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Li Z, Li Q. Study on the Anti-Inflammatory Mechanism of Coumarins in Peucedanum decursivum Based on Spatial Metabolomics Combined with Network Pharmacology. Molecules 2024; 29:3346. [PMID: 39064924 PMCID: PMC11280318 DOI: 10.3390/molecules29143346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024] Open
Abstract
Peucedanum decursivum (Miq.) Maxim (P. decursivum) is a traditional Chinese medicinal plant with pharmacological effects such as anti-inflammatory and anti-tumor effects, the root of which is widely used as medicine. Determining the spatial distribution and pharmacological mechanisms of metabolites is necessary when studying the effective substances of medicinal plants. As a means of obtaining spatial distribution information of metabolites, mass spectrometry imaging has high sensitivity and allows for molecule visualization. In this study, matrix-assisted laser desorption mass spectrometry (MALDI-TOF-MSI) and network pharmacology were used for the first time to visually study the spatial distribution and anti-inflammatory mechanism of coumarins, which are metabolites of P. decursivum, to determine their tissue localization and mechanism of action. A total of 27 coumarins were identified by MALDI-TOF-MSI, which mainly concentrated in the cortex, periderm, and phloem of the root of P. decursivum. Network pharmacology studies have identified key targets for the anti-inflammatory effect of P. decursivum, such as TNF, PTGS2, and PRAKA. GO enrichment and KEGG pathway analyses indicated that coumarins in P. decursivum mainly participated in biological processes such as inflammatory response, positive regulation of protein kinase B signaling, chemical carcinogenesis receptor activation, pathways in cancer, and other biological pathways. The molecular docking results indicated that there was good binding between components and targets. This study provides a basis for understanding the spatial distribution and anti-inflammatory mechanism of coumarins in P. decursivum.
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Affiliation(s)
| | - Qian Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
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2
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Xi Y, Sohn AL, Joignant AN, Cologna SM, Prentice BM, Muddiman DC. SMART: A data reporting standard for mass spectrometry imaging. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4904. [PMID: 36740651 PMCID: PMC10078510 DOI: 10.1002/jms.4904] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Mass spectrometry imaging (MSI) is an important analytical technique that simultaneously reports the spatial location and abundance of detected ions in biological, chemical, clinical, and pharmaceutical studies. As MSI grows in popularity, it has become evident that data reporting varies among different research groups and between techniques. The lack of consistency in data reporting inherently creates additional challenges in comparing intra- and inter-laboratory MSI data. In this tutorial, we propose a unified data reporting system, SMART, based on the common features shared between techniques. While there are limitations to any reporting system, SMART was decided upon after significant discussion to more easily understand and benchmark MSI data. SMART is not intended to be comprehensive but rather capture essential baseline information for a given MSI study; this could be within a study (e.g., effect of spot size on the measured ion signals) or between two studies (e.g., different MSI platform technologies applied to the same tissue type). This tutorial does not attempt to address the confidence with which annotations are made nor does it deny the importance of other parameters that are not included in the current SMART format. Ultimately, the goal of this tutorial is to discuss the necessity of establishing a uniform reporting system to communicate MSI data in publications and presentations in a simple format to readily interpret the parameters and baseline outcomes of the data.
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Affiliation(s)
- Ying Xi
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Alexandria L. Sohn
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Alena N. Joignant
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | | | | | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
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3
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Nwabufo CK, Aigbogun OP. The Role of Mass Spectrometry Imaging in Pharmacokinetic Studies. Xenobiotica 2022; 52:811-827. [PMID: 36048000 DOI: 10.1080/00498254.2022.2119900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Although liquid chromatography-tandem mass spectrometry is the gold standard analytical platform for the quantification of drugs, metabolites, and biomarkers in biological samples, it cannot localize them in target tissues.The localization and quantification of drugs and/or their associated metabolites in target tissues is a more direct measure of bioavailability, biodistribution, efficacy, and regional toxicity compared to the traditional substitute studies using plasma.Therefore, combining high spatial resolution imaging functionality with the superior selectivity and sensitivity of mass spectrometry into one analytical technique will be a valuable tool for targeted localization and quantification of drugs, metabolites, and biomarkers.Mass spectrometry imaging (MSI) is a tagless analytical technique that allows for the direct localization and quantification of drugs, metabolites, and biomarkers in biological tissues, and has been used extensively in pharmaceutical research.The overall goal of this current review is to provide a detailed description of the working principle of MSI and its application in pharmacokinetic studies encompassing absorption, distribution, metabolism, excretion, and toxicity processes, followed by a discussion of the strategies for addressing the challenges associated with the functional utility of MSI in pharmacokinetic studies that support drug development.
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Affiliation(s)
- Chukwunonso K Nwabufo
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Omozojie P Aigbogun
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada.,Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
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4
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Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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5
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Spruill ML, Maletic-Savatic M, Martin H, Li F, Liu X. Spatial analysis of drug absorption, distribution, metabolism, and toxicology using mass spectrometry imaging. Biochem Pharmacol 2022; 201:115080. [PMID: 35561842 PMCID: PMC9744413 DOI: 10.1016/j.bcp.2022.115080] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Mass spectrometry imaging (MSI) is emerging as a powerful analytical tool for detection, quantification, and simultaneous spatial molecular imaging of endogenous and exogenous molecules via in situ mass spectrometry analysis of thin tissue sections without the requirement of chemical labeling. The MSI generates chemically specific and spatially resolved ion distribution information for administered drugs and metabolites, which allows numerous applications for studies involving various stages of drug absorption, distribution, metabolism, excretion, and toxicity (ADMET). MSI-based pharmacokinetic imaging analysis provides a histological context and cellular environment regarding dynamic drug distribution and metabolism processes, and facilitates the understanding of the spatial pharmacokinetics and pharmacodynamic properties of drugs. Herein, we discuss the MSI's current technological developments that offer qualitative, quantitative, and spatial location information of small molecule drugs, antibody, and oligonucleotides macromolecule drugs, and their metabolites in preclinical and clinical tissue specimens. We highlight the macro and micro drug-distribution in the whole-body, brain, lung, liver, kidney, stomach, intestine tissue sections, organoids, and the latest applications of MSI in pharmaceutical ADMET studies.
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Affiliation(s)
- Michelle L Spruill
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Mirjana Maletic-Savatic
- Department of Pediatrics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | | | - Feng Li
- Center for Drug Discovery and Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; NMR and Drug Metabolism Core, Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Xinli Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA.
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6
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DeLaney K, Phetsanthad A, Li L. ADVANCES IN HIGH-RESOLUTION MALDI MASS SPECTROMETRY FOR NEUROBIOLOGY. MASS SPECTROMETRY REVIEWS 2022; 41:194-214. [PMID: 33165982 PMCID: PMC8106695 DOI: 10.1002/mas.21661] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/13/2020] [Indexed: 05/08/2023]
Abstract
Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
- To whom correspondence should be addressed. , Phone: (608) 265-8491, Fax: (608) 262-5345., Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53706
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7
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Sakallioglu IT, Barletta RG, Dussault PH, Powers R. Deciphering the mechanism of action of antitubercular compounds with metabolomics. Comput Struct Biotechnol J 2021; 19:4284-4299. [PMID: 34429848 PMCID: PMC8358470 DOI: 10.1016/j.csbj.2021.07.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB), one of the oldest and deadliest bacterial diseases, continues to cause serious global economic, health, and social problems. Current TB treatments are lengthy, expensive, and routinely ineffective against emerging drug resistant strains. Thus, there is an urgent need for the identification and development of novel TB drugs possessing comprehensive and specific mechanisms of action (MoAs). Metabolomics is a valuable approach to elucidating the MoA, toxicity, and potency of promising chemical leads, which is a critical step of the drug discovery process. Recent advances in metabolomics methodologies for deciphering MoAs include high-throughput screening techniques, the integration of multiple omics methods, mass spectrometry imaging, and software for automated analysis. This review describes recently introduced metabolomics methodologies and techniques for drug discovery, highlighting specific applications to the discovery of new antitubercular drugs and the elucidation of their MoAs.
