synthetic biology, relying on Design-Build-Test-Learn (DBTL) cycle, aims to solve medicine, manufacturing, and agriculture problems. However, the DBTL cycle's Learn (L) step lacks predictive power for the behavior of biological systems, resulting from the incompatibility between sparse testing data and chaotic metabolic networks. Herein, we develop a method, "RespectM," based on mass spectrometry imaging, which is able to detect metabolites at a rate of 500 cells per hour with high efficiency. In this study, 4,321 single cell level metabolomics data were acquired, representing metabolic heterogeneity. An optimizable deep neural network was applied to learn from metabolic heterogeneity and a "heterogeneity-powered learning (HPL)" based model was trained as well. By testing the HPL based model, we suggest minimal operations to achieve high triglyceride production for engineering. The HPL strategy could revolutionize rational design and reshape the DBTL cycle.
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Affiliation(s)
- Xuanlin Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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6
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Chen X, Wang Y, Luo Y, Gao Z, Han T, Zhou H. Composite PVK/SLGO As Matrix for MALDI-TOF MS Detection of Small Molecules in Dual-Ion Mode. ACS OMEGA 2022; 7:39028-39038. [PMID: 36340108 PMCID: PMC9631907 DOI: 10.1021/acsomega.2c04772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Currently, most matrices developed for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) for small-molecule detection are only suitable for the positive or negative ion mode and not the dual-ion mode, except for carbon-based nanomaterials. The lone-pair electrons on the N atom in poly n-vinylcarbazole (PVK) can serve as a Lewis base with strong electron-donation effects, which is favorable for negative ion mode detection. The surface of single-layer graphene oxide (SLGO) contains many oxygen atoms in carboxyl and hydroxyl groups that act as Lewis acids and thereby provides favorable protonation sites for positive ion mode detection. In this study, composite PVK/SLGO was prepared by combining the advantages of amorphous PVK and SLGO. PVK/SLGO was tested as a novel matrix for positive- and negative-ion-mode MALDI-TOF MS for the analysis of amino acids, nucleic acid bases, environmental endocrine disruptors, antibiotics, and various small molecules. PVK/SLGO was compared with PVK, SLGO, and commercially available matrices of 9-aminoacridine (9-AA) and α-cyano-4-hydroxycinnamic acid (CHCA). The PVK/SLGO matrix was demonstrated to be suitable for the positive and negative ion modes, exhibiting high signal intensity and detection sensitivity without background interference. The limits of detection of the aforementioned molecules ranged from 0.1 to 0.0001 and 0.01 to 0.0001 mg/mL in the positive and negative ion modes, respectively. The quantitative determination of enrofloxacin in milk was realized using an internal standard method with a linear range of 0.0001-0.1 mg/mL (R 2 = 0.9991). Furthermore, the PVK/SLGO matrix exhibited high salt tolerance (up to 1000 mmol/L) and stability over 28 consecutive days. Studies regarding its ionization mechanism revealed that the good performance originates from the combined materials acting synergistically. This study provides a foundation for developing bimodal composite matrices and further expands the scope of PVK/SLGO applications.
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Affiliation(s)
- Xiuying Chen
- Key
Laboratory of Medicinal Chemistry and Molecular Diagnosis, College
of Chemical and Environmental Sciences, Hebei University, Baoding 071002, China
- Tianjin
Key Laboratory of Risk Assessment and Control Technology for Environment
and Food Safety, Tianjin Institute of Environmental
and Operational Medicine, Tianjin 300050, China
- Nanpu
Development Zone Administrative Examination and Approval Bureau, Tangshan 063305, China
| | - Yonghui Wang
- Tianjin
Key Laboratory of Risk Assessment and Control Technology for Environment
and Food Safety, Tianjin Institute of Environmental
and Operational Medicine, Tianjin 300050, China
| | - Yuanyuan Luo
- Tianjin
Key Laboratory of Risk Assessment and Control Technology for Environment
and Food Safety, Tianjin Institute of Environmental
and Operational Medicine, Tianjin 300050, China
| | - Zhixian Gao
- Tianjin
Key Laboratory of Risk Assessment and Control Technology for Environment
and Food Safety, Tianjin Institute of Environmental
and Operational Medicine, Tianjin 300050, China
| | - Tie Han
- Tianjin
Key Laboratory of Risk Assessment and Control Technology for Environment
and Food Safety, Tianjin Institute of Environmental
and Operational Medicine, Tianjin 300050, China
| | - Huanying Zhou
- Tianjin
Key Laboratory of Risk Assessment and Control Technology for Environment
and Food Safety, Tianjin Institute of Environmental
and Operational Medicine, Tianjin 300050, China
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7
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Bien T, Koerfer K, Schwenzfeier J, Dreisewerd K, Soltwisch J. Mass spectrometry imaging to explore molecular heterogeneity in cell culture. Proc Natl Acad Sci U S A 2022; 119:e2114365119. [PMID: 35858333 PMCID: PMC9303856 DOI: 10.1073/pnas.2114365119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 05/13/2022] [Indexed: 01/13/2023] Open
Abstract
Molecular analysis on the single-cell level represents a rapidly growing field in the life sciences. While bulk analysis from a pool of cells provides a general molecular profile, it is blind to heterogeneities between individual cells. This heterogeneity, however, is an inherent property of every cell population. Its analysis is fundamental to understanding the development, function, and role of specific cells of the same genotype that display different phenotypical properties. Single-cell mass spectrometry (MS) aims to provide broad molecular information for a significantly large number of cells to help decipher cellular heterogeneity using statistical analysis. Here, we present a sensitive approach to single-cell MS based on high-resolution MALDI-2-MS imaging in combination with MALDI-compatible staining and use of optical microscopy. Our approach allowed analyzing large amounts of unperturbed cells directly from the growth chamber. Confident coregistration of both modalities enabled a reliable compilation of single-cell mass spectra and a straightforward inclusion of optical as well as mass spectrometric features in the interpretation of data. The resulting multimodal datasets permit the use of various statistical methods like machine learning-driven classification and multivariate analysis based on molecular profile and establish a direct connection of MS data with microscopy information of individual cells. Displaying data in the form of histograms for individual signal intensities helps to investigate heterogeneous expression of specific lipids within the cell culture and to identify subpopulations intuitively. Ultimately, t-MALDI-2-MSI measurements at 2-µm pixel sizes deliver a glimpse of intracellular lipid distributions and reveal molecular profiles for subcellular domains.
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Affiliation(s)
- Tanja Bien
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
| | - Krischan Koerfer
- Institute for Psychology, University of Münster, 48149 Münster, Germany
- Otto Creutzfeldt Center for Cognitive and Behavioural Neuroscience, University of Münster, 48149 Münster, Germany
| | - Jan Schwenzfeier
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
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8
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Wink K, van der Loh M, Hartner N, Polack M, Dusny C, Schmid A, Belder D. Quantification of Biocatalytic Transformations by Single Microbial Cells Enabled by Tailored Integration of Droplet Microfluidics and Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202204098. [PMID: 35511505 PMCID: PMC9401594 DOI: 10.1002/anie.202204098] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Indexed: 12/23/2022]
Abstract
Improving the performance of chemical transformations catalysed by microbial biocatalysts requires a deep understanding of cellular processes. While the cellular heterogeneity of cellular characteristics, such as the concentration of high abundant cellular content, is well studied, little is known about the reactivity of individual cells and its impact on the chemical identity, quantity, and purity of excreted products. Biocatalytic transformations were monitored chemically specific and quantifiable at the single-cell level by integrating droplet microfluidics, cell imaging, and mass spectrometry. Product formation rates for individual Saccharomyces cerevisiae cells were obtained by i) incubating nanolitre-sized droplets for product accumulation in microfluidic devices, ii) an imaging setup to determine the number of cells in the droplets, and iii) electrospray ionisation mass spectrometry for reading the chemical contents of individual droplets. These findings now enable the study of whole-cell biocatalysis at single-cell resolution.
