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Qi Z, Liu C. Metabolic characteristics and markers in viable but nonculturable state of Pseudomonas aeruginosa induced by chlorine stress. ENVIRONMENTAL RESEARCH 2022; 214:114111. [PMID: 35987374 DOI: 10.1016/j.envres.2022.114111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Many Gram-negative pathogens enter the viable but nonculturable (VBNC) state to resist external environmental stress (such as disinfection). However, little is known about the metabolic properties, especially for the metabolic markers, of VBNC bacteria, which impedes the development of efficient disinfection technologies and causes more potential health risks. In this study, we analyzed the metabolic characteristics of chlorine stress-induced VBNC Pseudomonas aeruginosa at the population and single-cell levels. The overall metabolic activity of VBNC bacteria showed a downward trend, but the glyoxylate cycle, fatty acid and glycerophospholipid metabolism pathways were up-regulated. Based on the metabolic profiles of VBNC bacteria, nine metabolic markers (pyruvate, glyoxylate, guanine, glutamate, sn glycero-3-phos-phocholine, fatty acid, D-alanine, glutathione, N-Butanoyl-D-homoserine lactone) were determined. The results of single-cell Raman spectroscopy showed that the metabolic activity of VBNC bacteria was significantly reduced, but showed more significant metabolic heterogeneity. The redshift of the Raman peaks of 15N and 13C labeled VBNC bacteria was significantly weaker than that of the culturable bacteria, suggesting that the VBNC bacteria have a reduced ability to synthesize proteins, nucleotides, phospholipids, and carbohydrates. The result of this study can help to better understand the metabolic mechanisms and energy management strategy of VBNC bacteria, to achieve precise identification and effective control of VBNC bacteria.
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Affiliation(s)
- Zheng Qi
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China
| | - Chunguang Liu
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong Province, PR China.
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2
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Dai X, Cai L, He F. Single-cell sequencing: expansion, integration and translation. Brief Funct Genomics 2022; 21:280-295. [PMID: 35753690 DOI: 10.1093/bfgp/elac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 12/11/2022] Open
Abstract
With the rapid advancement in sequencing technologies, the concept of omics has revolutionized our understanding of cellular behaviors. Conventional omics investigation approaches measure the averaged behaviors of multiple cells, which may easily hide signals represented by a small-cell cohort, urging for the development of techniques with enhanced resolution. Single-cell RNA sequencing, investigating cell transcriptomics at the resolution of a single cell, has been rapidly expanded to investigate other omics such as genomics, proteomics and metabolomics since its invention. The requirement for comprehensive understanding of complex cellular behavior has led to the integration of multi-omics and single-cell sequencing data with other layers of information such as spatial data and the CRISPR screening technique towards gained knowledge or innovative functionalities. The development of single-cell sequencing in both dimensions has rendered it a unique field that offers us a versatile toolbox to delineate complex diseases, including cancers.
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3
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Cahill JF, Kertesz V. Quantitation of amiodarone and N-desethylamiodarone in single HepG2 cells by single-cell printing-liquid vortex capture-mass spectrometry. Anal Bioanal Chem 2021; 413:6917-6927. [PMID: 34595558 DOI: 10.1007/s00216-021-03652-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Quantitative measure of a drug and its associated metabolite(s) with single-cell resolution is often limited by sampling throughput or other compromises that limit broad use. Here, we demonstrate the use of single-cell printing-liquid vortex capture-mass spectrometry (SCP-LVC-MS) to quantitatively measure the intracellular concentrations of amiodarone (AMIO) and its metabolite, N-desethylamiodarone (NDEA), from thousands of single cells across several AMIO incubation concentrations ranging from 0 to 10 μM. Concentrations obtained by SCP-LVC-MS were validated through comparison with average assays and traditional measurement of cells in bulk. Average of SCP-LVC-MS measurements and aggregate vial collection assay the concentrations differed by < 5%. Both AMIO and NDEA had clear log-normal distributions with similar standard deviation of concentrations in the cell population. The mean of both AMIO and NDEA intracellular concentrations were positively correlated with AMIO incubation concentration, increasing from 0.026 to 0.520 and 0.0055 to 0.048 mM for AMIO and NDEA, respectively. The standard deviation of AMIO and NDEA log-normal distribution fits were relatively similar in value across incubation concentrations, 0.15-0.19 log10 (mM), and exhibited a linear trend with respect to each other. The single cell-resolved conversion ratio of AMIO to NDEA increased with decreasing incubation concentration, 7 ± 2%, 18 ± 3%, and 20 ± 7% for 10.0, 1.0, and 0.1 μM AMIO incubation concentrations, respectively. Association with simultaneously measured lipids had several ions with statistically significant difference in intensity but no clear correlations with AMIO intracellular content was observed.
