1
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Good CJ, Butrico CE, Colley ME, Emmerson LN, Gibson-Corley KN, Cassat JE, Spraggins JM, Caprioli RM. Uncovering lipid dynamics in Staphylococcus aureus osteomyelitis using multimodal imaging mass spectrometry. Cell Chem Biol 2024:S2451-9456(24)00401-X. [PMID: 39389064 DOI: 10.1016/j.chembiol.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/20/2024] [Accepted: 09/18/2024] [Indexed: 10/12/2024]
Abstract
Osteomyelitis occurs when Staphylococcus aureus invades the bone microenvironment, resulting in a bone marrow abscess with a spatially defined architecture of cells and biomolecules. Imaging mass spectrometry and microscopy are tools that can be employed to interrogate the lipidome of S. aureus-infected murine femurs and reveal metabolic and signaling consequences of infection. Here, nearly 250 lipids were spatially mapped to healthy and infection-associated morphological features throughout the femur, establishing composition profiles for tissue types. Ether lipids and arachidonoyl lipids were altered between cells and tissue structures in abscesses, suggesting their roles in abscess formation and inflammatory signaling. Sterols, triglycerides, bis(monoacylglycero)phosphates, and gangliosides possessed ring-like distributions throughout the abscess, suggesting a hypothesized dysregulation of lipid metabolism in a population of cells that cannot be discerned with traditional microscopy. These data provide insight into the signaling function and metabolism of cells in the fibrotic border of abscesses, likely characteristic of lipid-laden macrophages.
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Affiliation(s)
- Christopher J Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Casey E Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madeline E Colley
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Lauren N Emmerson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA.
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Medicine, Vanderbilt University, Nashville, TN 37235, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
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2
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Zhang H, Lu KH, Ebbini M, Huang P, Lu H, Li L. Mass spectrometry imaging for spatially resolved multi-omics molecular mapping. NPJ IMAGING 2024; 2:20. [PMID: 39036554 PMCID: PMC11254763 DOI: 10.1038/s44303-024-00025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
The recent upswing in the integration of spatial multi-omics for conducting multidimensional information measurements is opening a new chapter in biological research. Mapping the landscape of various biomolecules including metabolites, proteins, nucleic acids, etc., and even deciphering their functional interactions and pathways is believed to provide a more holistic and nuanced exploration of the molecular intricacies within living systems. Mass spectrometry imaging (MSI) stands as a forefront technique for spatially mapping the metabolome, lipidome, and proteome within diverse tissue and cell samples. In this review, we offer a systematic survey delineating different MSI techniques for spatially resolved multi-omics analysis, elucidating their principles, capabilities, and limitations. Particularly, we focus on the advancements in methodologies aimed at augmenting the molecular sensitivity and specificity of MSI; and depict the burgeoning integration of MSI-based spatial metabolomics, lipidomics, and proteomics, encompassing the synergy with other imaging modalities. Furthermore, we offer speculative insights into the potential trajectory of MSI technology in the future.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Kelly H. Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Malik Ebbini
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
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3
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Colley ME, Esselman AB, Scott CF, Spraggins JM. High-Specificity Imaging Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:1-24. [PMID: 38594938 DOI: 10.1146/annurev-anchem-083023-024546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Imaging mass spectrometry (IMS) enables highly multiplexed, untargeted tissue mapping for a broad range of molecular classes, facilitating in situ biological discovery. Yet, challenges persist in molecular specificity, which is the ability to discern one molecule from another, and spatial specificity, which is the ability to link untargeted imaging data to specific tissue features. Instrumental developments have dramatically improved IMS spatial resolution, allowing molecular observations to be more readily associated with distinct tissue features across spatial scales, ranging from larger anatomical regions to single cells. High-performance mass analyzers and systems integrating ion mobility technologies are also becoming more prevalent, further improving molecular coverage and the ability to discern chemical identity. This review provides an overview of recent advancements in high-specificity IMS that are providing critical biological context to untargeted molecular imaging, enabling integrated analyses, and addressing advanced biomedical research applications.