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Affiliation(s)
- Konstantin Wink
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Marie van der Loh
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Nora Hartner
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Matthias Polack
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Christian Dusny
- Department Solar MaterialsHelmholtz Centre for Environmental Research (UFZ)04318LeipzigGermany
| | - Andreas Schmid
- Department Solar MaterialsHelmholtz Centre for Environmental Research (UFZ)04318LeipzigGermany
| | - Detlev Belder
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
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9
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Facile preparation of aqueous-soluble fluorescent polyethylene glycol functionalized carbon dots from palm waste by one-pot hydrothermal carbonization for colon cancer nanotheranostics. Sci Rep 2022; 12:10550. [PMID: 35732805 PMCID: PMC9217983 DOI: 10.1038/s41598-022-14704-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Carbon dots (CDs) are categorized as an emerging class of zero-dimension nanomaterials having high biocompatibility, photoluminescence, tunable surface, and hydrophilic property. CDs, therefore, are currently of interest for bio-imaging and nano-medicine applications. In this work, polyethylene glycol functionalized CDs (CD-PEG) were prepared from oil palm empty fruit bunch by a one-pot hydrothermal technique. PEG was chosen as a passivating agent for the enhancement of functionality and photoluminescence properties of CDs. To prepare the CDs-PEG, the effects of temperature, time, and concentration of PEG were investigated on the properties of CDs. The as-prepared CDs-PEG were characterized by several techniques including dynamic light scattering, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, fluorescence spectroscopy, Raman spectroscopy, Fourier-transform infrared spectroscopy and Thermogravimetric analysis. The as-prepared CDs under hydrothermal condition at 220 °C for 6 h had spherical morphology with an average diameter of 4.47 nm. Upon modification, CDs-PEG were photo-responsive with excellent photoluminescence property. The CDs-PEG was subsequently used as a drug carrier for doxorubicin [DOX] delivery to CaCo-2, colon cancer cells in vitro. DOX was successfully loaded onto CDs-PEG surface confirmed by FT-IR and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometer (MALDI-TOF/MS) patterns. The selective treatment of CDs-PEG-DOX against the colorectal cancer cells, , relative to normal human fibroblast cells was succesfully demonstrated.
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10
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Wink K, Loh M, Hartner N, Polack M, Dusny C, Schmid A, Belder D. Quantifizierung biokatalytischer Umwandlungen durch einzelne mikrobielle Zellen mittels maßgeschneiderter Integration von Tröpfchenmikrofluidik und Massenspektrometrie. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Konstantin Wink
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Marie Loh
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Nora Hartner
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Matthias Polack
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Christian Dusny
- Department Solare Materialien Helmholtz-Zentrum für Umweltforschung (UFZ) 04318 Leipzig Deutschland
| | - Andreas Schmid
- Department Solare Materialien Helmholtz-Zentrum für Umweltforschung (UFZ) 04318 Leipzig Deutschland
| | - Detlev Belder
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
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11
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Chen XY, Wang YH, Ren SY, Li S, Wang Y, Qin K, Li S, Han DP, Peng Y, Han T, Gao ZX, Gao BX, Zhou HY. Amorphous poly- N-vinylcarbazole polymer as a novel matrix for the determination of low molecular weight compounds by MALDI-TOF MS. RSC Adv 2022; 12:15215-15221. [PMID: 35693227 PMCID: PMC9116175 DOI: 10.1039/d2ra01602h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 12/18/2022] Open
Abstract
Traditional matrices for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) are usually crystalline small molecules. The heterogeneous co-crystallization of the analyte and the matrix creates a sweet spot effect and reduces point-to-point reproducibility. In this study, an amorphous poly-N-vinylcarbazole polymer (PVK) was studied as a novel matrix for MALDI-TOF MS to detect various low molecular weight compounds (LMWCs) in the negative ion mode. The PVK achieved excellent matrix action and showed high sensitivity, good salt tolerance, and reproducibility. These results significantly broaden the design rules for new and efficient polymeric MALDI matrices. Amorphous, highly salt tolerant and stable polymer PVK as a negative ion mode matrix was successfully achieved for the qualitative and quantitative detection of small molecule compounds by MALDI MS.![]()
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Affiliation(s)
- Xiu-Ying Chen
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, College of Chemical and Environmental Sciences, Hebei University Baoding 071002 China .,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China .,Nanpu Development Zone Administrative Examination and Approval Bureau Tangshan 063305 China
| | - Yong-Hui Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Shu-Yue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Kang Qin
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Sen Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Dian-Peng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Zhi-Xian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
| | - Bao-Xiang Gao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, College of Chemical and Environmental Sciences, Hebei University Baoding 071002 China
| | - Huan-Ying Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine Tianjin 300050 China
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12
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Cohen N, Kahana A, Schuldiner M. A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase. J Mol Biol 2022; 434:167478. [PMID: 35123996 PMCID: PMC9005783 DOI: 10.1016/j.jmb.2022.167478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/01/2022]
Abstract
Despite decades of research and the availability of the full genomic sequence of the baker's yeast Saccharomyces cerevisiae, still a large fraction of its genome is not functionally annotated. This hinders our ability to fully understand cellular activity and suggests that many additional processes await discovery. The recent years have shown an explosion of high-quality genomic and structural data from multiple organisms, ranging from bacteria to mammals. New computational methods now allow us to integrate these data and extract meaningful insights into the functional identity of uncharacterized proteins in yeast. Here, we created a database of sensitive sequence similarity predictions for all yeast proteins. We use this information to identify candidate enzymes for known biochemical reactions whose enzymes are unidentified, and show how this provides a powerful basis for experimental validation. Using one pathway as a test case we pair a new function for the previously uncharacterized enzyme Yhr202w, as an extra-cellular AMP hydrolase in the NAD degradation pathway. Yhr202w, which we now term Smn1 for Scavenger MonoNucleotidase 1, is a highly conserved protein that is similar to the human protein E5NT/CD73, which is associated with multiple cancers. Hence, our new methodology provides a paradigm, that can be adopted to other organisms, for uncovering new enzymatic functions of uncharacterized proteins.