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Affiliation(s)
- John F Cahill
- Bioanalytical Mass Spectrometry Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA.
| | - Vilmos Kertesz
- Bioanalytical Mass Spectrometry Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA
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4
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Olson NE, Cooke ME, Shi JH, Birbeck JA, Westrick JA, Ault AP. Harmful Algal Bloom Toxins in Aerosol Generated from Inland Lake Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4769-4780. [PMID: 32186187 PMCID: PMC11406200 DOI: 10.1021/acs.est.9b07727] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms (HABs) caused by cyanobacteria in freshwater environments produce toxins (e.g., microcystin) that are harmful to human and animal health. HAB frequency and intensity are increasing with greater nutrient runoff and a warming climate. Lake spray aerosol (LSA) released from freshwater lakes has been identified on lakeshores and after transport inland, including from lakes with HABs, but little is known about the potential for HAB toxins to be incorporated into LSA. In this study, freshwater samples were collected from two lakes in Michigan: Mona Lake during a severe HAB with microcystin concentrations (>200 μg/L) well above the Environmental Protection Agency (EPA) recommended "do not drink" level (1.6 μg/L) and Muskegon Lake without a HAB (<1 μg/L microcystin). Microcystin toxins were identified in freshwater, as well as aerosol particles generated in the laboratory from Mona Lake water by liquid chromatography-tandem mass spectrometry (LC-MS/MS) at atmospheric concentrations up to 50 ± 20 ng/m3. Enrichment of hydrophobic microcystin congeners (e.g., microcystin-LR) was observed in aerosol particles relative to bulk freshwater, while enrichment of hydrophilic microcystin (e.g., microcystin-RR) was lower. As HABs increase in a warming climate, understanding and quantifying the emissions of toxins into the atmosphere is crucial for evaluating the health consequences of HABs.
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Affiliation(s)
- Nicole E Olson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Madeline E Cooke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jia H Shi
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Johnna A Birbeck
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Judy A Westrick
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Andrew P Ault
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Mavroudakis L, Valsami EA, Grafanaki S, Andreadaki TP, Ghanotakis DF, Pergantis SA. The effect of nitrogen starvation on membrane lipids of Synechocystis sp. PCC 6803 investigated by using easy ambient sonic-spray ionization mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183027. [DOI: 10.1016/j.bbamem.2019.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 01/30/2023]
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Duncan KD, Fyrestam J, Lanekoff I. Advances in mass spectrometry based single-cell metabolomics. Analyst 2019; 144:782-793. [DOI: 10.1039/c8an01581c] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Single cell metabolomics using mass spectrometry can contribute to understanding biological activities in health and disease.
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7
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Metabolic heterogeneity in clonal microbial populations. Curr Opin Microbiol 2018; 45:30-38. [DOI: 10.1016/j.mib.2018.02.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 11/22/2022]
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May NW, Olson NE, Panas M, Axson JL, Tirella PS, Kirpes RM, Craig RL, Gunsch MJ, China S, Laskin A, Ault AP, Pratt KA. Aerosol Emissions from Great Lakes Harmful Algal Blooms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:397-405. [PMID: 29169236 DOI: 10.1021/acs.est.7b03609] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In freshwater lakes, harmful algal blooms (HABs) of Cyanobacteria (blue-green algae) produce toxins that impact human health. However, little is known about the lake spray aerosol (LSA) produced from wave-breaking in freshwater HABs. In this study, LSA were produced in the laboratory from freshwater samples collected from Lake Michigan and Lake Erie during HAB and nonbloom conditions. The incorporation of biological material within the individual HAB-influenced LSA particles was examined by single-particle mass spectrometry, scanning electron microscopy with energy-dispersive X-ray spectroscopy, and fluorescence microscopy. Freshwater with higher blue-green algae content produced higher number fractions of individual LSA particles that contained biological material, showing that organic molecules of biological origin are incorporated in LSA from HABs. The number fraction of individual LSA particles containing biological material also increased with particle diameter (greater than 0.5 μm), a size dependence that is consistent with previous studies of sea spray aerosol impacted by phytoplankton blooms. Similar to sea spray aerosol, organic carbon markers were most frequently observed in individual LSA particles less than 0.5 μm in diameter. Understanding the transfer of biological material from freshwater to the atmosphere via LSA is crucial for determining health and climate effects of HABs.
