1
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Geue N. Modern Electrospray Ionization Mass Spectrometry Techniques for the Characterization of Supramolecules and Coordination Compounds. Anal Chem 2024; 96:7332-7341. [PMID: 38686955 PMCID: PMC11099892 DOI: 10.1021/acs.analchem.4c01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Mass spectrometry is routinely used for myriad applications in clinical, industrial, and research laboratories worldwide. Developments in the areas of ionization sources, high-resolution mass analyzers, tandem mass spectrometry, and ion mobility have significantly extended the repertoire of mass spectrometrists; however, for coordination compounds and supramolecules, mass spectrometry remains underexplored and arguably underappreciated. Here, the reader is guided through different tools of modern electrospray ionization mass spectrometry that are suitable for larger inorganic complexes. All steps, from sample preparation and technical details to data analysis and interpretation are discussed. The main target audience of this tutorial is synthetic chemists as well as technicians/mass spectrometrists with little experience in characterizing labile inorganic compounds.
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Affiliation(s)
- Niklas Geue
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, Department
of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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2
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Stratigaki M, Armirotti A, Ottonello G, Manente S, Traviglia A. Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts. Sci Rep 2024; 14:7003. [PMID: 38523163 PMCID: PMC10961312 DOI: 10.1038/s41598-024-57228-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
Historical paper documents are susceptible to complex degradation processes, including biodeterioration, which can progressively compromise their aesthetic and structural integrity. This study analyses seventeenth century handwritten historical letters stored at the Correr Museum Library in Venice, Italy, exhibiting pronounced signs of biodeterioration. The techniques used encompassed traditional colony isolation on agar plates and proteomics analyses, employing nanoscale liquid chromatography coupled with high-resolution mass spectrometry (nano-LC-MS). Fluorescence microscopy was used for the first time in the historical paper biodeterioration context to supplement the conventional stereoscopic, optical, and scanning electron microscopic imaging techniques. This method enables the visualisation of microorganisms beyond and beneath the paper's surface through their natural intrinsic autofluorescence in a non-invasive and non-destructive way. The results demonstrate a diverse, complex, and abundant microbiota composed of coexisting fungal and bacterial species (Ascomycota, Mucoromycota, Basidiomycota, Proteobacteria, and Actinobacteria), along with mite carcasses, insects, parasites, and possibly protists. Furthermore, this study reveals certain species that were not previously documented in the biodeterioration of historical paper, including human pathogens, such as Histoplasma capsulatum, Brucella, Candida albicans, and species of Aspergillus (A. flavus, A. fumigatus, A. oryzae, A. terreus, A. niger) known to cause infections or produce mycotoxins, posing substantial risk to both artefacts and humans.
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Affiliation(s)
- Maria Stratigaki
- Center for Cultural Heritage Technology (CCHT), Istituto Italiano di Tecnologia, Via Torino 155, 30172, Venice, Italy.