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Affiliation(s)
- Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amit Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel. https://twitter.com/AmitKahana
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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13
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Liu Q, Lan J, Wu R, Begley A, Ge W, Zenobi R. Hybrid Ionization Source Combining Nanoelectrospray and Dielectric Barrier Discharge Ionization for the Simultaneous Detection of Polar and Nonpolar Compounds in Single Cells. Anal Chem 2022; 94:2873-2881. [PMID: 35113514 DOI: 10.1021/acs.analchem.1c04759] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Single-cell metabolomics is expected to deliver fast and dynamic information on cell function; therefore, it requires rapid analysis of a wide variety of very small quantities of metabolites in living cells. In this work, a hybrid ionization source that combines nanoelectrospray ionization (nanoESI) and dielectric barrier discharge ionization (DBDI) is proposed for single-cell analysis. A capillary with a 1 μm i.d. tip was inserted into cells for sampling and then directly used as the nanoESI source for ionization of polar metabolites. In addition, a DBDI source was employed as a post-ionization source to improve the ionization of apolar metabolites in cells that are not easily ionized by ESI. By increasing the voltage of the DBDI source from 0 to 3.2 kV, the classes of detected metabolites can be shifted from mostly polar to both polar and apolar to mainly apolar. Plant cells (onion) and human cells (PANC-1) were investigated in this study. After optimization, 50 compounds in onion cells and 40 compounds in PANC-1 cells were observed in ESI mode (3.5 kV) and an additional 49 compounds in onion cells and 73 compounds in PANC-1 cells were detected in ESI (3.5 kV)-DBDI (2.6 kV) hybrid mode. This hybrid ionization source improves the coverage, ionization efficiency, and limit of detection of metabolites with different polarities and could potentially contribute to the fast-growing field of single-cell metabolomics.
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Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jiayi Lan
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ri Wu
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Alina Begley
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Wenjie Ge
- Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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14
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Borisov RS, Matveeva MD, Zaikin VG. Reactive Matrices for Analytical Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry. Crit Rev Anal Chem 2021; 53:1027-1043. [PMID: 34969337 DOI: 10.1080/10408347.2021.2001309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
In recent years, a special focus is placed on the usage of reactive matrices for analytical matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Since 2003, when the term "reactive matrices" was suggested and the dignity of compounds, possessing dualistic properties as matrices and derivatization agents was demonstrated, corresponding approach has found application in various fields and, in particular, in bioanalysis (metabolomics, lipidomics, etc.). The main advantage of this methodology is that it reduces sample treatment time, simplifies the procedure of sample handling, improves the sensitivity of analysis, enhances the molecular identification and profiling. Within the framework of this review, the main attention is paid to "true" reactive matrices that interact with analyte molecules through an exchange or addition reactions. A special section discusses practical application of reactive matrices in the determination of the distribution of targeted and non-targeted organic substances on the surface of biological tissue sections by MALDI-MS imaging. In this critical review, a controversial proposal is made to consider protonating and deprotonating matrices as reactive, because they can undergo a chemical reaction such as proton transfer that occurs in both target solution and MALDI plume. In this respect, special attention is paid to "proton sponge" matrices that have found a wide application in the analysis of various acidic compounds by MALDI-MS in the negative mode. Historical data on the formation of ions and the fate of matrices in MALDI are considered at the beginning of this article.
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Affiliation(s)
- Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mariya D Matveeva
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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15
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Liu Q, Ge W, Wang T, Lan J, Martínez‐Jarquín S, Wolfrum C, Stoffel M, Zenobi R. High‐Throughput Single‐Cell Mass Spectrometry Reveals Abnormal Lipid Metabolism in Pancreatic Ductal Adenocarcinoma. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Wenjie Ge
- Department of Biology ETH Zurich Otto-Stern-Weg 7 8093 Zurich Switzerland
| | - Tongtong Wang
- Department of Health Sciences and Technology ETH Zurich Schorenstrasse 16 8603 Schwerzenbach Switzerland
| | - Jiayi Lan
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Sandra Martínez‐Jarquín
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Christian Wolfrum
- Department of Health Sciences and Technology ETH Zurich Schorenstrasse 16 8603 Schwerzenbach Switzerland
| | - Markus Stoffel
- Department of Biology ETH Zurich Otto-Stern-Weg 7 8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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16
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Liu Q, Ge W, Wang T, Lan J, Martínez‐Jarquín S, Wolfrum C, Stoffel M, Zenobi R. High-Throughput Single-Cell Mass Spectrometry Reveals Abnormal Lipid Metabolism in Pancreatic Ductal Adenocarcinoma. Angew Chem Int Ed Engl 2021; 60:24534-24542. [PMID: 34505339 PMCID: PMC8597026 DOI: 10.1002/anie.202107223] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/17/2021] [Indexed: 01/02/2023]
Abstract
Even populations of clonal cells are heterogeneous, which requires high-throughput analysis methods with single-cell sensitivity. Here, we propose a rapid, label-free single-cell analytical method based on active capillary dielectric barrier discharge ionization mass spectrometry, which can analyze multiple metabolites in single cells at a rate of 38 cells/minute. Multiple cell types (HEK-293T, PANC-1, CFPAC-1, H6c7, HeLa and iBAs) were discriminated successfully. We found evidence for abnormal lipid metabolism in pancreatic cancer cells. We also analyzed gene expression in a cancer genome atlas dataset and found that the mRNA level of a critical enzyme of lipid synthesis (ATP citrate lyase, ACLY) was upregulated in human pancreatic ductal adenocarcinoma (PDAC). Moreover, both an ACLY chemical inhibitor and a siRNA approach targeting ACLY could suppress the viability of PDAC cells. A significant reduction in lipid content in treated cells indicates that ACLY could be a potential target for treating pancreatic cancer.
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Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Wenjie Ge
- Department of BiologyETH ZurichOtto-Stern-Weg 78093ZurichSwitzerland
| | - Tongtong Wang
- Department of Health Sciences and TechnologyETH ZurichSchorenstrasse 168603SchwerzenbachSwitzerland
| | - Jiayi Lan
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Sandra Martínez‐Jarquín
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Christian Wolfrum
- Department of Health Sciences and TechnologyETH ZurichSchorenstrasse 168603SchwerzenbachSwitzerland
| | - Markus Stoffel
- Department of BiologyETH ZurichOtto-Stern-Weg 78093ZurichSwitzerland
| | - Renato Zenobi
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
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17
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Xu T, Li H, Feng D, Dou P, Shi X, Hu C, Xu G. Lipid Profiling of 20 Mammalian Cells by Capillary Microsampling Combined with High-Resolution Spectral Stitching Nanoelectrospray Ionization Direct-Infusion Mass Spectrometry. Anal Chem 2021; 93:10031-10038. [PMID: 34270220 DOI: 10.1021/acs.analchem.1c00373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Studies of cellular metabolism can provide profound insights into the underlying molecular mechanisms and metabolic function. To date, the majority of cellular metabolism studies based on chromatography-mass spectrometry (MS) require population cells to obtain informative metabolome. These methods are not only time-consuming but also not suitable for amount-limited cell samples such as circulating tumor cells, stem cells, and neurons. Therefore, it is extremely essential to develop analytical methods enabling to detect metabolome from tens of cells in a high-throughput and high-sensitivity way. In this work, a novel platform for rapid and sensitive detection of lipidome in 20 mammalian cells was proposed using capillary microsampling combined with high-resolution spectral stitching nanoelectrospray ionization direct-infusion MS. It can be used to collect cells rapidly and accurately via the capillary microprobe, extract lipids directly in a 96-well plate using a spray solvent, and detect more than 500 lipids covering 19 lipid subclasses within 3 min. This novel platform was successfully applied to study the lipid features of different cancer cell types and subtypes as well as target cells from tissue samples. This study provides a strategy for determining the lipid species with rich information in tens of cells and demonstrates great potential for clinical applications.