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Affiliation(s)
- Nathaniel W May
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Nicole E Olson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Mark Panas
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Jessica L Axson
- Department of Environmental Health Sciences, University of Michigan , Ann Arbor, Michigan, United States
| | - Peter S Tirella
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Rachel M Kirpes
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Rebecca L Craig
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Matthew J Gunsch
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
| | - Swarup China
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Alexander Laskin
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Andrew P Ault
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
- Department of Environmental Health Sciences, University of Michigan , Ann Arbor, Michigan, United States
| | - Kerri A Pratt
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan, United States
- Department of Earth and Environmental Sciences, University of Michigan , Ann Arbor, Michigan, United States
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Affiliation(s)
- Julia Laskin
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Alexander Laskin
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Sergey A Nizkorodov
- Department of Chemistry, University of California , Irvine, California 92697, United States
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Sun M, Yang Z, Wawrik B. Metabolomic Fingerprints of Individual Algal Cells Using the Single-Probe Mass Spectrometry Technique. FRONTIERS IN PLANT SCIENCE 2018; 9:571. [PMID: 29760716 PMCID: PMC5936784 DOI: 10.3389/fpls.2018.00571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/11/2018] [Indexed: 05/21/2023]
Abstract
Traditional approaches for the assessment of physiological responses of microbes in the environment rely on bulk filtration techniques that obscure differences among populations as well as among individual cells. Here, were report on the development on a novel micro-scale sampling device, referred to as the "Single-probe," which allows direct extraction of metabolites from living, individual phytoplankton cells for mass spectrometry (MS) analysis. The Single-probe is composed of dual-bore quartz tubing which is pulled using a laser pipette puller and fused to a silica capillary and a nano-ESI. For this study, we applied Single-probe MS technology to the marine dinoflagellate Scrippsiella trochoidea, assaying cells grown under different illumination levels and under nitrogen (N) limiting conditions as a proof of concept for the technology. In both experiments, significant differences in the cellular metabolome of individual cells could readily be identified, though the vast majority of detected metabolites could not be assigned to KEGG pathways. Using the same approach, significant changes in cellular lipid complements were observed, with individual lipids being both up- and down-regulated under light vs. dark conditions. Conversely, lipid content increased across the board under N limitation, consistent with an adjustment of Redfield stoichiometry to reflect higher C:N and C:P ratios. Overall, these data suggest that the Single-probe MS technique has the potential to allow for near in situ metabolomic analysis of individual phytoplankton cells, opening the door to targeted analyses that minimize cell manipulation and sampling artifacts, while preserving metabolic variability at the cellular level.