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Sabrina Manente
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
| | - Arianna Traviglia
- Center for Cultural Heritage Technology (CCHT), Istituto Italiano di Tecnologia, Via Torino 155, 30172, Venice, Italy
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3
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Prakash O, Dewala SR, Nimonkar Y, Patil SK, Chauhan A, Yadav A, Dhotre DP, Ranade DR. Culture-based and culture-independent approach for the study of the methanogens and obligate anaerobes from different landfill sites. Front Microbiol 2024; 14:1273037. [PMID: 38348306 PMCID: PMC10860756 DOI: 10.3389/fmicb.2023.1273037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/27/2023] [Indexed: 02/15/2024] Open
Abstract
The landfill is a cheap way of solid waste management in developing countries. The majority of landfills are non-sanitary and work as open garbage dumping sites and pose threats to public and environmental health. Therefore, an in-depth understanding of the chemistry and microbiology of landfills is imperative to develop the right policies for landfill management. In the current study, we investigated the chemistry and microbiology of three Indian landfill sites using culture-based and culture-independent molecular approaches. Our data indicate that the nature of landfills varies from site to site in terms of chemistry, pollutants, and pathogens. We also enriched and cultivated three methanogens using an optimized medium and constructed two high-quality draft genomes from enriched microbiomes using metagenome-assembled genome approaches. The phylogenomic study of one draft genome showed the highest 93% sequence similarity with members of Methanomassiliicoccaceae and was always enriched with Acholoplasma and Anaerohalosphaera lusitana. Despite all the efforts, we did not isolate it in pure culture and hypothesized that for the cultivation of some not-yet-cultured methanogen, the presence of other organisms plays an important role, and their syntrophic interaction must be discerned for its successful cultivation in the future. Co-cultivation of amino acid-degrading organisms indicates that their co-culture can assist in boosting the growth of methanogens. In addition, our data indicated that landfill leachate contains a heavy load of pollutants and treatment is a must before discharge in nature or use in irrigation or biofertilizer.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Sahab Ram Dewala
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Yogesh Nimonkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Shalaka K. Patil
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Ashvini Chauhan
- Environmental Biotechnology at the School of the Environment, Florida A&M University, Tallahassee, FL, United States
| | - Amit Yadav
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Dheeraj P. Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Dilip R. Ranade
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
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4
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Cheng KW, Su PR, Feller KJA, Chien MP, Hsu CC. Investigating the Metabolic Heterogeneity of Cancer Cells Using Functional Single-Cell Selection and nLC Combined with Multinozzle Emitter Mass Spectrometry. Anal Chem 2024; 96:624-629. [PMID: 38157203 DOI: 10.1021/acs.analchem.3c03688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Tumor metastasis and cancer recurrence are often a result of cell heterogeneity, where specific subpopulations of tumor cells may be resistant to radio- or chemotherapy. To investigate this physiological and phenotypic diversity, single-cell metabolomics provides a powerful approach at the chemical level, where distinct lipid profiles can be found in different tumor cells. Here, we established a highly sensitive platform using nanoflow liquid chromatography (nLC) combined with multinozzle emitter electrospray ionization mass spectrometry for more in-depth metabolomics profiling. Our platform identified 15 and 17 lipids from individual osteosarcoma (U2OS) and glioblastoma (GBM) cells when analyzing single-cell samples. Additionally, we used the functional single-cell selection (fSCS) pipeline to analyze the subpopulations of cells with a DNA damage response (DDR) in U2OS cells and fast migration in GBM cells. Specifically, we observed a down-regulation of polyunsaturated fatty acids (PUFAs) in U2OS cells undergoing DDR, such as fatty acids FA 20:3; O2 and FA 17:4; O3. Furthermore, ceramides (Cer 38:0; O3) and triglycerides (TG 36:0) were found to be down-regulated in fast-migrating GBM cells compared to the slow-migrating subpopulation. These findings suggest the potential roles of these metabolites and/or lipids in the cellular behavior of the subpopulations.
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Affiliation(s)
- Kai-Wen Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pin-Rui Su
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Kate Jo-Ann Feller
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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5
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Neef SK, Hofmann U, Mürdter TE, Schwab M, Haag M. Performance comparison of narrow-bore and capillary liquid-chromatography for non-targeted metabolomics profiling by HILIC-QTOF-MS. Talanta 2023; 260:124578. [PMID: 37119797 DOI: 10.1016/j.talanta.2023.124578] [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: 11/25/2022] [Revised: 03/13/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Clinical metabolomics studies often have to cope with limited sample amounts, thus miniaturized liquid chromatography (LC) systems are a promising alternative. Their applicability has already been demonstrated in various fields, including a few metabolomics studies that mainly used reversed-phase chromatography. However, hydrophilic interaction chromatography (HILIC), which is widely used in metabolomics due to its particular suitability for the analysis of polar molecules, has rarely been tested for miniaturized LC-MS analysis of small molecules. In the present work, the suitability of a capillary HILIC (CapHILIC)-QTOF-MS system for non-targeted metabolomics was evaluated based on extracts of porcine formalin-fixed, paraffin-embedded (FFPE) tissue samples. The performance was assessed with respect to the number and retention time span of metabolic features as well as the analytical repeatability, the signal-to-noise ratio and the signal intensity of 16 annotated metabolites from different compound classes. The results were compared with a well established narrow-bore HILIC-QTOF-MS system. Both platforms have detected a similar number of features and performed excellent with respect to retention time stability (median RT span <0.05 min) and analytical repeatability (>75% of features with CV < 20%). The signal areas of all metabolites assessed were increased up to 18-fold by the use of CapHILIC, although the signal-to-noise ratio was only improved for 50% of the metabolites. An even better reproducibility (median CV = 5.2%) and up to 80-fold increase in signal intensity were observed after optimization of CapHILIC conditions for analysis of bile acid standard solutions. Even though the observed improvement for specific bile acids (e.g. taurocholic acid) in biological matrix needs to be evaluated, the platform comparison indicates, that the tested CapHILIC system is particularly suitable for analyses of a less broad metabolite spectrum, and specifically optimized chromatography.