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Affiliation(s)
- Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Disheng Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Krivosheina MS, Borisov RS, Zhilyaev DI, Matveeva MD, Zaikin VG. New suitable deprotonating matrices for the analysis of carboxylic acids and some acidic compounds by matrix-assisted laser desorption/ionization mass spectrometry in negative ion mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8954. [PMID: 32979299 DOI: 10.1002/rcm.8954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Direct non-derivatization analysis of organic acids and acidic compounds by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) in positive ion mode is not always possible due to the low ionization efficiency of analytes. Some new efficient deprotonating matrices were suggested that allowed the production of negative ions from acidic compounds during MALDI-MS experiments. METHODS Various tested carboxyl-containing compounds as well as compounds with acidic properties were mixed with the suggested deprotonating matrices [4-dimethylaminobenzaldehyde (DMABA), N,N-dimethylamino-p-phenylenediamine or 3-aminoquinoline] and applied on a standard MALDI target followed by recording MALDI mass spectra in negative ion mode. RESULTS All the tested acidic compounds mixed with the suggested deprotonating matrices produced abundant [M - H]- ions under MALDI conditions. DMABA produced the strongest signals reflecting greater sensitivity of analysis. CONCLUSIONS The suggested deprotonating matrices are commercially available compounds and are good alternatives to well-known matrices of this kind and, in particular, the often used 9-aminoacridine. DMABA is the best of the tested potential matrices and is suitable for the detection of low molecular weight carboxyl-containing compounds, substituted phenols, and mixtures of naphthenic acids by (-)MALDI-MS.
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Affiliation(s)
- Mariya S Krivosheina
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
- People's Friendship University of Russia, ul. Miklukho-Maklay 6, Moscow, 117198, Russian Federation
| | - Dmitry I Zhilyaev
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
- People's Friendship University of Russia, ul. Miklukho-Maklay 6, Moscow, 117198, Russian Federation
| | - Mariya D Matveeva
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
| | - Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
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19
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Kumar R, Ghosh M, Kumar S, Prasad M. Single Cell Metabolomics: A Future Tool to Unmask Cellular Heterogeneity and Virus-Host Interaction in Context of Emerging Viral Diseases. Front Microbiol 2020; 11:1152. [PMID: 32582094 PMCID: PMC7286130 DOI: 10.3389/fmicb.2020.01152] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
Viral emergence is an unpredictable but obvious event, particularly in the era of climate change and globalization. Efficient management of viral outbreaks depends on pre-existing knowledge and alertness. The potential hotspots of viral emergence often remain neglected and the information related to them is insufficient, particularly for emerging viruses. Viral replication and transmission rely upon usurping the host metabolic machineries. So altered host metabolic pathways can be exploited for containment of these viruses. Metabolomics provides the insight for tracing out such checkpoints. Consequently introspection of metabolic alteration at virus-host interface has evolved as prime area in current virology research. Chromatographic separation followed by mass spectrometry has been used as the predominant analytical platform in bulk of the analyses followed by nuclear magnetic resonance (NMR) and fluorescence based techniques. Although valuable information regarding viral replication and modulation of host metabolic pathways have been extracted but ambiguity often superseded the real events due to population effect over the infected cells. Exploration of cellular heterogeneity and differentiation of infected cells from the nearby healthy ones has become essential. Single cell metabolomics (SCM) emerges as necessity to explore such minute details. Mass spectrometry imaging (MSI) coupled with several soft ionization techniques such as electrospray ionization (ESI), laser ablation electrospray ionization (LAESI), matrix assisted laser desorption/ionization (MALDI), matrix-free laser desorption ionization (LDI) have evolved as the best suited platforms for SCM analyses. The potential of SCM has already been exploited to resolve several biological conundrums. Thus SCM is knocking at the door of virus-host interface.
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Affiliation(s)
- Rajesh Kumar
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Mirzapur, India
| | - Sandeep Kumar
- Department of Veterinary Surgery and Radiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
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21
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Wu Z, Liu M, Liu Z, Tian Y. Real-Time Imaging and Simultaneous Quantification of Mitochondrial H 2O 2 and ATP in Neurons with a Single Two-Photon Fluorescence-Lifetime-Based Probe. J Am Chem Soc 2020; 142:7532-7541. [PMID: 32233469 DOI: 10.1021/jacs.0c00771] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial oxidative stress and energy metabolism are vital biological events and are involved in various physiological and pathological processes such as apoptosis and necrosis. However, it remains unclear how the dynamic patterns of mitochondrial hydrogen peroxide (H2O2) and adenosine-5'-triphosphate (ATP) change in these events and, more importantly, how they affect each other. Herein, we developed a single two-photon fluorescence-lifetime-based probe (TFP), which offered real-time imaging and the simultaneous determination of mitochondrial H2O2 and ATP changes in two well-separated fluorescence channels without spectral crosstalk. The fluorescence lifetime of TFP exhibited good responses and selectivity in the detection ranges of 0.4-10 μM H2O2 and 0.5-15 mM ATP, taking advantage of accuracy and the quantitative ability of fluorescence lifetime imaging. Using this useful probe, we studied the relationship between H2O2 and ATP in mitochondria and visualized the dynamic level changes of mitochondrial H2O2 and ATP induced by the superoxide anion (O2•-). It was discovered that O2•- stimulation in a short period of time (8 min) temporarily changes the levels of H2O2 and ATP in mitochondria, and neurons were capable of recovering to the initial state in a short time. However, increasing time of up to 50 min of O2•- stimulation led to permanent oxidative damage and an energy deficiency. Meanwhile, it was first found that the exogenous stimulation of O2•- and H2O2 had different impacts on the levels of mitochondrial H2O2 and ATP, in which O2•- demonstrated more severe and negative consequences. As a matter of fact, this work not only has provided a general molecular design methodology for multiple species imaging but also has revealed oxidative-stress-induced intracellular functions related to H2O2 and ATP in mitochondria based on this developed TFP probe.
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Affiliation(s)
- Zhou Wu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Zhichao Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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22
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Lin CH, Lee C, Wu YC, Lu IC. New Strategy to Preserve Phosphate by Ionic Liquid Matrices in Matrix-Assisted Laser Desorption/Ionization: A Case of Adenosine Nucleotides. Molecules 2020; 25:molecules25051217. [PMID: 32182713 PMCID: PMC7179418 DOI: 10.3390/molecules25051217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Adenosine -5′-triphosphate (ATP) plays a valuable role in metabolic activity to produce adequate energy in a biosystem. A high ATP/AMP ratio has a correlation with diabetes that induces suppression of AMP-activated protein kinase (AMPK). Matrix-assisted laser desorption/ionization (MALDI)–mass spectrometry (MS) has outstanding potential in determining the ratio of several types of adenosine phosphates in a sample to rapidly understand the primary energy transfer in metabolism. Although MALDI is viewed as a soft ionization technique for MS analysis, excess photon energy might crack the phosphate bonds leading to misinterpretation of the ATP level. In this work, ionic liquid matrices (ILMs) were employed to reduce fragmentation and increase the detection efficiency during the MALDI process. This study demonstrated for the first time that 2,5-dihydroxybenzoic acid pyridine (DHBP) is one of the most effective matrices for further quantitative analysis of adenosine nucleotides. This systematic screening of ILMs also enhances the fundamental understanding of MALDI.
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Affiliation(s)
- Chih-Hao Lin
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan; (C.-H.L.); (Y.-C.W.)
| | - Chuping Lee
- Department of Applied Chemistry, National Chiayi University, Chiayi City 60004, Taiwan;
| | - Yu-Cheng Wu
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan; (C.-H.L.); (Y.-C.W.)
| | - I-Chung Lu
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan; (C.-H.L.); (Y.-C.W.)