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Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska Lincoln, Lincoln, NE 68583-0905, USA
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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8
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Cordes J, Enzlein T, Marsching C, Hinze M, Engelhardt S, Hopf C, Wolf I. M2aia-Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data. Gigascience 2021; 10:giab049. [PMID: 34282451 PMCID: PMC8290197 DOI: 10.1093/gigascience/giab049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/19/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Mass spectrometry imaging (MSI) is a label-free analysis method for resolving bio-molecules or pharmaceuticals in the spatial domain. It offers unique perspectives for the examination of entire organs or other tissue specimens. Owing to increasing capabilities of modern MSI devices, the use of 3D and multi-modal MSI becomes feasible in routine applications-resulting in hundreds of gigabytes of data. To fully leverage such MSI acquisitions, interactive tools for 3D image reconstruction, visualization, and analysis are required, which preferably should be open-source to allow scientists to develop custom extensions. FINDINGS We introduce M2aia (MSI applications for interactive analysis in MITK), a software tool providing interactive and memory-efficient data access and signal processing of multiple large MSI datasets stored in imzML format. M2aia extends MITK, a popular open-source tool in medical image processing. Besides the steps of a typical signal processing workflow, M2aia offers fast visual interaction, image segmentation, deformable 3D image reconstruction, and multi-modal registration. A unique feature is that fused data with individual mass axes can be visualized in a shared coordinate system. We demonstrate features of M2aia by reanalyzing an N-glycan mouse kidney dataset and 3D reconstruction and multi-modal image registration of a lipid and peptide dataset of a mouse brain, which we make publicly available. CONCLUSIONS To our knowledge, M2aia is the first extensible open-source application that enables a fast, user-friendly, and interactive exploration of large datasets. M2aia is applicable to a wide range of MSI analysis tasks.
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Affiliation(s)
- Jonas Cordes
- Faculty of Computer Science, Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, University Heidelberg, Theodor Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Thomas Enzlein
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany
| | - Christian Marsching
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany
| | - Marven Hinze
- Faculty of Computer Science, Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany
| | - Sandy Engelhardt
- Working Group “Artificial Intelligence in Cardiovascular Medicine” (AICM), University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany
| | - Ivo Wolf
- Faculty of Computer Science, Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163 Mannheim, Germany
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9
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Zhvansky ES, Ivanov DG, Sorokin AA, Bugrova AE, Nikolaev EN, Popov IA. Interactive Estimation of Heterogeneity from Mass Spectrometry Imaging. Anal Chem 2021; 93:3706-3709. [PMID: 33591173 DOI: 10.1021/acs.analchem.1c00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we demonstrate a new approach for interactively assessing hyperspectral data spatial structures for heterogeneity using mass spectrometry imaging. This approach is based on the visualization of the cosine distance as the similarity levels between mass spectra of a chosen region and the rest of the image (sample). The applicability of the method is demonstrated on a set of mass spectrometry images of frontal mouse brain slices. Selection of the reference pixel of the mass spectrometric image and a further view of the corresponding cosine distance map helps to prepare supporting vectors for further analysis, select features, and carry out biological interpretation of different tissues in the mass spectrometry context with or without histological annotation. Visual inspection of the similarity maps reveals the spatial distribution of features in tissue samples, which can serve as the molecular histological annotation of a slide.
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Affiliation(s)
- Evgeny S Zhvansky
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia
| | - Daniil G Ivanov
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia.,Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia.,Institute of Cell Biophysics RAS, Institutskaya st., 3, 142290 Pushchino, Russia.,Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Anna E Bugrova
- Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences, Kosygina st. 4, 119334 Moscow, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Novaya Street, 100, 143025 Skolkovo, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Institutskij bystr. 9, 141700 Dolgoprudnyi, Moscow Region, Russia
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10
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He Q, Sun C, Liu J, Pan Y. MALDI-MSI analysis of cancer drugs: Significance, advances, and applications. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Flinders B, Morrell J, Marshall PS, Ranshaw LE, Heeren RMA, Clench MR. Monitoring the three-dimensional distribution of endogenous species in the lungs by matrix-assisted laser desorption/ionization mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8957. [PMID: 32990347 DOI: 10.1002/rcm.8957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is routinely employed to monitor the distribution of compounds in tissue sections and generate two-dimensional (2D) images. Whilst informative the images do not represent the distribution of the analyte of interest through the entire organ. The generation of 3D images is an exciting field that can provide a deeper view of the analyte of interest throughout an entire organ. METHODS Serial sections of mouse and rat lung tissue were obtained at 120 μm depth intervals and imaged individually. Homogenate registration markers were incorporated in order to aid the final 3D image construction. Using freely available software packages, the images were stacked together to generate a 3D image that showed the distribution of endogenous species throughout the lungs. RESULTS Preliminary tests were performed on 16 serial tissue sections of mouse lungs. A 3D model showing the distribution of phosphocholine at m/z 184.09 was constructed, which defined the external structure of the lungs and trachea. Later, a second experiment was performed using 24 serial tissue sections of the left lung of a rat. Two molecular markers, identified as [PC (32:1) + K]+ at m/z 770.51 and [PC (36:4) + K]+ at m/z 820.52, were used to generate 3D models of the parenchyma and airways, respectively. CONCLUSIONS A straightforward method to generate 3D MALDI-MS images of selected molecules in lung tissue has been presented. Using freely available imaging software, the 3D distributions of molecules related to different anatomical features were determined.
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Affiliation(s)
- Bryn Flinders
- Centre for Mass Spectrometry Imaging, Biomedical Research Centre, City Campus, Sheffield Hallam University, Sheffield, S1 1WB, UK
- Hair Diagnostix, Dutch Screening Group, Gaetano Martinolaan 63A, Maastricht, 6229 GS, The Netherlands
- Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands
| | - Josie Morrell
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | | | - Lisa E Ranshaw
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomedical Research Centre, City Campus, Sheffield Hallam University, Sheffield, S1 1WB, UK
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Mohamed SA, Taube ET, Thiele H, Noack F, Nebrich G, Mohamady K, Hanke T, Klein O. Evaluation of the Aortopathy in the Ascending Aorta: The Novelty of Using Matrix-Assisted Laser Desorption/Ionization Imaging. Proteomics Clin Appl 2021; 15:e2000047. [PMID: 33270371 DOI: 10.1002/prca.202000047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
PURPOSE Histopathological evaluation presents conflicting reports regarding aortic abnormalities. The authors aim to present proof-of-concept study to explore the feasibility of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) in combination with histopathology for characterizing alterations in the aneurysmal ascending formalin-fixed paraffin-embedded (FFPE) aorta tissue. EXPERIMENTAL DESIGN The authors assess FFPE specimens from patients with a dilated aorta and bicuspid aortic valve (BAV), those with a standard tricuspid aortic valve (TAV), and those with Marfan syndrome (MFS) via histopathology and grade the conditions for elastic fiber fragmentation (EFF) and MALDI-IMS. The proteins using liquid chromatographic-mass spectrometry are identified and the results are confirmed by immunohistochemistry. RESULTS There is significant difference in terms of EFF between MFS and BAV, and TAV and BAV. Characteristic peptide signatures and m/z values in the EFF facilitate the characterization among the aortic specimens of BAV, MFS, and TAV. The m/z values from the aortic alpha smooth muscle actin and myosin heavy chains significantly increase in BAV compared with MFS and TAV. These findings are confirmed by immunohistochemistry. CONCLUSION The results represent a strategy that uses MALDI-IMS in combination with histopathology as promising approaches to characterize spatial alteration in the structure of the aneurysmal ascending aorta.