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Affiliation(s)
- Madeline E Colley
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison B Esselman
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Claire F Scott
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeffrey M Spraggins
- 1Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA;
- 2Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
- 3Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- 4Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- 5Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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4
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Rahman MM, Islam A, Mamun MA, Afroz MS, Nabi MM, Sakamoto T, Sato T, Kahyo T, Takahashi Y, Okino A, Setou M. Low-Temperature Plasma Pretreatment Enhanced Cholesterol Detection in Brain by Desorption Electrospray Ionization-Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1227-1236. [PMID: 38778699 DOI: 10.1021/jasms.4c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Cholesterol is a primary lipid molecule in the brain that contains one-fourth of the total body cholesterol. Abnormal cholesterol homeostasis is associated with neurodegenerative disorders. Mass spectrometry imaging (MSI) technique is a powerful tool for studying lipidomics and metabolomics. Among the MSI techniques, desorption electrospray ionization-MSI (DESI-MSI) has been used advantageously to study brain lipidomics due to its soft and ambient ionization nature. However, brain cholesterol is poorly ionized. To this end, we have developed a new method for detecting brain cholesterol by DESI-MSI using low-temperature plasma (LTP) pretreatment as an ionization enhancement. In this method, the brain sections were treated with LTP for 1 and 2 min prior to DESI-MSI analyses. Interestingly, the MS signal intensity of cholesterol (at m/z 369.35 [M + H - H2O]+) was more than 2-fold higher in the 1 min LTP-treated brain section compared to the untreated section. In addition, we detected cholesterol, more specifically excluding isomers by targeted-DESI-MSI in multiple reaction monitoring (MRM) mode and similar results were observed: the signal intensity of each cholesterol transition (m/z 369.4 → 95.1, 109.1, 135.1, 147.1, and 161.1) was increased by more than 2-fold due to 1 min LTP treatment. Cholesterol showed characteristic distributions in the fiber tract region, including the corpus callosum and anterior commissure, anterior part of the brain where LTP markedly (p < 0.001) enhanced the cholesterol intensity. In addition, the distributions of some unknown analytes were exclusively detected in the LTP-treated section. Our study revealed LTP pretreatment as a potential strategy to ionize molecules that show poor ionization efficiency in the MSI technique.
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Affiliation(s)
- Md Muedur Rahman
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Preppers Co., Ltd., Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Ariful Islam
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Preppers Co., Ltd., Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Department of Biochemistry and Microbiology, School of Health and Life Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Al Mamun
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Preppers Co., Ltd., Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Mst Sayela Afroz
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Md Mahamodun Nabi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Takumi Sakamoto
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Preppers Co., Ltd., Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tomohito Sato
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tomoaki Kahyo
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Quantum Imaging Laboratory, International Mass Imaging and Spatial Omics Center, Institute of Photonics Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Yutaka Takahashi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- Preppers Co., Ltd., Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Akitoshi Okino
- Laboratory for Future Interdisciplinary Research of Science and Technology, Institute of Innovative Research, Tokyo Institute of Technology, J2-32, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
- International Mass Imaging and Spatial Omics Center, Institute of Photonics Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Chuo-ku, Hamamatsu, Shizuoka 431-3192, Japan
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5
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Bitto V, Hönscheid P, Besso MJ, Sperling C, Kurth I, Baumann M, Brors B. Enhancing mass spectrometry imaging accessibility using convolutional autoencoders for deriving hypoxia-associated peptides from tumors. NPJ Syst Biol Appl 2024; 10:57. [PMID: 38802379 PMCID: PMC11130291 DOI: 10.1038/s41540-024-00385-x] [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: 01/12/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Mass spectrometry imaging (MSI) allows to study cancer's intratumoral heterogeneity through spatially-resolved peptides, metabolites and lipids. Yet, in biomedical research MSI is rarely used for biomarker discovery. Besides its high dimensionality and multicollinearity, mass spectrometry (MS) technologies typically output mass-to-charge ratio values but not the biochemical compounds of interest. Our framework makes particularly low-abundant signals in MSI more accessible. We utilized convolutional autoencoders to aggregate features associated with tumor hypoxia, a parameter with significant spatial heterogeneity, in cancer xenograft models. We highlight that MSI captures these low-abundant signals and that autoencoders can preserve them in their latent space. The relevance of individual hyperparameters is demonstrated through ablation experiments, and the contribution from original features to latent features is unraveled. Complementing MSI with tandem MS from the same tumor model, multiple hypoxia-associated peptide candidates were derived. Compared to random forests alone, our autoencoder approach yielded more biologically relevant insights for biomarker discovery.
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Affiliation(s)
- Verena Bitto
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- HIDSS4Health - Helmholtz Information and Data Science School for Health, Karlsruhe/Heidelberg, Heidelberg, Germany.
- Faculty for Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany.
| | - Pia Hönscheid
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Hospital Carl Gustav Carus (UKD), Technische Universität Dresden, Institute of Pathology, Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - María José Besso
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Sperling
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Hospital Carl Gustav Carus (UKD), Technische Universität Dresden, Institute of Pathology, Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ina Kurth
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
| | - Michael Baumann
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
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6
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Klein D, Rivera ES, Caprioli RM, Spraggins JM. Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. Anal Chem 2024; 96:5065-5070. [PMID: 38517028 PMCID: PMC10993197 DOI: 10.1021/acs.analchem.3c05252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (∼10 pixels/s) 10 μm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS.