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Affiliation(s)
- Sylvia K Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Thomas E Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany; Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany.
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6
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Beltekin B, Alharthi S, Aydoğan C. Novel open‐tubular columns with highly hydrophobic stationary phase for peptide and protein separation by nano‐liquid chromatography. SEPARATION SCIENCE PLUS 2023. [DOI: 10.1002/sscp.202200111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Büşra Beltekin
- Food Analysis and Research Laboratory Bingöl University Bingöl Türkiye
| | - Sarah Alharthi
- Department of Chemistry, College of Science Taif University Taif Saudi Arabia
| | - Cemil Aydoğan
- Food Analysis and Research Laboratory Bingöl University Bingöl Türkiye
- Department of Chemistry Bingöl University Bingöl Türkiye
- Department of Food Engineering Bingöl University Bingöl Türkiye
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7
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Two-dimensional liquid chromatography-mass spectrometry for lipidomics using off-line coupling of hydrophilic interaction liquid chromatography with 50 cm long reversed phase capillary columns. J Chromatogr A 2023; 1687:463707. [PMID: 36516490 DOI: 10.1016/j.chroma.2022.463707] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Comprehensive characterization of the lipidome remains a challenge requiring development of new analytical approaches to expand lipid coverage in complex samples. In this work, offline two-dimensional liquid chromatography-mass spectrometry was investigated for lipidomics from human plasma. Hydrophilic interaction liquid chromatography was implemented in the first dimension to fractionate lipid classes. Nine fractions were collected and subjected to a second-dimension separation utilizing 50 cm capillary columns packed with 1.7 µm C18 particles operated on custom-built instrumentation at 35 kpsi. Online coupling with time-of-flight mass spectrometry allowed putative lipid identification from precursor-mass based library searching. The method had good orthogonality (fractional coverage of ∼40%), achieved a peak capacity of approximately 1900 in 600 min, and detected over 1000 lipids from a 5 µL injection of a human plasma extract while consuming less than 3 mL of solvent. The results demonstrate the expected gains in peak capacity when employing long columns and two-dimensional separations and illustrate practical approaches for improving lipidome coverage from complex biological samples.
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8
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Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022; 21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Denis K Naplekov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Oleg V Krokhin
- Department of Internal Medicine, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, WinnipegR3E 3P4, Manitoba, Canada
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Jiří Urban
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Ken Broeckhoven
- Department of Chemical Engineering (CHIS), Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050Brussel, Belgium
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
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9
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Gautam S, Hiemstra S, Goli M, Mechref Y. Development of an In-Source Peltier Heater for Pulled Capillary Nanospray Emitter Columns. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1799-1802. [PMID: 35881499 DOI: 10.1021/jasms.2c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Column compartments in liquid chromatography (LC) systems house the LC columns. These compartments are responsible for maintaining a suitable column environment for achieving optimal chromatographic performance. However, the advancements in instrument and column designs demand newer technologies. It is a well-established concept that decreasing the dead volume of the column improves the column resolution, thereby providing enhanced chromatographic separation. One of the major contributors in the dead volume is the line connecting the column in the LC compartment to the ion source in the mass spectrometer. Using in-source emitter columns is one strategy to enhance the resolution. However, ion sources without temperature control are not suitable for columns that are used at high temperatures. In this work, we are introducing a nano electrospray ionization source with an integrated Peltier heater designed for pulled capillary nanospray emitter columns. Although the performance of the device is demonstrated by showing the isomeric separation of permethylated glycans using a mesoporous graphitized carbon packed pulled capillary emitter, it can easily be paired with any nanospray emitter column that requires temperature control.