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Affiliation(s)
- Salah A Mohamed
- Department of Cardiac and Thoracic Vascular Surgery, UKSH-Campus Luebeck, Luebeck, 23538, Germany
| | - Eliane T Taube
- Charité-Universitaetsmedizin, Institute for Pathology, Berlin, 10117, Germany
| | - Herbert Thiele
- Fraunhofer Institute for Digital Medicine MEVIS, Luebeck, 23538, Germany
| | - Frank Noack
- Institute of Pathology Martin-Luther Hospital, Berlin, 14193, Germany
| | - Grit Nebrich
- Berlin Institute of Health Center for Regenerative Therapies & Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Campus Virchow Klinikum (CVK), Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | | | | | - Oliver Klein
- Berlin Institute of Health Center for Regenerative Therapies & Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Campus Virchow Klinikum (CVK), Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, 13353, Germany
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13
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Pappritz K, Klein O, Dong F, Hamdani N, Kovacs A, O'Flynn L, Elliman S, O'Brien T, Tschöpe C, Van Linthout S. MALDI-IMS as a Tool to Determine the Myocardial Response to Syndecan-2-Selected Mesenchymal Stromal Cell Application in an Experimental Model of Diabetic Cardiomyopathy. Proteomics Clin Appl 2021; 15:e2000050. [PMID: 33068073 DOI: 10.1002/prca.202000050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/12/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE Mesenchymal stromal cells (MSC) are an attractive tool for treatment of diabetic cardiomyopathy. Syndecan-2/CD362 has been identified as a functional marker for MSC isolation. Imaging mass spectrometry (IMS) allows for the characterization of therapeutic responses in the left ventricle. This study aims to investigate whether IMS can assess the therapeutic effect of CD362+ -selected MSC on early onset experimental diabetic cardiomyopathy. EXPERIMENTAL DESIGN 1 × 106 wild type (WT), CD362- , or CD362+ MSC are intravenously injected into db/db mice. Four weeks later, mice are hemodynamically characterized and subsequently sacrificed for IMS combined with bottom-up mass spectrometry, and isoform and phosphorylation analyses of cardiac titin. RESULTS Overall alterations of the cardiac proteome signatures, especially titin, are observed in db/db compared to control mice. Interestingly, only CD362+ MSC can overcome the reduced titin intensity distribution and shifts the isoform ratio toward the more compliant N2BA form. In contrast, WT and CD362- MSCs improve all-titin phosphorylation and protein kinase G activity, which is reflected in an improvement in diastolic performance. CONCLUSIONS AND CLINICAL RELEVANCE IMS enables the characterization of differences in titin intensity distribution following MSC application. However, further analysis of titin phosphorylation is needed to allow for the assessment of the therapeutic efficacy of MSC.
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Affiliation(s)
- Kathleen Pappritz
- Berlin-Brandenburg Center for Regenerative Therapies and Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Berlin, 13353 and 10178, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, 13347, Germany
| | - Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies and Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Berlin, 13353 and 10178, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, 13347, Germany
| | - Fengquan Dong
- Berlin-Brandenburg Center for Regenerative Therapies and Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Berlin, 13353 and 10178, Germany
| | - Nazha Hamdani
- Department of Physiology, Institute of Physiology, Ruhr University Bochum, Bochum, 44780, Germany
| | - Arpad Kovacs
- Department of Physiology, Institute of Physiology, Ruhr University Bochum, Bochum, 44780, Germany
| | - Lisa O'Flynn
- Orbsen Therapeutics, National University of Ireland (NUIG), Galway, H91 TK33, Ireland
| | - Steve Elliman
- Orbsen Therapeutics, National University of Ireland (NUIG), Galway, H91 TK33, Ireland
| | - Timothy O'Brien
- Regenerative Medicine Institute and Department of Medicine, NUIG, Galway, H91 TK33, Ireland
| | - Carsten Tschöpe
- Berlin-Brandenburg Center for Regenerative Therapies and Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Berlin, 13353 and 10178, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, 13347, Germany
- Department of Cardiology, Charité - Universitätsmedizin Berlin, CVK, Berlin, 13353, Germany
| | - Sophie Van Linthout
- Berlin-Brandenburg Center for Regenerative Therapies and Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Berlin, 13353 and 10178, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, 13347, Germany
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Tuck M, Blanc L, Touti R, Patterson NH, Van Nuffel S, Villette S, Taveau JC, Römpp A, Brunelle A, Lecomte S, Desbenoit N. Multimodal Imaging Based on Vibrational Spectroscopies and Mass Spectrometry Imaging Applied to Biological Tissue: A Multiscale and Multiomics Review. Anal Chem 2020; 93:445-477. [PMID: 33253546 DOI: 10.1021/acs.analchem.0c04595] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tuck
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Landry Blanc
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Rita Touti
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, United States
| | - Sebastiaan Van Nuffel
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sandrine Villette
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Jean-Christophe Taveau
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Andreas Römpp
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Alain Brunelle
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR 8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Sophie Lecomte
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nicolas Desbenoit
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
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15
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Tobias F, Hummon AB. Considerations for MALDI-Based Quantitative Mass Spectrometry Imaging Studies. J Proteome Res 2020; 19:3620-3630. [PMID: 32786684 DOI: 10.1021/acs.jproteome.0c00443] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Significant advances in mass spectrometry imaging (MSI) have pushed the boundaries in obtaining spatial information and quantification in biological samples. Quantitative MSI (qMSI) has typically been challenging to achieve because of matrix and tissue heterogeneity, inefficient analyte extraction, and ion suppression effects, but recent studies have demonstrated approaches to obtain highly robust methods and reproducible results. In this perspective, we share our insights into sample preparation, how the choice of matrix influences sensitivity, construction of calibration curves, signal normalization, and visualization of MSI data. We hope that by articulating these guidelines that qMSI can be routinely conducted while retaining the analytical merits of other mass spectrometry modalities.