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Affiliation(s)
- Dustin
R. Klein
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Emilio S. Rivera
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Richard M. Caprioli
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Mass
Spectrometry Research Center, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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7
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Sarretto T, Gardner W, Brungs D, Napaki S, Pigram PJ, Ellis SR. A Machine Learning-Driven Comparison of Ion Images Obtained by MALDI and MALDI-2 Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:466-475. [PMID: 38407924 DOI: 10.1021/jasms.3c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enables label-free imaging of biomolecules in biological tissues. However, many species remain undetected due to their poor ionization efficiencies. MALDI-2 (laser-induced post-ionization) is the most widely used post-ionization method for improving analyte ionization efficiencies. Mass spectra acquired using MALDI-2 constitute a combination of ions generated by both MALDI and MALDI-2 processes. Until now, no studies have focused on a detailed comparison between the ion images (as opposed to the generated m/z values) produced by MALDI and MALDI-2 for mass spectrometry imaging (MSI) experiments. Herein, we investigated the ion images produced by both MALDI and MALDI-2 on the same tissue section using correlation analysis (to explore similarities in ion images for ions common to both MALDI and MALDI-2) and a deep learning approach. For the latter, we used an analytical workflow based on the Xception convolutional neural network, which was originally trained for human-like natural image classification but which we adapted to elucidate similarities and differences in ion images obtained using the two MSI techniques. Correlation analysis demonstrated that common ions yielded similar spatial distributions with low-correlation species explained by either poor signal intensity in MALDI or the generation of additional unresolved signals using MALDI-2. Using the Xception-based method, we identified many regions in the t-SNE space of spatially similar ion images containing MALDI and MALDI-2-related signals. More notably, the method revealed distinct regions containing only MALDI-2 ion images with unique spatial distributions that were not observed using MALDI. These data explicitly demonstrate the ability of MALDI-2 to reveal molecular features and patterns as well as histological regions of interest that are not visible when using conventional MALDI.
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Affiliation(s)
- Tassiani Sarretto
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia, 2522
| | - Wil Gardner
- Centre for Materials and Surface Science and Department of Mathematical and Physical Sciences, La Trobe University, Bundoora, Australia, 3086
| | - Daniel Brungs
- Graduate School of Medicine, University of Wollongong, Wollongong, Australia, 2522
| | - Sarbar Napaki
- Graduate School of Medicine, University of Wollongong, Wollongong, Australia, 2522
| | - Paul J Pigram
- Centre for Materials and Surface Science and Department of Mathematical and Physical Sciences, La Trobe University, Bundoora, Australia, 3086
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia, 2522
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8
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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9
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Good CJ, Butrico CE, Colley ME, Gibson-Corley KN, Cassat JE, Spraggins JM, Caprioli RM. In situ lipidomics of Staphylococcus aureus osteomyelitis using imaging mass spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569690. [PMID: 38077019 PMCID: PMC10705574 DOI: 10.1101/2023.12.01.569690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Osteomyelitis occurs when Staphylococcus aureus invades the bone microenvironment, resulting in a bone marrow abscess with a spatially defined architecture of cells and biomolecules. Imaging mass spectrometry and microscopy are invaluable tools that can be employed to interrogate the lipidome of S. aureus-infected murine femurs to reveal metabolic and signaling consequences of infection. Here, nearly 250 lipids were spatially mapped to healthy and infection-associated morphological features throughout the femur, establishing composition profiles for tissue types. Ether lipids and arachidonoyl lipids were significantly altered between cells and tissue structures in abscesses, suggesting their roles in abscess formation and inflammatory signaling. Sterols, triglycerides, bis(monoacylglycero)phosphates, and gangliosides possessed ring-like distributions throughout the abscess, indicating dysregulated lipid metabolism in a subpopulation of leukocytes that cannot be discerned with traditional microscopy. These data provide chemical insight into the signaling function and metabolism of cells in the fibrotic border of abscesses, likely characteristic of lipid-laden macrophages.
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Affiliation(s)
- Christopher J. Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Casey E. Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madeline E. Colley
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Katherine N. Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E. Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Medicine, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
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10
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Abstract
Imaging mass spectrometry is a well-established technology that can easily and succinctly communicate the spatial localization of molecules within samples. This review communicates the recent advances in the field, with a specific focus on matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) applied on tissues. The general sample preparation strategies for different analyte classes are explored, including special considerations for sample types (fresh frozen or formalin-fixed,) strategies for various analytes (lipids, metabolites, proteins, peptides, and glycans) and how multimodal imaging strategies can leverage the strengths of each approach is mentioned. This work explores appropriate experimental design approaches and standardization of processes needed for successful studies, as well as the various data analysis platforms available to analyze data and their strengths. The review concludes with applications of imaging mass spectrometry in various fields, with a focus on medical research, and some examples from plant biology and microbe metabolism are mentioned, to illustrate the breadth and depth of MALDI IMS.
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Affiliation(s)
- Jessica L Moore
- Department of Proteomics, Discovery Life Sciences, Huntsville, Alabama 35806, United States
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, Connecticut 06520, United States
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11
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Lai YH, Wang YS. Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions. MASS SPECTROMETRY REVIEWS 2023; 42:2426-2445. [PMID: 35686331 DOI: 10.1002/mas.21790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/27/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.
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Affiliation(s)
- Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National United University, Miaoli, Taiwan, R.O.C
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, Taiwan, R.O.C
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
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12
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Degnan DJ, Zemaitis KJ, Lewis LA, McCue LA, Bramer LM, Fulcher JM, Veličković D, Paša-Tolić L, Zhou M. IsoMatchMS: Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2061-2064. [PMID: 37523489 DOI: 10.1021/jasms.3c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. Visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.