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Affiliation(s)
- Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Scott Hiemstra
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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10
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Vargas Medina DA, Pereira dos Santos NG, Maciel EVS, Lanças FM. Current prospects on nano liquid chromatography coupled to electron ionization mass spectrometry (nanoLC-EI-MS). J LIQ CHROMATOGR R T 2022. [DOI: 10.1080/10826076.2022.2110114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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11
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Fitz V, El Abiead Y, Berger D, Koellensperger G. Systematic Investigation of LC Miniaturization to Increase Sensitivity in Wide-Target LC-MS-Based Trace Bioanalysis of Small Molecules. Front Mol Biosci 2022; 9:857505. [PMID: 35923463 PMCID: PMC9340153 DOI: 10.3389/fmolb.2022.857505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/06/2022] [Indexed: 01/23/2023] Open
Abstract
Covering a wide spectrum of molecules is essential for global metabolome assessment. While metabolomics assays are most frequently carried out in microbore LC-MS analysis, reducing the size of the analytical platform has proven its ability to boost sensitivity for specific -omics applications. In this study, we elaborate the impact of LC miniaturization on exploratory small-molecule LC-MS analysis, focusing on chromatographic properties with critical impact on peak picking and statistical analysis. We have assessed a panel of small molecules comprising endogenous metabolites and environmental contaminants covering three flow regimes—analytical, micro-, and nano-flow. Miniaturization to the micro-flow regime yields moderately increased sensitivity as compared to the nano setup, where median sensitivity gains around 80-fold are observed in protein-precipitated blood plasma extract. This gain resulting in higher coverage at low µg/L concentrations is compound dependent. At the same time, the nano-LC-high-resolution mass spectrometry (HRMS) approach reduces the investigated chemical space as a consequence of the trap-and-elute nano-LC platform. Finally, while all three setups show excellent retention time stabilities, rapid gradients jeopardize the peak area repeatability of the nano-LC setup. Micro-LC offers the best compromise between improving signal intensity and metabolome coverage, despite the fact that only incremental gains can be achieved. Hence, we recommend using micro-LC for wide-target small-molecule trace bioanalysis and global metabolomics of abundant samples.
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Affiliation(s)
- Veronika Fitz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Daniel Berger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- Chemistry Meets Biology, University of Vienna, Vienna, Austria
- *Correspondence: Gunda Koellensperger,
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12
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Quantification of endocannabinoids in human cerebrospinal fluid using a novel micro-flow liquid chromatography-mass spectrometry method. Anal Chim Acta 2022; 1210:339888. [DOI: 10.1016/j.aca.2022.339888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/13/2022] [Accepted: 04/28/2022] [Indexed: 11/19/2022]
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13
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Dong C, Donnarumma F, Murray KK. Infrared Laser Ablation Microsampling for Small Volume Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1003-1010. [PMID: 35536596 DOI: 10.1021/jasms.2c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Infrared (IR) laser ablation was used to remove localized tissue regions from which proteins were extracted and processed with a low volume sample preparation workflow for bottom-up proteomics by liquid chromatography tandem mass spectrometry (LC-MS/MS). A polytetrafluoroethylene (PTFE) coated glass slide with 2 mm diameter microwells was used to capture ablated rat brain tissue for in situ protein digestion with submicroliter solution volumes. The resulting peptides were analyzed with LC-MS/MS for protein identification and label-free quantification. The method was used to identify an average of 600, 1350, and 1900 proteins from ablation areas of 0.01, 0.04, and 0.1 mm2, respectively, from a 50 μm thick rat brain tissue section. Differential proteomics of 0.01 mm2 regions captured from cerebral cortex and corpus callosum was accomplished to demonstrate the capabilities of the approach.