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Kulbe H, Klein O, Wu Z, Taube ET, Kassuhn W, Horst D, Darb-Esfahani S, Jank P, Abobaker S, Ringel F, du Bois A, Heitz F, Sehouli J, Braicu EI. Discovery of Prognostic Markers for Early-Stage High-Grade Serous Ovarian Cancer by Maldi-Imaging. Cancers (Basel) 2020; 12:cancers12082000. [PMID: 32707805 PMCID: PMC7463791 DOI: 10.3390/cancers12082000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 12/31/2022] Open
Abstract
With regard to relapse and survival, early-stage high-grade serous ovarian (HGSOC) patients comprise a heterogeneous group and there is no clear consensus on first-line treatment. Currently, no prognostic markers are available for risk assessment by standard targeted immunohistochemistry and novel approaches are urgently required. Here, we applied MALDI-imaging mass spectrometry (MALDI-IMS), a new method to identify distinct mass profiles including protein signatures on paraffin-embedded tissue sections. In search of prognostic biomarker candidates, we compared proteomic profiles of primary tumor sections from early-stage HGSOC patients with either recurrent (RD) or non-recurrent disease (N = 4; each group) as a proof of concept study. In total, MALDI-IMS analysis resulted in 7537 spectra from the malignant tumor areas. Using receiver operating characteristic (ROC) analysis, 151 peptides were able to discriminate between patients with RD and non-RD (AUC > 0.6 or < 0.4; p < 0.01), and 13 of them could be annotated to proteins. Strongest expression levels of specific peptides linked to Keratin type1 and Collagen alpha-2(I) were observed and associated with poor prognosis (AUC > 0.7). These results confirm that in using IMS, we could identify new candidates to predict clinical outcome and treatment extent for patients with early-stage HGSOC.
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Affiliation(s)
- Hagen Kulbe
- Tumorbank Ovarian Cancer Network, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (H.K.); (W.K.); (S.A.); (F.R.); (J.S.)
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Oliver Klein
- BIH Center for Regenerative Therapies BCRT, Charité – Universitätsmedizin Berlin, 10117 Berlin, Germany; (O.K.); (Z.W.)
| | - Zhiyang Wu
- BIH Center for Regenerative Therapies BCRT, Charité – Universitätsmedizin Berlin, 10117 Berlin, Germany; (O.K.); (Z.W.)
| | - Eliane T. Taube
- Institute of Pathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (E.T.T.); (D.H.); (P.J.)
| | - Wanja Kassuhn
- Tumorbank Ovarian Cancer Network, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (H.K.); (W.K.); (S.A.); (F.R.); (J.S.)
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (E.T.T.); (D.H.); (P.J.)
| | | | - Paul Jank
- Institute of Pathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (E.T.T.); (D.H.); (P.J.)
- Institute of Pathology, Philipps-University Marburg, 35032 Marburg, Germany
| | - Salem Abobaker
- Tumorbank Ovarian Cancer Network, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (H.K.); (W.K.); (S.A.); (F.R.); (J.S.)
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Frauke Ringel
- Tumorbank Ovarian Cancer Network, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (H.K.); (W.K.); (S.A.); (F.R.); (J.S.)
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Andreas du Bois
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, 45136 Essen, Germany (F.H.)
| | - Florian Heitz
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, 45136 Essen, Germany (F.H.)
| | - Jalid Sehouli
- Tumorbank Ovarian Cancer Network, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (H.K.); (W.K.); (S.A.); (F.R.); (J.S.)
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elena I. Braicu
- Tumorbank Ovarian Cancer Network, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; (H.K.); (W.K.); (S.A.); (F.R.); (J.S.)
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- Correspondence: ; Tel.: +49-(0)30-450-664469
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The choice of tissue fixative is a key determinant for mass spectrometry imaging based tumor metabolic reprogramming characterization. Anal Bioanal Chem 2020; 412:3123-3134. [PMID: 32236659 DOI: 10.1007/s00216-020-02562-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/03/2020] [Accepted: 02/28/2020] [Indexed: 12/12/2022]
Abstract
The application of mass spectrometry imaging (MSI) for the study of spatiotemporal alterations of the metabolites in tumors has brought a number of significant biological results. At present, metabolite profiling based on MSI is typically performed on frozen tissue sections; however, the majority of clinical specimens need to be fixed in tissue fixative to avoid autolysis and to preserve antigenicity. In this study, we present the global impacts of different fixatives on the MS imaging of gastric cancer tissue metabolites. The MSI performances of 17 kinds of metabolites, such as amino acids, polyamines, cholines, organic acids, polypeptides, nucleotides, nucleosides, nitrogen bases, cholesterols, fatty acids, and phospholipids, in untreated, 10% formalin-, 4% paraformaldehyde-, acetone-, and 95% ethanol-fixed gastric cancer tissues were thoroughly explored for the first time. Furthermore, we also investigated the spatial expressions of 6 metabolic enzymes, namely, GLS, FASN, CHKA, PLD2, cPLA2, and EGFR, closely related to tumor-associated metabolites. Immunohistochemical staining carried out on the same tissue sections' which have undergone MSI analysis' suggests that enzymatic characterization is feasible after metabolite imaging. Combining the spatial signatures of metabolites and pathway-related metabolic enzymes in heterogeneous tumor tissues offers an insight to understand the complex tumor metabolism. Graphical abstract.
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18
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Föll MC, Moritz L, Wollmann T, Stillger MN, Vockert N, Werner M, Bronsert P, Rohr K, Grüning BA, Schilling O. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. Gigascience 2019; 8:giz143. [PMID: 31816088 PMCID: PMC6901077 DOI: 10.1093/gigascience/giz143] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/10/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial distribution of hundreds of analytes in a sample. Being at the interface of proteomics/metabolomics and imaging, the acquired datasets are large and complex and often analyzed with proprietary software or in-house scripts, which hinders reproducibility. Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many mass spectrometry imaging (MSI) researchers. FINDINGS We have integrated 18 dedicated mass spectrometry imaging tools into the Galaxy framework to allow accessible, reproducible, and transparent data analysis. Our tools are based on Cardinal, MALDIquant, and scikit-image and enable all major MSI analysis steps such as quality control, visualization, preprocessing, statistical analysis, and image co-registration. Furthermore, we created hands-on training material for use cases in proteomics and metabolomics. To demonstrate the utility of our tools, we re-analyzed a publicly available N-linked glycan imaging dataset. By providing the entire analysis history online, we highlight how the Galaxy framework fosters transparent and reproducible research. CONCLUSION The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access, together with high levels of reproducibility and transparency.
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Affiliation(s)
- Melanie Christine Föll
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Lennart Moritz
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
| | - Thomas Wollmann
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Maren Nicole Stillger
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany
| | - Niklas Vockert
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Martin Werner
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Medicine - University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Peter Bronsert
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Medicine - University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Björn Andreas Grüning
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Medicine - University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Hugstetter Straße 55, 79106 Freiburg, Germany
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Condina MR, Mittal P, Briggs MT, Oehler MK, Klingler-Hoffmann M, Hoffmann P. Egg White as a Quality Control in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI). Anal Chem 2019; 91:14846-14853. [PMID: 31660720 DOI: 10.1021/acs.analchem.9b03091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The strength of MALDI-MSI is to analyze and visualize spatial intensities of molecular features from an intact tissue. The distribution of the intensities can then be visualized within a single tissue section or compared in between sections, acquired consecutively. This method can be reliably used to reveal physiological structures and has the potential to identify molecular details, which correlate with biological outcomes. MALDI-MSI implementation in clinical laboratories requires the ability to ensure method quality and validation to meet diagnostic expectations. To be able to get consistent qualitative and quantitative results, standardized sample preparation and data acquisition are of highest priority. We have previously shown that the deposition of internal standards onto the tissue section during sample preparation can be used to improve the mass accuracy of monitored m/z features across the sample. Here, we present the use of external and internal controls for the quality check of sample preparation and data acquisition, which is particularly relevant when either many spectra are acquired during a single MALDI-MSI experiment or data from independent experiments are processed together. To monitor detector performance and sample preparation, we use egg white as an external control for peptide and N-glycan MALDI-MSI throughout the experiment. We have also identified endogenous peptides from cytoskeletal proteins, which can be reliably monitored in gynecological tissue samples. Lastly, we summarize our standard quality control workflow designed to produce reliable and comparable MALDI-MSI data from single sections and tissue microarrays (TMAs).