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Affiliation(s)
- Mei Sun
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Boris Wawrik
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Boris Wawrik,
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Ozdemir A, Lin JL, Gulfen M, Lai SH, Hsiao CJ, Chen NG, Chen CH. ESI MS for Microsized Bioparticles. Anal Chem 2017; 89:13195-13202. [DOI: 10.1021/acs.analchem.7b02937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abdil Ozdemir
- Department
of Chemistry, Faculty of Arts and Sciences, Sakarya University, Esentepe, 54187 Sakarya, Turkey
| | - Jung-Lee Lin
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Mustafa Gulfen
- Department
of Chemistry, Faculty of Arts and Sciences, Sakarya University, Esentepe, 54187 Sakarya, Turkey
| | - Szu-Hsueh Lai
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Jen Hsiao
- Genomics
Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Nelson G. Chen
- Department
of Electrical and Computer Engineering, National Chiao Tung University, 1001 Da Xue Road, Hsinchu 30010, Taiwan
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Sultana CM, Collins DB, Prather KA. Effect of Structural Heterogeneity in Chemical Composition on Online Single-Particle Mass Spectrometry Analysis of Sea Spray Aerosol Particles. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3660-3668. [PMID: 28299935 DOI: 10.1021/acs.est.6b06399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Knowledge of the surface composition of sea spray aerosols (SSA) is critical for understanding and predicting climate-relevant impacts. Offline microscopy and spectroscopy studies have shown that dry supermicron SSA tend to be spatially heterogeneous particles with sodium- and chloride-rich cores surrounded by organic enriched surface layers containing minor inorganic seawater components such as magnesium and calcium. At the same time, single-particle mass spectrometry reveals several different mass spectral ion patterns, suggesting that there may be a number of chemically distinct particle types. This study investigates factors controlling single particle mass spectra of nascent supermicron SSA. Depth profiling experiments conducted on SSA generated by a fritted bubbler and total ion intensity analysis of SSA generated by a marine aerosol reference tank were compared with observations of ambient SSA observed at two coastal locations. Analysis of SSA produced by utilizing controlled laboratory methods reveals that single-particle mass spectra with weak sodium ion signals can be produced by the desorption of the surface of typical dry SSA particles composed of salt cores and organic-rich coatings. Thus, this lab-based study for the first time unifies findings from offline and online measurements as well as lab and field studies of the SSA particle-mixing state.
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Affiliation(s)
- Camille M Sultana
- Department of Chemistry and Biochemistry and ‡Scripps Institution of Oceanography, University of California , San Diego, La Jolla, California 92093, United States
| | - Douglas B Collins
- Department of Chemistry and Biochemistry and ‡Scripps Institution of Oceanography, University of California , San Diego, La Jolla, California 92093, United States
| | - Kimberly A Prather
- Department of Chemistry and Biochemistry and ‡Scripps Institution of Oceanography, University of California , San Diego, La Jolla, California 92093, United States
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Cahill JF, Kertesz V, Van Berkel GJ. Laser dissection sampling modes for direct mass spectral analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:611-9. [PMID: 26842582 DOI: 10.1002/rcm.7477] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 05/12/2023]
Abstract
RATIONALE Laser microdissection coupled directly with mass spectrometry provides the capability of on-line analysis of substrates with high spatial resolution, high collection efficiency, and freedom on shape and size of the sampling area. Establishing the merits and capabilities of the different sampling modes that the system provides is necessary in order to select the best sampling mode for characterizing analytically challenging samples. METHODS The capabilities of laser ablation spot sampling, laser ablation raster sampling, and laser 'cut and drop' sampling modes of a hybrid optical microscopy/laser ablation liquid vortex capture electrospray ionization mass spectrometry system were compared for the analysis of single cells and tissue. RESULTS Single Chlamydomonas reinhardtii cells were monitored for their monogalactosyldiacylglycerol (MGDG) and diacylglyceryltrimethylhomo-Ser (DGTS) lipid content using the laser spot sampling mode, which was capable of ablating individual cells (~4-15 μm) even when agglomerated together. Turbid Allium Cepa cells (~150 μm) having unique shapes difficult to precisely measure using the other sampling modes could be ablated in their entirety using laser raster sampling. Intact microdissections of specific regions of a cocaine-dosed mouse brain tissue were compared using laser 'cut and drop' sampling. Since in laser 'cut and drop' sampling whole and otherwise unmodified sections are captured into the probe, 100% collection efficiencies were achieved. Laser ablation spot sampling has the highest spatial resolution of any sampling mode, while laser ablation raster sampling has the highest sampling area adaptability of the sampling modes. CONCLUSIONS Laser ablation spot sampling has the highest spatial resolution of any sampling mode, useful in this case for the analysis of single cells. Laser ablation raster sampling was best for sampling regions with unique shapes that are difficult to measure using other sampling modes. Laser 'cut and drop' sampling can be used for cases where the highest sensitivity is needed, for example, monitoring drugs present in trace amounts in tissue.
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Affiliation(s)
- John F Cahill
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA
| | - Vilmos Kertesz
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA
| | - Gary J Van Berkel
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6131, USA
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