- Correspondence: ; Tel.: +886-4-22840411 (ext. 502); Fax: +886-4-22862547
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23
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Abstract
Mass spectrometry (MS) is an indispensable analytical technique for bioanalysis. Based on the measurement of mass/charge ratios (m/z) of ions, MS can be used for sensitive detection and accurate identification of species of interest. In traditional studies, MS is utilized to measure analytes in prepared solutions or gas-phase samples. Benefited from recent development of sampling and ionization approaches, MS has been extensively applied to the analysis of broad ranges of biological samples. We have developed a new device, the Single-probe, that can be used for in situ, real-time MS analysis of metabolites inside individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip size smaller than 10 μm, we can insert the Single-probe tip into single cells to extract intracellular compounds, which are analyzed using MS in real-time. We have successfully used the Single-probe MS technique to detect a variety of endogenous and exogenous cellular metabolites in individual eukaryotic cells. Single cell mass spectrometry (SCMS) is a new scientific technology that has the potential to reshape approaches in biological and pharmaceutical bioanalytical research.
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Affiliation(s)
- Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Wei Rao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
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24
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Krismer J, Sobek J, Steinhoff RF, Brönnimann R, Pabst M, Zenobi R. A MALDI-MS Methodology for Studying Metabolic Heterogeneity of Single Cells in a Population. Methods Mol Biol 2020; 2064:113-124. [PMID: 31565770 DOI: 10.1007/978-1-4939-9831-9_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mass spectrometry based metabolomics is the highly multiplexed, label-free analysis of small molecules such as metabolites or lipids in biological systems, and thus one of the most direct ways to characterize phenotypes. However, the phenotyping of populations with single-cell resolution is a great challenge due to the small number of molecules contained in an individual cell. Here we describe a microarray-based sample preparation workflow for MALDI mass spectrometry that has single-cell sensitivity and allows high-throughput analysis of lipids and pigments in single algae cells. The microarray targets receive individual cells in 1430 separate spots that allow the cells to be lysed individually without cross-contamination. Using positive ion mode and 2,5-dihydroxybenzoic acid as the MALDI matrix, the mass spectra unveil information about the relative composition of more than 20 different lipids/pigments in each individual cell within the population. Thus, the method allows the analysis of cellular phenotypes in a population on a completely new level.
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Affiliation(s)
- Jasmin Krismer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Jens Sobek
- Functional Genomics Center Zürich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Robert F Steinhoff
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Rolf Brönnimann
- Swiss Federal Laboratories for Materials Science, Dübendorf, Switzerland
| | - Martin Pabst
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
- TU Delft, Department of Biotechnology, Delft, The Netherlands
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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25
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Applications of MicroArrays for Mass Spectrometry (MAMS) in Single-Cell Metabolomics. Methods Mol Biol 2019. [PMID: 31565767 DOI: 10.1007/978-1-4939-9831-9_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]
Abstract
The metabolic network is the endpoint in the flow of information that begins with the "gene" and ends with "phenotype" (observable function) of the cell. Previously, due to the variety of metabolites analyzed inside cells, the metabolomic measurements were performed with samples including multiple cells. Unfortunately, this sampling process may mask important metabolic phenomena, such as cell-to-cell heterogeneity. For these studies, we must use analytical techniques that can robustly deliver reproducible results with single-cell sensitivity. In this chapter, we summarize laser-based methods for single-cell analysis and a novel approach of MicroArrays for Mass Spectrometry (or MAMS) is described in full detail. This particular type of microarrays was tailored for the study of cells grown in liquid medium using multiple-analytical read-outs, such as optical and laser desorption/ionization (LDI) or MALDI mass spectrometry.
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26
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Eveque-Mourroux MR, Emans PJ, Zautsen RRM, Boonen A, Heeren RMA, Cillero-Pastor B. Spatially resolved endogenous improved metabolite detection in human osteoarthritis cartilage by matrix assisted laser desorption ionization mass spectrometry imaging. Analyst 2019; 144:5953-5958. [PMID: 31418440 DOI: 10.1039/c9an00944b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Osteoarthritis (OA) is one of the most common musculoskeletal diseases, characterized by the progressive deterioration of articular cartilage. Although the disease has been well studied in the past few years, the endogenous metabolic composition and more importantly the spatial information of these molecules in cartilage is still poorly understood. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has been previously used for the investigation of the bimolecular distribution of proteins and lipids through the in situ analysis of cartilage tissue sections. MALDI-MSI as a tool to detect metabolites remains challenging, as these species have low abundance and degrade rapidly. In this work, we present a complete methodology, from sample preparation to data analysis for the detection of endogenous metabolites on cartilage by MSI. Our results demonstrate for the first time the ability to detect small molecules in fragile, challenging tissues through an optimized protocol, and render MSI as a tool towards a better understanding of OA.
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Affiliation(s)
- M R Eveque-Mourroux
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, the Netherlands.
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27
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Exploring the Fundamental Structures of Life: Non-Targeted, Chemical Analysis of Single Cells and Subcellular Structures. Angew Chem Int Ed Engl 2019; 58:9348-9364. [PMID: 30500998 PMCID: PMC6542728 DOI: 10.1002/anie.201811951] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 01/14/2023]
Abstract
Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares numerous aspects that are common to all living organisms. While there are many approaches for studying this chemical diversity, only a few are non-targeted and capable of analyzing hundreds of different chemicals at cellular resolution. Here, we review the non-targeted approaches used to perform comprehensive chemical analyses, provide chemical imaging information, or obtain high-throughput single-cell profiling data. Single-cell measurement capabilities are rapidly increasing in terms of throughput, limits of detection, and completeness of the chemical analyses; these improvements enable their application to understand ever more complex physiological phenomena, such as learning, memory, and behavior.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Thanh D. Do
- Department of Chemistry, 1420 Circle Drive, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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28
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Dusny C, Lohse M, Reemtsma T, Schmid A, Lechtenfeld OJ. Quantifying a Biocatalytic Product from a Few Living Microbial Cells Using Microfluidic Cultivation Coupled to FT-ICR-MS. Anal Chem 2019; 91:7012-7018. [DOI: 10.1021/acs.analchem.9b00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christian Dusny
- Helmholtz-Centre for Environmental Research - UFZ Leipzig, and Leipzig 04318, Germany
| | - Martin Lohse
- Helmholtz-Centre for Environmental Research - UFZ Leipzig, and Leipzig 04318, Germany
| | - Thorsten Reemtsma
- Helmholtz-Centre for Environmental Research - UFZ Leipzig, and Leipzig 04318, Germany
- University of Leipzig, Institute of Analytical Chemistry, Linnéstrasse 3, Leipzig 04103, Germany
| | - Andreas Schmid
- Helmholtz-Centre for Environmental Research - UFZ Leipzig, and Leipzig 04318, Germany
| | - Oliver J. Lechtenfeld
- Helmholtz-Centre for Environmental Research - UFZ Leipzig, and Leipzig 04318, Germany
- Helmholtz Centre for Environmental Research - UFZ, ProVIS - Centre for Chemical Microscopy, 04318 Leipzig, Germany
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29
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Erforschung der fundamentalen Strukturen des Lebens: Nicht zielgerichtete chemische Analyse von Einzelzellen und subzellulären Strukturen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Thanh D. Do
- Department of ChemistryUniversity of Tennessee 1420 Circle Drive Knoxville TN 37996 USA
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
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30
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Yin Z, Cheng X, Liu R, Li X, Hang L, Hang W, Xu J, Yan X, Li J, Tian Z. Chemical and Topographical Single‐Cell Imaging by Near‐Field Desorption Mass Spectrometry. Angew Chem Int Ed Engl 2019; 58:4541-4546. [DOI: 10.1002/anie.201813744] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Zhibin Yin
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xiaoling Cheng
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Rong Liu
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xiaoping Li
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Le Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Wei Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 China
| | - Jingyi Xu
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xiaomei Yan
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Jianfeng Li
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- State Key Laboratory of Physical Chemistry of Solid Surfaces College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhongqun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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31
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Yin Z, Cheng X, Liu R, Li X, Hang L, Hang W, Xu J, Yan X, Li J, Tian Z. Chemical and Topographical Single‐Cell Imaging by Near‐Field Desorption Mass Spectrometry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zhibin Yin
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xiaoling Cheng
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Rong Liu
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xiaoping Li
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Le Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Wei Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- State Key Laboratory of Marine Environmental Science Xiamen University Xiamen 361005 China
| | - Jingyi Xu
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xiaomei Yan
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Jianfeng Li
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- State Key Laboratory of Physical Chemistry of Solid Surfaces College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhongqun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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32
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Wang R, Zhao H, Zhang X, Zhao X, Song Z, Ouyang J. Metabolic Discrimination of Breast Cancer Subtypes at the Single-Cell Level by Multiple Microextraction Coupled with Mass Spectrometry. Anal Chem 2019; 91:3667-3674. [DOI: 10.1021/acs.analchem.8b05739] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ruihua Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hansen Zhao
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaochao Zhang
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xu Zhao
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhe Song
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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33
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Xu M, Pan R, Zhu Y, Jiang D, Chen HY. Molecular profiling of single axons and dendrites in living neurons using electrosyringe-assisted electrospray mass spectrometry. Analyst 2019; 144:954-960. [DOI: 10.1039/c8an00483h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electrosyringe-assisted electrospray mass spectrometry (MS) is established for the first time to achieve intracellular sampling from one axon or dendrite in living neurons for mass spectrometric analysis.