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Affiliation(s)
- Mark R Condina
- Future Industries Institute , The University of South Australia , Adelaide , South Australia 5095 , Australia
| | - Parul Mittal
- Adelaide Proteomics Centre , The University of Adelaide , Adelaide , South Australia 5005 , Austrailia
| | - Matthew T Briggs
- Future Industries Institute , The University of South Australia , Adelaide , South Australia 5095 , Australia
| | - Martin K Oehler
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute , The University of Adelaide , Adelaide , South Australia 5000 , Australia.,Department of Gynaecological Oncology , Royal Adelaide Hospital , Adelaide , South Australia 5005 , Australia
| | - Manuela Klingler-Hoffmann
- Future Industries Institute , The University of South Australia , Adelaide , South Australia 5095 , Australia
| | - Peter Hoffmann
- Future Industries Institute , The University of South Australia , Adelaide , South Australia 5095 , Australia
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Chen G, Fan M, Liu Y, Sun B, Liu M, Wu J, Li N, Guo M. Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques. Front Chem 2019; 7:703. [PMID: 31709232 PMCID: PMC6819514 DOI: 10.3389/fchem.2019.00703] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Minxia Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meixian Liu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Jianlin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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21
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Barry JA, Ait-Belkacem R, Hardesty WM, Benakli L, Andonian C, Licea-Perez H, Stauber J, Castellino S. Multicenter Validation Study of Quantitative Imaging Mass Spectrometry. Anal Chem 2019; 91:6266-6274. [PMID: 30938516 DOI: 10.1021/acs.analchem.9b01016] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The aim of this study was to assess potential sources of variability in quantitative imaging mass spectrometry (IMS) across multiple sites, analysts, and instruments. A sample from rat liver perfused with clozapine was distributed to three sites for analysis by three analysts using a predefined protocol to standardize the sample preparation, acquisition, and data analysis parameters. In addition, two commonly used approaches to IMS quantification, the mimetic tissue model and dilution series, were used to quantify clozapine and its major metabolite norclozapine in isolated perfused rat liver. The quantification was evaluated in terms of precision and accuracy with comparison to liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The results of this study showed that, across three analysts with six replicates each, both quantitative IMS methods achieved relative standard deviations in the low teens and accuracies of around 80% compared to LC-MS/MS quantification of adjacent tissue sections. The utility of a homogeneously coated stable-isotopically labeled standard (SIL) for normalization was appraised in terms of its potential to improve precision and accuracy of quantification as well as qualitatively reduce variability in the sample tissue images. SIL normalization had a larger influence on the dilution series, where the use of the internal standard was necessary to achieve accuracy and precision comparable to the non-normalized mimetic tissue model data. Normalization to the internal standard appeared most effective when the intensity ratio of the analyte to internal standard was approximately one, and thus precludes this method as a universal normalization approach for all ions in the acquisition.
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Affiliation(s)
- Jeremy A Barry
- Bioimaging , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Rima Ait-Belkacem
- Imabiotech SAS, Parc Eurasanté , 152 rue du Docteur Yersin , 59120 Loos , France
| | - William M Hardesty
- Bioimaging , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Lydia Benakli
- Imabiotech SAS, Parc Eurasanté , 152 rue du Docteur Yersin , 59120 Loos , France
| | - Clara Andonian
- Bioanalysis , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Hermes Licea-Perez
- Bioanalysis , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Jonathan Stauber
- Imabiotech SAS, Parc Eurasanté , 152 rue du Docteur Yersin , 59120 Loos , France.,Imabiotech Corp , 44 Manning Rd , Billerica , Massachusetts 01821 , United States
| | - Stephen Castellino
- Bioimaging , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , United States
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22
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Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
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Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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23
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Michno W, Wehrli PM, Blennow K, Zetterberg H, Hanrieder J. Molecular imaging mass spectrometry for probing protein dynamics in neurodegenerative disease pathology. J Neurochem 2018; 151:488-506. [PMID: 30040875 DOI: 10.1111/jnc.14559] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022]
Abstract
Recent advances in the understanding of basic pathological mechanisms in various neurological diseases depend directly on the development of novel bioanalytical technologies that allow sensitive and specific chemical imaging at high resolution in cells and tissues. Mass spectrometry-based molecular imaging (IMS) has gained increasing popularity in biomedical research for mapping the spatial distribution of molecular species in situ. The technology allows for comprehensive, untargeted delineation of in situ distribution profiles of metabolites, lipids, peptides and proteins. A major advantage of IMS over conventional histochemical techniques is its superior molecular specificity. Imaging mass spectrometry has therefore great potential for probing molecular regulations in CNS-derived tissues and cells for understanding neurodegenerative disease mechanism. The goal of this review is to familiarize the reader with the experimental workflow, instrumental developments and methodological challenges as well as to give a concise overview of the major advances and recent developments and applications of IMS-based protein and peptide profiling with particular focus on neurodegenerative diseases. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Wojciech Michno
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Patrick M Wehrli
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK.,Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
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24
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Race AM, Römpp A. Error-Free Data Visualization and Processing through imzML and mzML Validation. Anal Chem 2018; 90:13378-13384. [PMID: 30220203 DOI: 10.1021/acs.analchem.8b03059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Open data formats are key to facilitating data processing, sharing, and integration. The imzML format ( http://imzml.org/ ) has drastically improved these aspects of mass spectrometry imaging data. Efficient processing of data depends on data sets which are consistent and adhere to the specifications; however, this is not always the case. Here we present a validation tool for data stored in both imzML and the HUPO-PSI mass spectrometery counterpart, mzML, to identify any deviations from the published (i)mzML standard which could cause issues for the user when visualizing or processing data. The tool is released in two forms, a graphical user interface (GUI) for ease of use, and a command line version to fit into existing workflows and pipelines. When certain known issues are encountered, such as the presence of negative values for the location of the binary data, the validator resolves the issue automatically upon saving. The GUI version of the validator also allows editing of the metadata included within the (i)mzML files in order to resolve inconsistencies. We also present a means of performing conditional validation on the metadata within (i)mzML files, where user-defined rules are validated against depending on whether specific metadata are present (or not). For example, if the MALDI term is present, then additional rules related to MALDI (such as the requirement of inclusion of laser parameters) can be validated against this. This enables a flexible and more thorough automated validation of (i)mzML data. Such a system is necessary for validating data against more comprehensive sets of metadata such as minimum reporting guidelines or metadata requirements prior to submission and acceptance of data to data repositories. We demonstrate how this tool can be used to validate against the proposed minimum reporting guidelines in MSI as well as institute specific metadata criteria. The validator tool is endorsed for validation of imzML ( http://imzml.org/ ) and mzML ( http://www.psidev.info/mzml ) and is made available through the respective Web sites. The validator is also released as open source under Mozilla Public License 2.0 at https://gitlab.com/imzML/imzMLValidator .