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Affiliation(s)
- David J Degnan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin J Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Logan A Lewis
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - James M Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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13
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Sharman K, Patterson NH, Migas LG, Neumann EK, Allen J, Gibson-Corley KN, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. MALDI IMS-Derived Molecular Contour Maps: Augmenting Histology Whole-Slide Images. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:905-912. [PMID: 37061946 PMCID: PMC10787559 DOI: 10.1021/jasms.2c00370] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Imaging mass spectrometry (IMS) provides untargeted, highly multiplexed maps of molecular distributions in tissue. Ion images are routinely presented as heatmaps and can be overlaid onto complementary microscopy images that provide greater context. However, heatmaps use transparency blending to visualize both images, obscuring subtle quantitative differences and distribution gradients. Here, we developed a contour mapping approach that combines information from IMS ion intensity distributions with that of stained microscopy. As a case study, we applied this approach to imaging data from Staphylococcus aureus-infected murine kidney. In a univariate, or single molecular species, use-case of the contour map representation of IMS data, certain lipids colocalizing with regions of infection were selected using Pearson's correlation coefficient. Contour maps of these lipids overlaid with stained microscopy showed enhanced visualization of lipid distributions and spatial gradients in and around the bacterial abscess as compared to traditional heatmaps. The full IMS data set comprising hundreds of individual ion images was then grouped into a smaller subset of representative patterns using non-negative matrix factorization (NMF). Contour maps of these multivariate NMF images revealed distinct molecular profiles of the major abscesses and surrounding immune response. This contour mapping workflow also enabled a molecular visualization of the transition zone at the host-pathogen interface, providing potential clues about the spatial molecular dynamics beyond what histological staining alone provides. In summary, we developed a new IMS-based contour mapping approach to augment classical stained microscopy images, providing an enhanced and more interpretable visualization of IMS-microscopy multimodal molecular imaging data sets.
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Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jamie Allen
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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14
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Kaya I, Schembri LS, Nilsson A, Shariatgorji R, Baijnath S, Zhang X, Bezard E, Svenningsson P, Odell LR, Andrén PE. On-Tissue Chemical Derivatization for Comprehensive Mapping of Brain Carboxyl and Aldehyde Metabolites by MALDI-MS Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:836-846. [PMID: 37052344 PMCID: PMC10161219 DOI: 10.1021/jasms.2c00336] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The visualization of small metabolites by MALDI mass spectrometry imaging in brain tissue sections is challenging due to low detection sensitivity and high background interference. We present an on-tissue chemical derivatization MALDI mass spectrometry imaging approach for the comprehensive mapping of carboxyls and aldehydes in brain tissue sections. In this approach, the AMPP (1-(4-(aminomethyl)phenyl)pyridin-1-ium chloride) derivatization reagent is used for the covalent charge-tagging of molecules containing carboxylic acid (in the presence of peptide coupling reagents) and aldehydes. This includes free fatty acids and the associated metabolites, fatty aldehydes, dipeptides, neurotoxic reactive aldehydes, amino acids, neurotransmitters and associated metabolites, as well as tricarboxylic acid cycle metabolites. We performed sensitive ultrahigh mass resolution MALDI-MS detection and imaging of various carboxyl- and aldehyde-containing endogenous metabolites simultaneously in rodent brain tissue sections. We verified the AMPP-derivatized metabolites by tandem MS for structural elucidation. This approach allowed us to image numerous aldehydes and carboxyls, including certain metabolites which had been undetectable in brain tissue sections. We also demonstrated the application of on-tissue derivatization to carboxyls and aldehydes in coronal brain tissue sections of a nonhuman primate Parkinson's disease model. Our methodology provides a powerful tool for the sensitive, simultaneous spatial molecular imaging of numerous aldehydes and carboxylic acids during pathological states, including neurodegeneration, in brain tissue.
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Affiliation(s)
- Ibrahim Kaya
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, SE-75124 Uppsala, Sweden
| | | | - Anna Nilsson
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, SE-75124 Uppsala, Sweden
| | - Reza Shariatgorji
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, SE-75124 Uppsala, Sweden
| | - Sooraj Baijnath
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, SE-75124 Uppsala, Sweden
| | - Xiaoqun Zhang
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Erwan Bezard
- Université de Bordeaux, Institut des Maladies Neurodégénératives, F-33000 Bordeaux, France
| | - Per Svenningsson
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Luke R Odell
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, SE-75124 Uppsala, Sweden
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15
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Post-translational modifications on the metal-sequestering protein calprotectin. Biometals 2023:10.1007/s10534-023-00493-x. [PMID: 36826733 PMCID: PMC10393864 DOI: 10.1007/s10534-023-00493-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
Human calprotectin (CP, S100A8/S100A9 oligomer) is an abundant neutrophil protein that contributes to innate immunity by sequestering nutrient metal ions in the extracellular space. This process starves invading microbial pathogens of essential metal nutrients, which can inhibit growth and colonization. Over the past decade, fundamental and clinical studies have revealed that the S100A8 and S100A9 subunits of CP exhibit a variety of post-translational modifications (PTMs). This review summarizes PTMs on the CP subunits that have been detected and highlights two recent studies that evaluated the structural and functional consequences of methionine and cysteine oxidation on CP. Collectively, these investigations indicate that the molecular speciation of extracellular CP is complex and composed of multiple proteoforms. Moreover, PTMs may impact biological function and the lifetime of the protein. It is therefore important that post-translationally modified CP species receive consideration and integration into the current working model for how CP functions in nutritional immunity.