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Affiliation(s)
- Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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14
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Zhou Y, Guo G, Wang X. Development of
Ultranarrow‐Bore
Open Tubular High Efficiency Liquid Chromatography. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yingyan Zhou
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology Beijing 100124 China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology Beijing 100124 China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology Beijing 100124 China
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15
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Mining Proteome Research Reports: A Bird's Eye View. Proteomes 2021; 9:proteomes9020029. [PMID: 34200663 PMCID: PMC8293458 DOI: 10.3390/proteomes9020029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 01/25/2023] Open
Abstract
The complexity of data has burgeoned to such an extent that scientists of every realm are encountering the incessant challenge of data management. Modern-day analytical approaches with the help of free source tools and programming languages have facilitated access to the context of the various domains as well as specific works reported. Here, with this article, an attempt has been made to provide a systematic analysis of all the available reports at PubMed on Proteome using text mining. The work is comprised of scientometrics as well as information extraction to provide the publication trends as well as frequent keywords, bioconcepts and most importantly gene–gene co-occurrence network. Out of 33,028 PMIDs collected initially, the segregation of 24,350 articles under 28 Medical Subject Headings (MeSH) was analyzed and plotted. Keyword link network and density visualizations were provided for the top 1000 frequent Mesh keywords. PubTator was used, and 322,026 bioconcepts were able to extracted under 10 classes (such as Gene, Disease, CellLine, etc.). Co-occurrence networks were constructed for PMID-bioconcept as well as bioconcept–bioconcept associations. Further, for creation of subnetwork with respect to gene–gene co-occurrence, a total of 11,100 unique genes participated with mTOR and AKT showing the highest (64) number of connections. The gene p53 was the most popular one in the network in accordance with both the degree and weighted degree centrality, which were 425 and 1414, respectively. The present piece of study is an amalgam of bibliometrics and scientific data mining methods looking deeper into the whole scale analysis of available literature on proteome.
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Zamith-Miranda D, Peres da Silva R, Couvillion SP, Bredeweg EL, Burnet MC, Coelho C, Camacho E, Nimrichter L, Puccia R, Almeida IC, Casadevall A, Rodrigues ML, Alves LR, Nosanchuk JD, Nakayasu ES. Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles. Front Genet 2021; 12:648524. [PMID: 34012462 PMCID: PMC8126698 DOI: 10.3389/fgene.2021.648524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all kingdoms of life. The diverse biogenesis pathways of EVs result in a wide variety of physical properties and functions across different organisms. Fungal EVs were first described in 2007 and different omics approaches have been fundamental to understand their composition, biogenesis, and function. In this review, we discuss the role of omics in elucidating fungal EVs biology. Transcriptomics, proteomics, metabolomics, and lipidomics have each enabled the molecular characterization of fungal EVs, providing evidence that these structures serve a wide array of functions, ranging from key carriers of cell wall biosynthetic machinery to virulence factors. Omics in combination with genetic approaches have been instrumental in determining both biogenesis and cargo loading into EVs. We also discuss how omics technologies are being employed to elucidate the role of EVs in antifungal resistance, disease biomarkers, and their potential use as vaccines. Finally, we review recent advances in analytical technology and multi-omic integration tools, which will help to address key knowledge gaps in EVs biology and translate basic research information into urgently needed clinical applications such as diagnostics, and immuno- and chemotherapies to fungal infections.
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Affiliation(s)
- Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erin L. Bredeweg
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Meagan C. Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carolina Coelho
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Emma Camacho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Leonardo Nimrichter
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Igor C. Almeida
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, United States
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Marcio L. Rodrigues
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas-FIOCRUZ PR, Curitiba, Brazil
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
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17
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Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Anal Chem 2021; 93:519-545. [PMID: 33249827 PMCID: PMC7807424 DOI: 10.1021/acs.analchem.0c04698] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Evelyn Rampler
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Mate Rusz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Institute of Inorganic
Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Veronika Fitz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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