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Affiliation(s)
- Alan M Race
- Chair of Bioanalytical Sciences and Food Analysis , University of Bayreuth , 95447 Bayreuth , Germany
| | - Andreas Römpp
- Chair of Bioanalytical Sciences and Food Analysis , University of Bayreuth , 95447 Bayreuth , Germany
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25
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Gustafsson OJR, Winderbaum LJ, Condina MR, Boughton BA, Hamilton BR, Undheim EAB, Becker M, Hoffmann P. Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments. Gigascience 2018; 7:5074354. [PMID: 30124809 PMCID: PMC6203951 DOI: 10.1093/gigascience/giy102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/24/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023] Open
Abstract
Reproducibility, or a lack thereof, is an increasingly important topic across many research fields. A key aspect of reproducibility is accurate reporting of both experiments and the resulting data. Herein, we propose a reporting guideline for mass spectrometry imaging (MSI). Previous standards have laid out guidelines sufficient to guarantee a certain quality of reporting; however, they set a high bar and as a consequence can be exhaustive and broad, thus limiting uptake.To help address this lack of uptake, we propose a reporting supplement-Minimum Information About a Mass Spectrometry Imaging Experiment (MIAMSIE)-and its abbreviated reporting standard version, MSIcheck. MIAMSIE is intended to improve author-driven reporting. It is intentionally not exhaustive, but is rather designed for extensibility and could therefore eventually become analogous to existing standards that aim to guarantee reporting quality. Conversely, its abbreviated form MSIcheck is intended as a diagnostic tool focused on key aspects in MSI reporting.We discuss how existing standards influenced MIAMSIE/MSIcheck and how these new approaches could positively impact reporting quality, followed by test implementation of both standards to demonstrate their use. For MIAMSIE, we report on author reviews of four articles and a dataset. For MSIcheck, we show a snapshot review of a one-month subset of the MSI literature that indicated issues with data provision and the reporting of both data analysis steps and calibration settings for MS systems. Although our contribution is MSI specific, we believe the underlying approach could be considered as a general strategy for improving scientific reporting.
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Affiliation(s)
- Ove J R Gustafsson
- ARC Centre of Excellence in Convergent Bio-Nano Science & Technology (CBNS), University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Lyron J Winderbaum
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Mark R Condina
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael Becker
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riss 88397, Germany
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
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26
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Klein O, Strohschein K, Nebrich G, Fuchs M, Thiele H, Giavalisco P, Duda GN, Winkler T, Kobarg JH, Trede D, Geissler S. Unraveling local tissue changes within severely injured skeletal muscles in response to MSC-based intervention using MALDI Imaging mass spectrometry. Sci Rep 2018; 8:12677. [PMID: 30140012 PMCID: PMC6107672 DOI: 10.1038/s41598-018-30990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Pre-clinical and clinical studies are now beginning to demonstrate the high potential of cell therapies in enhancing muscle regeneration. We previously demonstrated functional benefit after the transplantation of autologous bone marrow mesenchymal stromal cells (MSC-TX) into a severe muscle crush trauma model. Despite our increasing understanding of the molecular and cellular mechanisms underlying MSC's regenerative function, little is known about the local molecular alterations and their spatial distribution within the tissue after MSC-TX. Here, we used MALDI imaging mass spectrometry (MALDI-IMS) in combination with multivariate statistical strategies to uncover previously unknown peptide alterations within severely injured skeletal muscles. Our analysis revealed that very early molecular alterations in response to MSC-TX occur largely in the region adjacent to the trauma and only to a small extent in the actual trauma region. Using "bottom up" mass spectrometry, we subsequently identified the proteins corresponding to the differentially expressed peptide intensity distributions in the specific muscle regions and used immunohistochemistry to validate our results. These findings extend our current understanding about the early molecular processes of muscle healing and highlights the critical role of trauma adjacent tissue during the early therapeutic response upon treatment with MSC.
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Affiliation(s)
- Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Kristin Strohschein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Grit Nebrich
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Michael Fuchs
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Herbert Thiele
- Fraunhofer - Inst. Medical Image Computing MEVIS, Maria-Goeppert-Straße 3, 23562, Lübeck, Germany
| | - Patrick Giavalisco
- Experimental Systems Biology Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, 14476, Golm, Germany
| | - Georg N Duda
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Tobias Winkler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan Hendrik Kobarg
- SCiLS, Zweigniederlassung Bremen der Bruker Daltonik, Fahrenheitstr. 1, 28359, Bremen, Germany
| | - Dennis Trede
- SCiLS, Zweigniederlassung Bremen der Bruker Daltonik, Fahrenheitstr. 1, 28359, Bremen, Germany
| | - Sven Geissler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
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27
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Huber K, Khamehgir-Silz P, Schramm T, Gorshkov V, Spengler B, Römpp A. Approaching cellular resolution and reliable identification in mass spectrometry imaging of tryptic peptides. Anal Bioanal Chem 2018; 410:5825-5837. [PMID: 30066193 PMCID: PMC6096711 DOI: 10.1007/s00216-018-1199-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/24/2018] [Accepted: 06/13/2018] [Indexed: 01/19/2023]
Abstract
On-tissue digestion has become the preferred method to identify proteins in mass spectrometry (MS) imaging. In this study, we report advances in data acquisition and protein identification for MS imaging after on-tissue digestion. Tryptic peptides in a coronal mouse brain section were measured at 50 μm pixel size and revealed detailed histological structures, e.g., the ependyma (consisting of one to two cell layers), which was confirmed by H&E staining. This demonstrates that MS imaging of tryptic peptides at or close to cellular resolution is within reach. We also describe a detailed identification workflow which resulted in the identification of 99 proteins (with 435 corresponding peptides), based on comparison with LC-MS/MS data and in silico digest. These results were obtained with stringent parameters, including high mass accuracy in imaging mode (RSME < 3 ppm) and at least two unique peptides per protein showing consistent spatial distribution. We identified almost 50% of proteins with at least four corresponding peptides. As there is no agreed approach for identification of proteins after on-tissue digestion yet, we discuss our workflow in detail and make the corresponding mass spectral data available as “open data” via ProteomeXchange (identifier PXD003172). With this, we would like to contribute to a more effective discussion and the development of new approaches for tryptic peptide identification in MS imaging. From an experimental point of view, we demonstrate the improvement due to the combination of high spatial resolution and high mass resolution/mass accuracy on a measurement at 25 μm pixel size in mouse cerebellum tissue. A whole body section of a mouse pub imaged at 50 μm pixel size (40 GB, 230,000 spectra) demonstrates the stability of our protocol. For this data set, we developed a workflow that is based on conversion to the common data format imzML and sequential application of freely available software tools. In combination, the presented results for spatial resolution, protein identification, and data processing constitute significant improvements for the field of on-tissue digestion. MS imaging of coronal mouse brain cerebellum with a pixel size of 25 μm: A Optical image, B myelin staining, C H&E staining, and D MS image overlay (RGB) of tryptic peptides m/z = 726.4045 ± 0.005, HGFLPR + H+ (red), m/z = 536.3173 ± 0.005, AKPAK + Na+ (green), and m/z = 994.5436 ± 0.005, WRQLIEK + Na+ (blue) ![]()
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Affiliation(s)
- Katharina Huber
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Pegah Khamehgir-Silz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Thorsten Schramm
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Vladimir Gorshkov
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany. .,Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitaetsstrasse 30, 95440, Bayreuth, Germany.