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16
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Surface-sampling mass spectrometry to study proteins and protein complexes. Essays Biochem 2023; 67:229-241. [PMID: 36748325 PMCID: PMC10070487 DOI: 10.1042/ebc20220191] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
This review aims to summarise the current capabilities of surface mass spectrometry (MS) approaches that offer intact protein analysis, and that of non-covalent complexes. Protein analysis is largely achieved via matrix-assisted laser desorption/ionisation (MALDI), which is in itself a surface analysis approach or solvent-based electrospray ionisation (ESI). Several surface sampling approaches have been developed based on ESI, and those that have been used for intact protein analysis will be discussed below. The extent of protein coverage, top-down elucidation, and probing of protein structure for native proteins and non-covalent complexes will be discussed for each approach. Strategies for improving protein analysis, ranging from sample preparation, and sampling methods to instrument modifications and the inclusion of ion mobility separation in the workflow will also be discussed. The relative benefits and drawbacks of each approach will be summarised, providing an overview of current capabilities.
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17
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Djambazova KV, Dufresne M, Migas LG, Kruse ARS, Van de Plas R, Caprioli RM, Spraggins JM. MALDI TIMS IMS of Disialoganglioside Isomers─GD1a and GD1b in Murine Brain Tissue. Anal Chem 2023; 95:1176-1183. [PMID: 36574465 DOI: 10.1021/acs.analchem.2c03939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gangliosides are acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or more sialic acid residue(s) and are highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of gangliosides, among other biomolecules, directly from tissue sections. Integrating trapped ion mobility spectrometry with MALDI IMS allows for the analysis of isomeric lipid structures in situ. Here, we demonstrate the gas-phase separation and identification of disialoganglioside isomers GD1a and GD1b that differ in the position of a sialic acid residue, in multiple samples, including a standard mixture of both isomers, a biological extract, and directly from thin tissue sections. The unique spatial distributions of GD1a/b (d36:1) and GD1a/b (d38:1) isomers were determined in rat hippocampus and spinal cord tissue sections, demonstrating the ability to structurally characterize and spatially map gangliosides based on both the carbohydrate chain and ceramide moieties.
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Affiliation(s)
- Katerina V Djambazova
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Angela R S Kruse
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 1161 21st Avenue S, Nashville, Tennessee 37232, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue S #3218, Nashville, Tennessee 37232, United States
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18
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Lausecker F, Lennon R, Randles MJ. The kidney matrisome in health, aging, and disease. Kidney Int 2022; 102:1000-1012. [PMID: 35870643 DOI: 10.1016/j.kint.2022.06.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Dysregulated extracellular matrix is the hallmark of fibrosis, and it has a profound impact on kidney function in disease. Furthermore, perturbation of matrix homeostasis is a feature of aging and is associated with declining kidney function. Understanding these dynamic processes, in the hope of developing therapies to combat matrix dysregulation, requires the integration of data acquired by both well-established and novel technologies. Owing to its complexity, the extracellular proteome, or matrisome, still holds many secrets and has great potential for the identification of clinical biomarkers and drug targets. The molecular resolution of matrix composition during aging and disease has been illuminated by cutting-edge mass spectrometry-based proteomics in recent years, but there remain key questions about the mechanisms that drive altered matrix composition. Basement membrane components are particularly important in the context of kidney function; and data from proteomic studies suggest that switches between basement membrane and interstitial matrix proteins are likely to contribute to organ dysfunction during aging and disease. Understanding the impact of such changes on physical properties of the matrix, and the subsequent cellular response to altered stiffness and viscoelasticity, is of critical importance. Likewise, the comparison of proteomic data sets from multiple organs is required to identify common matrix biomarkers and shared pathways for therapeutic intervention. Coupled with single-cell transcriptomics, there is the potential to identify the cellular origin of matrix changes, which could enable cell-targeted therapy. This review provides a contemporary perspective of the complex kidney matrisome and draws comparison to altered matrix in heart and liver disease.
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Affiliation(s)
- Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Michael J Randles
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK.