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Affiliation(s)
- Mingchen Xu
- The State Key Lab of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- Jiangsu 210093
| | - Rongrong Pan
- The State Key Lab of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- Jiangsu 210093
| | - Yue Zhu
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae and Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization
- Nanjing University of Chinese Medicine
- Nanjing
- China
| | - Dechen Jiang
- The State Key Lab of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- Jiangsu 210093
| | - Hong-Yuan Chen
- The State Key Lab of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- Jiangsu 210093
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34
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Demling P, Westerwalbesloh C, Noack S, Wiechert W, Kohlheyer D. Quantitative measurements in single-cell analysis: towards scalability in microbial bioprocess development. Curr Opin Biotechnol 2018; 54:121-127. [DOI: 10.1016/j.copbio.2018.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/02/2018] [Accepted: 01/22/2018] [Indexed: 10/17/2022]
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35
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Yang B, Patterson NH, Tsui T, Caprioli RM, Norris JL. Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29. [PMID: 29536413 PMCID: PMC5943162 DOI: 10.1007/s13361-018-1899-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. Graphical Abstract.
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Affiliation(s)
- Bo Yang
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA.
- Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA.
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36
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Tocci N, Gaid M, Kaftan F, Belkheir AK, Belhadj I, Liu B, Svatoš A, Hänsch R, Pasqua G, Beerhues L. Exodermis and endodermis are the sites of xanthone biosynthesis in Hypericum perforatum roots. THE NEW PHYTOLOGIST 2018; 217:1099-1112. [PMID: 29210088 DOI: 10.1111/nph.14929] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/20/2017] [Indexed: 05/09/2023]
Abstract
Xanthones are specialized metabolites with antimicrobial properties, which accumulate in roots of Hypericum perforatum. This medicinal plant provides widely taken remedies for depressive episodes and skin disorders. Owing to the array of pharmacological activities, xanthone derivatives attract attention for drug design. Little is known about the sites of biosynthesis and accumulation of xanthones in roots. Xanthone biosynthesis is localized at the transcript, protein, and product levels using in situ mRNA hybridization, indirect immunofluorescence detection, and high lateral and mass resolution mass spectrometry imaging (AP-SMALDI-FT-Orbitrap MSI), respectively. The carbon skeleton of xanthones is formed by benzophenone synthase (BPS), for which a cDNA was cloned from root cultures of H. perforatum var. angustifolium. Both the BPS protein and the BPS transcripts are localized to the exodermis and the endodermis of roots. The xanthone compounds as the BPS products are detected in the same tissues. The exodermis and the endodermis, which are the outermost and innermost cell layers of the root cortex, respectively, are not only highly specialized barriers for controlling the passage of water and solutes but also preformed lines of defence against soilborne pathogens and predators.
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Affiliation(s)
- Noemi Tocci
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Mariam Gaid
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Filip Kaftan
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Asma K Belkheir
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Ines Belhadj
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
| | - Aleš Svatoš
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Robert Hänsch
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, 38106, Braunschweig, Germany
| | - Gabriella Pasqua
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstraße 1, 38106, Braunschweig, Germany
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37
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Yoon S, Park S, Kim MS, Lee CY. Concomitant desalting and concentration of neuropeptides on a donut-shaped surface pattern for MALDI mass spectrometry. Chem Commun (Camb) 2018; 54:5688-5691. [DOI: 10.1039/c8cc02168f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We demonstrate a functional surface pattern that desalts and concentrates a highly saline solution of neuropeptides in a single step.
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Affiliation(s)
- Sook Yoon
- School of Energy and Chemical Engineering
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Republic of Korea
| | - Sanghwan Park
- School of Energy and Chemical Engineering
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Republic of Korea
| | - Min Sun Kim
- Scientific Instruments Reliability Assessment Center
- Korea Basic Science Institute
- Daejeon 34133
- Republic of Korea
| | - Chang Young Lee
- School of Energy and Chemical Engineering
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 44919
- Republic of Korea
- School of Life Sciences
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38
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Fujimura Y, Miura D, Tachibana H. A Phytochemical-Sensing Strategy Based on Mass Spectrometry Imaging and Metabolic Profiling for Understanding the Functionality of the Medicinal Herb Green Tea. Molecules 2017; 22:molecules22101621. [PMID: 28953237 PMCID: PMC6151411 DOI: 10.3390/molecules22101621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 11/25/2022] Open
Abstract
Low-molecular-weight phytochemicals have health benefits and reduce the risk of diseases, but the mechanisms underlying their activities have remained elusive because of the lack of a methodology that can easily visualize the exact behavior of such small molecules. Recently, we developed an in situ label-free imaging technique, called mass spectrometry imaging, for visualizing spatially-resolved biotransformations based on simultaneous mapping of the major bioactive green tea polyphenol and its phase II metabolites. In addition, we established a mass spectrometry-based metabolic profiling technique capable of evaluating the bioactivities of diverse green tea extracts, which contain multiple phytochemicals, by focusing on their compositional balances. This methodology allowed us to simultaneously evaluate the relative contributions of the multiple compounds present in a multicomponent system to its bioactivity. This review highlights small molecule-sensing techniques for visualizing the complex behaviors of herbal components and linking such information to an enhanced understanding of the functionalities of multicomponent medicinal herbs.