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28
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Falcetta F, Morosi L, Ubezio P, Giordano S, Decio A, Giavazzi R, Frapolli R, Prasad M, Franceschi P, D'Incalci M, Davoli E. Past-in-the-Future. Peak detection improves targeted mass spectrometry imaging. Anal Chim Acta 2018; 1042:1-10. [PMID: 30428975 DOI: 10.1016/j.aca.2018.06.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/19/2018] [Accepted: 06/24/2018] [Indexed: 11/30/2022]
Abstract
Mass spectrometry imaging is a valuable tool for visualizing the localization of drugs in tissues, a critical issue especially in cancer pharmacology where treatment failure may depend on poor drug distribution within the tumours. Proper preprocessing procedures are mandatory to obtain quantitative data of drug distribution in tumours, even at low intensity, through reliable ion peak identification and integration. We propose a simple preprocessing and quantification pipeline. This pipeline was designed starting from classical peak integration methods, developed when "microcomputers" became available for chromatography, now applied to MSI. This pre-processing approach is based on a novel method using the fixed mass difference between the analyte and its 5 d derivatives to set up a mass range gate. We demonstrate the use of this pipeline for the evaluating the distribution of the anticancer drug paclitaxel in tumour sections. The procedure takes advantage of a simple peak analysis and allows to quantify the drug concentration in each pixel with a limit of detection below 0.1 pmol mm-2 or 10 μg g-1. Quantitative images of paclitaxel distribution in different tumour models were obtained and average paclitaxel concentrations were compared with HPLC measures in the same specimens, showing <20% difference. The scripts are developed in Python and available through GitHub, at github.com/FrancescaFalcetta/Imaging_of_drugs_distribution_and_quantifications.git.
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Affiliation(s)
- Francesca Falcetta
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Lavinia Morosi
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Paolo Ubezio
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Silvia Giordano
- Mass Spectrometry Laboratory, Department of Environmental Health Sciences, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Alessandra Decio
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Raffaella Giavazzi
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Roberta Frapolli
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Mridula Prasad
- IMM/Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ, Nijmegen, Netherlands; Biostatistics and Data Management Group, Fondazione Edmund Mach, 38010, San Michele all' Adige, Italy; Nanotechnology in Medicinal Chemistry, Department of Molecular Biotechnology and Health Sciences, Università di Torino, 10126, Torino, Italy
| | - Pietro Franceschi
- Biostatistics and Data Management Group, Fondazione Edmund Mach, 38010, San Michele all' Adige, Italy
| | - Maurizio D'Incalci
- Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy
| | - Enrico Davoli
- Mass Spectrometry Laboratory, Department of Environmental Health Sciences, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa, 19-20156, Milan, Italy.
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29
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Mueller C, Haymond A, Davis JB, Williams A, Espina V. Protein biomarkers for subtyping breast cancer and implications for future research. Expert Rev Proteomics 2018; 15:131-152. [PMID: 29271260 PMCID: PMC6104835 DOI: 10.1080/14789450.2018.1421071] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure. Areas covered: This review provides a summary of immunohistochemistry, reverse phase protein array, mass spectrometry, and integrative studies that are revealing differences in biological functions within and between breast cancer subtypes. We conclude with a discussion of rigor and reproducibility for proteomic-based biomarker discovery. Expert commentary: Innovations in proteomics, including implementation of assay guidelines and standards, are facilitating refinement of breast cancer subtypes. Proteomic and phosphoproteomic information distinguish biologically functional subtypes, are predictive of recurrence, and indicate likelihood of drug resistance. Actionable, activated signal transduction pathways can now be quantified and characterized. Proteomic biomarker validation in large, well-designed studies should become a public health priority to capitalize on the wealth of information gleaned from the proteome.
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Affiliation(s)
- Claudius Mueller
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Amanda Haymond
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin B Davis
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Alexa Williams
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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30
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Bøgeskov Schmidt F, Heskes AM, Thinagaran D, Lindberg Møller B, Jørgensen K, Boughton BA. Mass Spectrometry Based Imaging of Labile Glucosides in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:892. [PMID: 30002667 PMCID: PMC6031732 DOI: 10.3389/fpls.2018.00892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/07/2018] [Indexed: 05/19/2023]
Abstract
Mass spectrometry based imaging is a powerful tool to investigate the spatial distribution of a broad range of metabolites across a variety of sample types. The recent developments in instrumentation and computing capabilities have increased the mass range, sensitivity and resolution and rendered sample preparation the limiting step for further improvements. Sample preparation involves sectioning and mounting followed by selection and application of matrix. In plant tissues, labile small molecules and specialized metabolites are subject to degradation upon mechanical disruption of plant tissues. In this study, the benefits of cryo-sectioning, stabilization of fragile tissues and optimal application of the matrix to improve the results from MALDI mass spectrometry imaging (MSI) is investigated with hydroxynitrile glucosides as the main experimental system. Denatured albumin proved an excellent agent for stabilizing fragile tissues such as Lotus japonicus leaves. In stem cross sections of Manihot esculenta, maintaining the samples frozen throughout the sectioning process and preparation of the samples by freeze drying enhanced the obtained signal intensity by twofold to fourfold. Deposition of the matrix by sublimation improved the spatial information obtained compared to spray. The imaging demonstrated that the cyanogenic glucosides (CNglcs) were localized in the vascular tissues in old stems of M. esculenta and in the periderm and vascular tissues of tubers. In MALDI mass spectrometry, the imaged compounds are solely identified by their m/z ratio. L. japonicus MG20 and the mutant cyd1 that is devoid of hydroxynitrile glucosides were used as negative controls to verify the assignment of the observed masses to linamarin, lotaustralin, and linamarin acid.
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Affiliation(s)
- Frederik Bøgeskov Schmidt
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
| | - Allison M. Heskes
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dinaiz Thinagaran
- Metabolomics Australia, School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Birger Lindberg Møller,
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Copenhagen, Denmark
- Center for Synthetic Biology, University of Copenhagen, Copenhagen, Denmark
| | - Berin A. Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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31
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Spatial Metabolite Profiling by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:291-321. [DOI: 10.1007/978-3-319-47656-8_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Abstract
Over the last decade mass spectrometry imaging (MSI) has been integrated in to many areas of drug discovery and development. It can have significant impact in oncology drug discovery as it allows efficacy and safety of compounds to be assessed against the backdrop of the complex tumour microenvironment. We will discuss the roles of MSI in investigating compound and metabolite biodistribution and defining pharmacokinetic -pharmacodynamic relationships, analysis that is applicable to all drug discovery projects. We will then look more specifically at how MSI can be used to understand tumour metabolism and other applications specific to oncology research. This will all be described alongside the challenges of applying MSI to industry research with increased use of metrology for MSI.
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Rzagalinski I, Volmer DA. Quantification of low molecular weight compounds by MALDI imaging mass spectrometry - A tutorial review. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:726-739. [PMID: 28012871 DOI: 10.1016/j.bbapap.2016.12.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 12/01/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) permits label-free in situ analysis of chemical compounds directly from the surface of two-dimensional biological tissue slices. It links qualitative molecular information of compounds to their spatial coordinates and distribution within the investigated tissue. MALDI-MSI can also provide the quantitative amounts of target compounds in the tissue, if proper calibration techniques are performed. Obviously, as the target molecules are embedded within the biological tissue environment and analysis must be performed at their precise locations, there is no possibility for extensive sample clean-up routines or chromatographic separations as usually performed with homogenized biological materials; ion suppression phenomena therefore become a critical side effect of MALDI-MSI. Absolute quantification by MALDI-MSI should provide an accurate value of the concentration/amount of the compound of interest in relatively small, well-defined region of interest of the examined tissue, ideally in a single pixel. This goal is extremely challenging and will not only depend on the technical possibilities and limitations of the MSI instrument hardware, but equally on the chosen calibration/standardization strategy. These strategies are the main focus of this article and are discussed and contrasted in detail in this tutorial review. 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)
- Ignacy Rzagalinski
- Institute of Bioanalytical Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, 66123 Saarbrücken, Germany.