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19
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Prasad M, Postma G, Franceschi P, Buydens LMC, Jansen JJ. Evaluation and comparison of unsupervised methods for the extraction of spatial patterns from mass spectrometry imaging data (MSI). Sci Rep 2022; 12:15687. [PMID: 36127378 PMCID: PMC9489880 DOI: 10.1038/s41598-022-19365-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
For the extraction of spatially important regions from mass spectrometry imaging (MSI) data, different clustering methods have been proposed. These clustering methods are based on certain assumptions and use different criteria to assign pixels into different classes. For high-dimensional MSI data, the curse of dimensionality also limits the performance of clustering methods which are usually overcome by pre-processing the data using dimension reduction techniques. In summary, the extraction of spatial patterns from MSI data can be done using different unsupervised methods, but the robust evaluation of clustering results is what is still missing. In this study, we have performed multiple simulations on synthetic and real MSI data to validate the performance of unsupervised methods. The synthetic data were simulated mimicking important spatial and statistical properties of real MSI data. Our simulation results confirmed that K-means clustering with correlation distance and Gaussian Mixture Modeling clustering methods give optimal performance in most of the scenarios. The clustering methods give efficient results together with dimension reduction techniques. From all the dimension techniques considered here, the best results were obtained with the minimum noise fraction (MNF) transform. The results were confirmed on both synthetic and real MSI data. However, for successful implementation of MNF transform the MSI data requires to be of limited dimensions.
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Affiliation(s)
- Mridula Prasad
- IMM/Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ, Nijmegen, The Netherlands.,Unit of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, 38010, San Michele all' Adige, Italy
| | - Geert Postma
- IMM/Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ, Nijmegen, The Netherlands.
| | - Pietro Franceschi
- Unit of Computational Biology, Research and Innovation Center, Fondazione Edmund Mach, 38010, San Michele all' Adige, Italy
| | - Lutgarde M C Buydens
- IMM/Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen J Jansen
- IMM/Analytical Chemistry, Radboud University, Heyendaalseweg, 6525 AJ, Nijmegen, The Netherlands
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20
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Zemaitis KJ, Veličković D, Kew W, Fort KL, Reinhardt-Szyba M, Pamreddy A, Ding Y, Kaushik D, Sharma K, Makarov AA, Zhou M, Paša-Tolić L. Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. Anal Chem 2022; 94:12604-12613. [PMID: 36067026 PMCID: PMC10064997 DOI: 10.1021/acs.analchem.2c01034] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Core histones including H2A, H2B, H3, and H4 are key modulators of cellular repair, transcription, and replication within eukaryotic cells, playing vital roles in the pathogenesis of disease and cellular responses to environmental stimuli. Traditional mass spectrometry (MS)-based bottom-up and top-down proteomics allows for the comprehensive identification of proteins and of post-translational modification (PTM) harboring proteoforms. However, these methodologies have difficulties preserving near-cellular spatial distributions because they typically require laser capture microdissection (LCM) and advanced sample preparation techniques. Herein, we coupled a matrix-assisted laser desorption/ionization (MALDI) source with a Thermo Scientific Q Exactive HF Orbitrap MS upgraded with ultrahigh mass range (UHMR) boards for the first demonstration of complementary high-resolution accurate mass (HR/AM) measurements of proteoforms up to 16.5 kDa directly from tissues using this benchtop mass spectrometer. The platform achieved isotopic resolution throughout the detected mass range, providing confident assignments of proteoforms with low ppm mass error and a considerable increase in duty cycle over other Fourier transform mass analyzers. Proteoform mapping of core histones was demonstrated on sections of human kidney at near-cellular spatial resolution, with several key distributions of histone and other proteoforms noted within both healthy biopsy and a section from a renal cell carcinoma (RCC) containing nephrectomy. The use of MALDI-MS imaging (MSI) for proteoform mapping demonstrates several steps toward high-throughput accurate identification of proteoforms and provides a new tool for mapping biomolecule distributions throughout tissue sections in extended mass ranges.
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Affiliation(s)
- Kevin J Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kyle L Fort
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | | | - Annapurna Pamreddy
- Center for Renal Precision Medicine, Department of Medicine, University of Texas Health, San Antonio, Texas 78284, United States
| | - Yanli Ding
- Department of Pathology and Laboratory Medicine, University of Texas Health, San Antonio, Texas 78284, United States
| | - Dharam Kaushik
- Department of Urology, University of Texas Health, San Antonio, Texas 78284, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, Department of Medicine, University of Texas Health, San Antonio, Texas 78284, United States.,Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, Texas 78284, United States
| | - Alexander A Makarov
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584, The Netherlands
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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21
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Perry WJ, Grunenwald CM, Van de Plas R, Witten JC, Martin DR, Apte SS, Cassat JE, Pettersson GB, Caprioli RM, Skaar EP, Spraggins JM. Visualizing Staphylococcus aureus pathogenic membrane modification within the host infection environment by multimodal imaging mass spectrometry. Cell Chem Biol 2022; 29:1209-1217.e4. [PMID: 35654040 PMCID: PMC9308753 DOI: 10.1016/j.chembiol.2022.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/10/2021] [Accepted: 05/11/2022] [Indexed: 11/30/2022]
Abstract
Bacterial pathogens have evolved virulence factors to colonize, replicate, and disseminate within the vertebrate host. Although there is an expanding body of literature describing how bacterial pathogens regulate their virulence repertoire in response to environmental signals, it is challenging to directly visualize virulence response within the host tissue microenvironment. Multimodal imaging approaches enable visualization of host-pathogen molecular interactions. Here we demonstrate multimodal integration of high spatial resolution imaging mass spectrometry and microscopy to visualize Staphylococcus aureus envelope modifications within infected murine and human tissues. Data-driven image fusion of fluorescent bacterial reporters and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance imaging mass spectrometry uncovered S. aureus lysyl-phosphatidylglycerol lipids, localizing to select bacterial communities within infected tissue. Absence of lysyl-phosphatidylglycerols is associated with decreased pathogenicity during vertebrate colonization as these lipids provide protection against the innate immune system. The presence of distinct staphylococcal lysyl-phosphatidylglycerol distributions within murine and human infections suggests a heterogeneous, spatially oriented microbial response to host defenses.