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Affiliation(s)
- Yoshinori Fujimura
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Daisuke Miura
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Hirofumi Tachibana
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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Abstract
Budding yeast has from the beginning been a major eukaryotic model for the study of metabolic network structure and function. This is attributable to both its genetic and biochemical capacities and its role as a workhorse in food production and biotechnology. New inventions in analytical technologies allow accurate, simultaneous detection and quantification of metabolites, and a series of recent findings have placed the metabolic network at center stage in the physiology of the cell. For example, metabolism might have facilitated the origin of life, and in modern organisms it not only provides nutrients to the cell but also serves as a buffer to changes in the cellular environment, a regulator of cellular processes, and a requirement for cell growth. These findings have triggered a rapid and massive renaissance in this important field. Here, we provide an introduction to analysis of metabolomics in yeast.
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Affiliation(s)
- Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
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40
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Hansen RL, Lee YJ. High-Spatial Resolution Mass Spectrometry Imaging: Toward Single Cell Metabolomics in Plant Tissues. CHEM REC 2017; 18:65-77. [PMID: 28685965 DOI: 10.1002/tcr.201700027] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/27/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool that has advanced our understanding of complex biological processes by enabling unprecedented details of metabolic biology to be uncovered. Through the use of high-spatial resolution MSI, metabolite localizations can be obtained with high precision. Here we describe our recent progress to enhance the spatial resolution of matrix-assisted laser desorption/ionization (MALDI) MSI from ∼50 μm with the commercial configuration to ∼5 μm. Additionally, we describe our efforts to develop a 'multiplex MSI' data acquisition method to allow more chemical information to be obtained on a single tissue in a single instrument run, and the development of new matrices to improve the ionization efficiency for a variety of small molecule metabolites. In combination, these contributions, along with the efforts of others, will bring MSI experiments closer to achieving metabolomic scale.
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Affiliation(s)
- Rebecca L Hansen
- Department of Chemistry, Iowa State University, 35 A Roy J Carver Co-Lab, 1111 WOI Road Ames, IA 50011, United States of America
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, 35 A Roy J Carver Co-Lab, 1111 WOI Road Ames, IA 50011, United States of America
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41
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Guillaume-Gentil O, Rey T, Kiefer P, Ibáñez AJ, Steinhoff R, Brönnimann R, Dorwling-Carter L, Zambelli T, Zenobi R, Vorholt JA. Single-Cell Mass Spectrometry of Metabolites Extracted from Live Cells by Fluidic Force Microscopy. Anal Chem 2017; 89:5017-5023. [PMID: 28363018 DOI: 10.1021/acs.analchem.7b00367] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-cell metabolite analysis provides valuable information on cellular function and response to external stimuli. While recent advances in mass spectrometry reached the sensitivity required to investigate metabolites in single cells, current methods commonly isolate and sacrifice cells, inflicting a perturbed state and preventing complementary analyses. Here, we propose a two-step approach that combines nondestructive and quantitative withdrawal of intracellular fluid with subpicoliter resolution using fluidic force microscopy, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The developed method enabled the detection and identification of 20 metabolites recovered from the cytoplasm of individual HeLa cells. The approach was further validated in 13C-glucose feeding experiments, which showed incorporation of labeled carbon atoms into different metabolites. Metabolite sampling, followed by mass spectrometry measurements, enabled the preservation of the physiological context and the viability of the analyzed cell, providing opportunities for complementary analyses of the cell before, during, and after metabolite analysis.
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Affiliation(s)
- Orane Guillaume-Gentil
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Timo Rey
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Patrick Kiefer
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Alfredo J Ibáñez
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Robert Steinhoff
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Rolf Brönnimann
- Swiss Federal Laboratories for Material Science and Technology EMPA , 8600 Dübendorf, Switzerland
| | - Livie Dorwling-Carter
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich , 8093 Zurich, Switzerland
| | - Tomaso Zambelli
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich , 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Julia A Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
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42
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Organic matrices, ionic liquids, and organic matrices@nanoparticles assisted laser desorption/ionization mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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43
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Si X, Xiong X, Zhang S, Fang X, Zhang X. Detecting Low-Abundance Molecules at Single-Cell Level by Repeated Ion Accumulation in Ion Trap Mass Spectrometer. Anal Chem 2017; 89:2275-2281. [PMID: 28192947 DOI: 10.1021/acs.analchem.6b03390] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Low-abundance metabolites or proteins in single-cell samples are usually undetectable by mass spectrometry (MS) due to the limited amount of substances in single cells. This limitation inspired us to further enhance the sensitivity of commercial mass spectrometers. Herein, we developed a technique named repeated ion accumulation by ion trap MS, which is capable of enhancing the sensitivity by selectively and repeatedly accumulating ions in a linear ion trap for up to 25 cycles. The increase in MS sensitivity was positively correlated with the number of repeated cycles. When ions were repeatedly accumulated for 25 cycles, the sensitivity of adenosine triphosphate detection was increased by 22-fold within 1.8 s. Our technique could stably detect low-abundance ions, especially MSn ions, at the single-cell level, such as 5-methylcytosine hydrolyzed from sample equivalent to ∼0.2 MCF7 cell. The strategy presented in this study offers the possibility to aid single-cell analysis by enhancing MS detection sensitivity.
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Affiliation(s)
- Xingyu Si
- Beijing Key Laboratory for Microanalytical Methods, Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
| | - Xingchuang Xiong
- Beijing Key Laboratory for Microanalytical Methods, Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
| | - Sichun Zhang
- Beijing Key Laboratory for Microanalytical Methods, Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
| | - Xiang Fang
- Beijing Key Laboratory for Microanalytical Methods, Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
| | - Xinrong Zhang
- Beijing Key Laboratory for Microanalytical Methods, Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, People's Republic of China
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44
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Wang X, Han J, Hardie DB, Yang J, Pan J, Borchers CH. Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:755-767. [PMID: 28017863 DOI: 10.1016/j.bbapap.2016.12.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022]
Abstract
In this work, we combined the use of two MALDI matrices (quercetin and 9-aminoacridine), a recently developed new matrix coating technique - matrix coating assisted by an electric field (MCAEF), and matrix-assisted laser desorption/ionization - Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) to detect and image endogenous compounds in the cancerous and non-cancerous regions of three human prostate cancer (stage II) tissue specimens. After three rounds of imaging data acquisitions (i.e., quercetin for positive and negative ion detection and 9-aminoacridine for negative ion detection), and metabolite identification, a total of 1091 metabolites including 1032 lipids and 59 other metabolites were routinely detected and successfully localized. Of these compounds, 250 and 217 were only detected in either the cancerous or the non-cancerous regions respectively, although we cannot rule out the presence of these metabolites at concentrations below the detection limit. In addition, 152 of the other 624 metabolites showed differential distributions (p<0.05, t-test) between the two regions of the tissues. Further studies on a larger number of clinical specimens will need to be carried out to confirm this large number of apparently cancer-related metabolites. The successful determination of the spatial locations and abundances of these endogenous biomolecules indicated significant metabolism abnormalities - e.g., increased energy charge and under-expression of neutral acyl glycerides, in the prostate cancer samples. To our knowledge, this work has resulted in MALDI-MS imaging of the largest group of metabolites in prostate cancer thus far and demonstrated the importance of using complementary matrices for comprehensive metabolomic imaging by MALDI-MS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Jingxi Pan
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
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45
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Yang M, Nelson R, Ros A. Toward Analysis of Proteins in Single Cells: A Quantitative Approach Employing Isobaric Tags with MALDI Mass Spectrometry Realized with a Microfluidic Platform. Anal Chem 2016; 88:6672-9. [PMID: 27257853 DOI: 10.1021/acs.analchem.5b03419] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein identification and quantification in individual cells is essential to understand biological processes such as those involved in cell apoptosis, cancer, biomarker discovery, disease diagnostics, pathology, or therapy. Compared with present single cell genome analysis, probing the protein content of single cells has been hampered by the lack of a protein amplification technique. Here, we report the development of a quantitative mass spectrometric approach combined with microfluidic technology reaching the detection sensitivity of high abundant proteins in single cells. A microfluidic platform with a series of chambers and valves, ensuring a set of defined wells for absolute quantification of targeted proteins, was developed and combined with isotopic labeling strategies employing isobaric tags for relative and absolute quantitation (iTRAQ)-labels. To this aim, we adapted iTRAQ labeling to an on-chip protocol. Simultaneous protein digestion and labeling performed on the microfluidic platform rendered the labeling strategy compatible with all necessary manipulation steps on-chip, including the matrix delivery for MALDI-TOF analysis. We demonstrate this approach with the apoptosis related protein Bcl-2 and quantitatively assess the number of Bcl-2 molecules detected. We anticipate that this approach will eventually allow quantification of protein expression on the single cell level.