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An experimental guideline for the analysis of histologically heterogeneous tumors by MALDI-TOF mass spectrometry imaging. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:957-966. [PMID: 27725306 DOI: 10.1016/j.bbapap.2016.09.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/26/2016] [Accepted: 09/30/2016] [Indexed: 12/11/2022]
Abstract
Mass spectrometry imaging (MSI) has been widely used for the direct molecular assessment of tissue samples and has demonstrated great potential to complement current histopathological methods in cancer research. It is now well established that tissue preparation is key to a successful MSI experiment; for histologically heterogeneous tumor tissues, other parts of the workflow are equally important to the experiment's success. To demonstrate these facets here we describe a matrix-assisted laser desorption/ionization MSI biomarker discovery investigation of high-grade, complex karyotype sarcomas, which often have histological overlap and moderate response to chemo-/radio-therapy. Multiple aspects of the workflow had to be optimized, ranging from the tissue preparation and data acquisition protocols, to the post-MSI histological staining method, data quality control, histology-defined data selection, data processing and statistical analysis. Only as a result of developing every step of the biomarker discovery workflow was it possible to identify a panel of protein signatures that could distinguish between different subtypes of sarcomas or could predict patient survival outcome. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Visualization of in vivo metabolic flows reveals accelerated utilization of glucose and lactate in penumbra of ischemic heart. Sci Rep 2016; 6:32361. [PMID: 27581923 PMCID: PMC5007669 DOI: 10.1038/srep32361] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 08/05/2016] [Indexed: 11/25/2022] Open
Abstract
Acute ischemia produces dynamic changes in labile metabolites. To capture snapshots of such acute metabolic changes, we utilized focused microwave treatment to fix metabolic flow in vivo in hearts of mice 10 min after ligation of the left anterior descending artery. The left ventricle was subdivided into short-axis serial slices and the metabolites were analyzed by capillary electrophoresis mass spectrometry and matrix-assisted laser desorption/ionization imaging mass spectrometry. These techniques allowed us to determine the fate of exogenously administered 13C6-glucose and 13C3-lactate. The penumbra regions, which are adjacent to the ischemic core, exhibited the greatest adenine nucleotide energy charge and an adenosine overflow extending from the ischemic core, which can cause ischemic hyperemia. Imaging analysis of metabolic pathway flows revealed that the penumbra executes accelerated glucose oxidation, with remaining lactate utilization for tricarboxylic acid cycle for energy compensation, suggesting unexpected metabolic interplays of the penumbra with the ischemic core and normoxic regions.
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36
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Label-free quantification of peptides in solution by disposable patterned hydrophilic chip based MALDI imaging. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA. A public repository for mass spectrometry imaging data. Anal Bioanal Chem 2015; 407:2027-33. [PMID: 25542566 PMCID: PMC4357645 DOI: 10.1007/s00216-014-8357-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Schubertstrasse 60, 35392, Giessen, Germany,
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Boughton BA, Thinagaran D, Sarabia D, Bacic A, Roessner U. Mass spectrometry imaging for plant biology: a review. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2015; 15:445-488. [PMID: 27340381 PMCID: PMC4870303 DOI: 10.1007/s11101-015-9440-2] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/25/2015] [Indexed: 05/09/2023]
Abstract
Mass spectrometry imaging (MSI) is a developing technique to measure the spatio-temporal distribution of many biomolecules in tissues. Over the preceding decade, MSI has been adopted by plant biologists and applied in a broad range of areas, including primary metabolism, natural products, plant defense, plant responses to abiotic and biotic stress, plant lipids and the developing field of spatial metabolomics. This review covers recent advances in plant-based MSI, general aspects of instrumentation, analytical approaches, sample preparation and the current trends in respective plant research.
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Affiliation(s)
- Berin A. Boughton
- />Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Dinaiz Thinagaran
- />School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Daniel Sarabia
- />School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Antony Bacic
- />School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
- />ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, VIC 3010 Australia
- />Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010 Australia
| | - Ute Roessner
- />School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
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39
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Munyeza CF, Shobo A, Baijnath S, Bratkowska D, Naiker S, Bester LA, Singh SD, Maguire GEM, Kruger HG, Naicker T, Govender T. Rapid and widespread distribution of doxycycline in rat brain: a mass spectrometric imaging study. Xenobiotica 2015; 46:385-92. [DOI: 10.3109/00498254.2015.1081307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Shobo A, Bratkowska D, Baijnath S, Naiker S, Somboro AM, Bester LA, Singh SD, Naicker T, Kruger HG, Govender T. Tissue distribution of pretomanid in rat brain via mass spectrometry imaging. Xenobiotica 2015. [PMID: 26207565 DOI: 10.3109/00498254.2015.1067935] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
1. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) combines the sensitivity and selectivity of mass spectrometry with spatial analysis to provide a new dimension for histological analyses of the distribution of drugs in tissue. Pretomanid is a pro-drug belonging to a class of antibiotics known as nitroimidizoles, which have been proven to be active under hypoxic conditions and to the best of our knowledge there have been no studies investigating the distribution and localisation of this class of compounds in the brain using MALDI MSI. 2. Herein, we report on the distribution of pretomanid in the healthy rat brain after intraperitoneal administration (20 mg/kg) using MALDI MSI. Our findings showed that the drug localises in specific compartments of the rat brain viz. the corpus callosum, a dense network of neurons connecting left and right cerebral hemispheres. 3. This study proves that MALDI MSI technique has great potential for mapping the pretomanid distribution in uninfected tissue samples, without the need for molecular labelling.
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Affiliation(s)
- Adeola Shobo
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Dominika Bratkowska
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Sooraj Baijnath
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Suhashni Naiker
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Anou M Somboro
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Linda A Bester
- b Biomedical Resource Unit , University of KwaZulu-Natal , Durban , South Africa
| | - Sanil D Singh
- b Biomedical Resource Unit , University of KwaZulu-Natal , Durban , South Africa
| | - Tricia Naicker
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Hendrik G Kruger
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
| | - Thavendran Govender
- a School of Pharmacy and Pharmacology, University of KwaZulu-Natal , Durban , South Africa and
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Addie RD, Balluff B, Bovée JVMG, Morreau H, McDonnell LA. Current State and Future Challenges of Mass Spectrometry Imaging for Clinical Research. Anal Chem 2015; 87:6426-33. [DOI: 10.1021/acs.analchem.5b00416] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ruben D. Addie
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Liam A. McDonnell
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
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42
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Römpp A, Both JP, Brunelle A, Heeren RMA, Laprévote O, Prideaux B, Seyer A, Spengler B, Stoeckli M, Smith DF. Mass spectrometry imaging of biological tissue: an approach for multicenter studies. Anal Bioanal Chem 2015; 407:2329-35. [DOI: 10.1007/s00216-014-8410-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/03/2014] [Accepted: 12/12/2014] [Indexed: 12/11/2022]
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43
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Crecelius AC, Schubert US, von Eggeling F. MALDI mass spectrometric imaging meets “omics”: recent advances in the fruitful marriage. Analyst 2015; 140:5806-20. [DOI: 10.1039/c5an00990a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) is a method that allows the investigation of the molecular content of surfaces, in particular, tissues, within its morphological context.
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Affiliation(s)
- A. C. Crecelius
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - U. S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - F. von Eggeling
- Jena Center for Soft Matter (JCSM)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Institute of Physical Chemistry
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