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Affiliation(s)
- William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA
| | - Caroline M Grunenwald
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Delft Center for Systems and Control, Delft University of Technology - TU Delft, Delft, the Netherlands; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
| | - James C Witten
- Department of Thoracic and Cardiovascular Surgery, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Daniel R Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - James E Cassat
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gösta B Pettersson
- Department of Thoracic and Cardiovascular Surgery, Cleveland Clinic Heart and Vascular Institute, Cleveland, OH 44195, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37212, USA; Department of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA; Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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22
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Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
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23
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Høiem TS, Andersen MK, Martin‐Lorenzo M, Longuespée R, Claes BS, Nordborg A, Dewez F, Balluff B, Giampà M, Sharma A, Hagen L, Heeren RM, Bathen TF, Giskeødegård GF, Krossa S, Tessem M. An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue. Proteomics 2022; 22:e2100223. [PMID: 35170848 PMCID: PMC9285595 DOI: 10.1002/pmic.202100223] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/19/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
MALDI MS imaging (MSI) is a powerful analytical tool for spatial peptide detection in heterogeneous tissues. Proper sample preparation is crucial to achieve high quality, reproducible measurements. Here we developed an optimized protocol for spatially resolved proteolytic peptide detection with MALDI time-of-flight MSI of fresh frozen prostate tissue sections. The parameters tested included four different tissue washes, four methods of protein denaturation, four methods of trypsin digestion (different trypsin densities, sprayers, and incubation times), and five matrix deposition methods (different sprayers, settings, and matrix concentrations). Evaluation criteria were the number of detected and excluded peaks, percentage of high mass peaks, signal-to-noise ratio, spatial localization, and average intensities of identified peptides, all of which were integrated into a weighted quality evaluation scoring system. Based on these scores, the optimized protocol included an ice-cold EtOH+H2 O wash, a 5 min heating step at 95°C, tryptic digestion incubated for 17h at 37°C and CHCA matrix deposited at a final amount of 1.8 μg/mm2 . Including a heat-induced protein denaturation step after tissue wash is a new methodological approach that could be useful also for other tissue types. This optimized protocol for spatial peptide detection using MALDI MSI facilitates future biomarker discovery in prostate cancer and may be useful in studies of other tissue types.
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Affiliation(s)
- Therese S. Høiem
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Maria K. Andersen
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Marta Martin‐Lorenzo
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Rémi Longuespée
- Department of Clinical Pharmacology and PharmacoepidemiologyHeidelberg University HospitalHeidelbergGermany
| | - Britt S.R. Claes
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Anna Nordborg
- Department of Biotechnology and NanomedicineSINTEF IndustryTrondheimNorway
| | - Frédéric Dewez
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Marco Giampà
- Department of Clinical and Molecular MedicineNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Animesh Sharma
- Department of Clinical and Molecular MedicineNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- PROMEC Core Facility for Proteomics and ModomicsNTNU ‐ Norwegian University of Science and Technology and the Central Norway Regional Health Authority NorwayTrondheimNorway
| | - Lars Hagen
- Department of Clinical and Molecular MedicineNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- PROMEC Core Facility for Proteomics and ModomicsNTNU ‐ Norwegian University of Science and Technology and the Central Norway Regional Health Authority NorwayTrondheimNorway
- Clinic of Laboratory MedicineSt. Olavs HospitalTrondheim University HospitalTrondheimNorway
| | - Ron M.A. Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4I)Maastricht UniversityMaastrichtNetherlands
| | - Tone F. Bathen
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- Department of radiology and nuclear medicineSt. Olavs HospitalTrondheim University HospitalTrondheimNorway
| | - Guro F. Giskeødegård
- K.G. Jebsen Center for Genetic EpidemiologyDepartment of Public Health and NursingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - Sebastian Krossa
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
| | - May‐Britt Tessem
- Department of Circulation and Medical ImagingNTNU ‐ Norwegian University of Science and TechnologyTrondheimNorway
- Department of SurgerySt. Olavs HospitalTrondheim University HospitalTrondheimNorway
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24
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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
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25
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Metal sequestration by S100 proteins in chemically diverse environments. Trends Microbiol 2022; 30:654-664. [DOI: 10.1016/j.tim.2021.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/22/2022]
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26
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Hipper E, Blech M, Hinderberger D, Garidel P, Kaiser W. Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques. Pharmaceutics 2021; 14:72. [PMID: 35056968 PMCID: PMC8779573 DOI: 10.3390/pharmaceutics14010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.