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Affiliation(s)
- Mian Yang
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Randall Nelson
- Molecular Biomarkers Laboratory, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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46
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Koutsoumanis KP, Aspridou Z. Individual cell heterogeneity in Predictive Food Microbiology: Challenges in predicting a "noisy" world. Int J Food Microbiol 2016; 240:3-10. [PMID: 27412586 DOI: 10.1016/j.ijfoodmicro.2016.06.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/13/2016] [Accepted: 06/19/2016] [Indexed: 11/25/2022]
Abstract
Gene expression is a fundamentally noisy process giving rise to a significant cell to cell variability at the phenotype level. The phenotypic noise is manifested in a wide range of microbial traits. Heterogeneous behavior of individual cells is observed at the growth, survival and inactivation responses and should be taken into account in the context of Predictive Food Microbiology (PMF). Recent methodological advances can be employed for the study and modeling of single cell dynamics leading to a new generation of mechanistic models which can provide insight into the link between phenotype, gene-expression, protein and metabolic functional units at the single cell level. Such models however, need to deal with an enormous amount of interactions and processes that influence each other, forming an extremely complex system. In this review paper, we discuss the importance of noise and present the future challenges in predicting the "noisy" microbial responses in foods.
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Affiliation(s)
- Konstantinos P Koutsoumanis
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | - Zafiro Aspridou
- Laboratory of Food Microbiology and Hygiene, Department of Food Science and Technology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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47
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Du R, Zhu L, Gan J, Wang Y, Qiao L, Liu B. Ultrasensitive Detection of Low-Abundance Protein Biomarkers by Mass Spectrometry Signal Amplification Assay. Anal Chem 2016; 88:6767-72. [PMID: 27253396 DOI: 10.1021/acs.analchem.6b01063] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A mass spectrometry signal amplification method is developed for the ultrasensitive and selective detection of low-abundance protein biomarkers by utilizing tag molecules on gold nanoparticles (AuNPs). EpCAM and thrombin as model targets are captured by specific aptamers immobilized on the AuNPs. With laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS), the mass tag molecules are detected to represent the protein biomarkers. Benefiting from the MS signal amplification, the assay can achieve a limit of detection of 100 aM. The method is further applied to detect thrombin in fetal bovine serum and EpCAM in cell lysates to demonstrate its selectivity and feasibility in complex biological samples. With the high sensitivity and specificity, the protocol shows great promise for providing a new route to single-cell analysis and early disease diagnosis.
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Affiliation(s)
- Ruijun Du
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University , Handan Road 220, Shanghai 200433, China
| | - Lina Zhu
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University , Handan Road 220, Shanghai 200433, China
| | - Jinrui Gan
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University , Handan Road 220, Shanghai 200433, China
| | - Yuning Wang
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University , Handan Road 220, Shanghai 200433, China
| | - Liang Qiao
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University , Handan Road 220, Shanghai 200433, China.,Shanghai Stomatological Hospital, Fudan University , East Beijing Road 356, Shanghai 200001, China
| | - Baohong Liu
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institutes of Biomedical Sciences, Fudan University , Handan Road 220, Shanghai 200433, China.,Shanghai Stomatological Hospital, Fudan University , East Beijing Road 356, Shanghai 200001, China
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48
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Wang Y, Gao D, Chen Y, Hu G, Liu H, Jiang Y. Development of N,S-doped carbon dots as a novel matrix for the analysis of small molecules by negative ion MALDI-TOF MS. RSC Adv 2016. [DOI: 10.1039/c6ra12131d] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The synthesized N,S-CDs was firstly used as a matrix for small molecule analysis with good reproducibility, high sensitivity and high salt tolerance.
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Affiliation(s)
- Yanwei Wang
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- China
| | - Dan Gao
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- China
| | - Yongli Chen
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- China
| | - Guangnan Hu
- Department of Medicine
- University of Massachusetts Medical School
- Worcester
- USA
| | - Hongxia Liu
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- China
| | - Yuyang Jiang
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- China
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49
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Gong X, Xiong X, Wang S, Li Y, Zhang S, Fang X, Zhang X. Desalting by crystallization: detection of attomole biomolecules in picoliter buffers by mass spectrometry. Anal Chem 2015; 87:9745-51. [PMID: 26312607 DOI: 10.1021/acs.analchem.5b01877] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Sensitive detection of biomolecules in small-volume samples by mass spectrometry is, in many cases, challenging because of the use of buffers to maintain the biological activities of proteins and cells. Here, we report a highly effective desalting method for picoliter samples. It was based on the spontaneous separation of biomolecules from salts during crystallization of the salts. After desalting, the biomolecules were deposited in the tip of the quartz pipet because of the evaporation of the solvent. Subsequent detection of the separated biomolecules was achieved using solvent assisted electric field induced desorption/ionization (SAEFIDI) coupled with mass spectrometry. It allowed for direct desorption/ionization of the biomolecules in situ from the tip of the pipet. The organic component in the assistant solvent inhibited the desorption/ionization of salts, thus assured successful detection of biomolecules. Proteins and peptides down to 50 amol were successfully detected using our method even if there were 3 × 10(5) folds more amount of salts in the sample. The concentration and ion species of the salts had little influence on the detection results.
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Affiliation(s)
- Xiaoyun Gong
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China.,National Institute of Metrology , Beijing 100013, China
| | | | - Song Wang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Yanyan Li
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Sichun Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xiang Fang
- National Institute of Metrology , Beijing 100013, China
| | - Xinrong Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University , Beijing 100084, China
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50
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Cahill JF, Darlington TK, Fitzgerald C, Schoepp NG, Beld J, Burkart MD, Prather KA. Online Analysis of Single Cyanobacteria and Algae Cells under Nitrogen-Limited Conditions Using Aerosol Time-of-Flight Mass Spectrometry. Anal Chem 2015; 87:8039-46. [DOI: 10.1021/acs.analchem.5b02326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- John F. Cahill
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | | | | | - Nathan G. Schoepp
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | - Joris Beld
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | - Michael D. Burkart
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | - Kimberly A. Prather
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
- Scripps
Institution of Oceanography, University of California, La Jolla, California 92093, United States
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