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Affiliation(s)
- Elena Hipper
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Dariush Hinderberger
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Wolfgang Kaiser
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
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27
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Lee PY, Yeoh Y, Omar N, Pung YF, Lim LC, Low TY. Molecular tissue profiling by MALDI imaging: recent progress and applications in cancer research. Crit Rev Clin Lab Sci 2021; 58:513-529. [PMID: 34615421 DOI: 10.1080/10408363.2021.1942781] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) imaging is an emergent technology that has been increasingly adopted in cancer research. MALDI imaging is capable of providing global molecular mapping of the abundance and spatial information of biomolecules directly in the tissues without labeling. It enables the characterization of a wide spectrum of analytes, including proteins, peptides, glycans, lipids, drugs, and metabolites and is well suited for both discovery and targeted analysis. An advantage of MALDI imaging is that it maintains tissue integrity, which allows correlation with histological features. It has proven to be a valuable tool for probing tumor heterogeneity and has been increasingly applied to interrogate molecular events associated with cancer. It provides unique insights into both the molecular content and spatial details that are not accessible by other techniques, and it has allowed considerable progress in the field of cancer research. In this review, we first provide an overview of the MALDI imaging workflow and approach. We then highlight some useful applications in various niches of cancer research, followed by a discussion of the challenges, recent developments and future prospect of this technique in the field.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, Selangor, Malaysia
| | - Lay Cheng Lim
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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28
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Fincher JA, Djambazova KV, Klein DR, Dufresne M, Migas LG, Van de Plas R, Caprioli RM, Spraggins JM. Molecular Mapping of Neutral Lipids Using Silicon Nanopost Arrays and TIMS Imaging Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2519-2527. [PMID: 34435768 DOI: 10.1021/jasms.1c00159] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate the utility of combining silicon nanopost arrays (NAPA) and trapped ion mobility imaging mass spectrometry (TIMS IMS) for high spatial resolution and specificity mapping of neutral lipid classes in tissue. Ionization of neutral lipid species such as triglycerides (TGs), cholestryl esters (CEs), and hexosylceramides (HexCers) from biological tissues has remained a challenge for imaging applications. NAPA, a matrix-free laser desorption ionization substrate, provides enhanced ionization efficiency for the above-mentioned neutral lipid species, providing complementary lipid coverage to matrix-assisted laser desorption ionization (MALDI). The combination of NAPA and TIMS IMS enables imaging of neutral lipid species at 20 μm spatial resolution while also increasing molecular coverage greater than 2-fold using gas-phase ion mobility separations. This is a significant improvement with respect to sensitivity, specificity, and spatial resolution compared to previously reported imaging studies using NAPA alone. Improved specificity for neutral lipid analysis using TIMS IMS was shown using rat kidney tissue to separate TGs, CEs, HexCers, and phospholipids into distinct ion mobility trendlines. Further, this technology allowed for the separation of isomeric species, including mobility resolved isomers of Cer(d42:2) (m/z 686.585) with distinct spatial localizations measured in rat kidney tissue section.
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Affiliation(s)
- Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Lukasz G Migas
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 442 Robinson Research Building, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Cell & Developmental Biology, Vanderbilt University, 465 21st Ave S #9160, Nashville, Tennessee 37235, United States
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29
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Zhang J, Sans M, Garza KY, Eberlin LS. MASS SPECTROMETRY TECHNOLOGIES TO ADVANCE CARE FOR CANCER PATIENTS IN CLINICAL AND INTRAOPERATIVE USE. MASS SPECTROMETRY REVIEWS 2021; 40:692-720. [PMID: 33094861 DOI: 10.1002/mas.21664] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Developments in mass spectrometry technologies have driven a widespread interest and expanded their use in cancer-related research and clinical applications. In this review, we highlight the developments in mass spectrometry methods and instrumentation applied to direct tissue analysis that have been tailored at enhancing performance in clinical research as well as facilitating translation and implementation of mass spectrometry in clinical settings, with a focus on cancer-related studies. Notable studies demonstrating the capabilities of direct mass spectrometry analysis in biomarker discovery, cancer diagnosis and prognosis, tissue analysis during oncologic surgeries, and other clinically relevant problems that have the potential to substantially advance cancer patient care are discussed. Key challenges that need to be addressed before routine clinical implementation including regulatory efforts are also discussed. Overall, the studies highlighted in this review demonstrate the transformative potential of mass spectrometry technologies to advance clinical research and care for cancer patients. © 2020 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Jialing Zhang
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Marta Sans
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Kyana Y Garza
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Livia S Eberlin
- Department of Chemistry, University of Texas at Austin, Austin, TX
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30
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Nicolardi S, Joseph AA, Zhu Q, Shen Z, Pardo-Vargas A, Chiodo F, Molinaro A, Silipo A, van der Burgt YEM, Yu B, Seeberger PH, Wuhrer M. Analysis of Synthetic Monodisperse Polysaccharides by Wide Mass Range Ultrahigh-Resolution MALDI Mass Spectrometry. Anal Chem 2021; 93:4666-4675. [PMID: 33667082 PMCID: PMC8034773 DOI: 10.1021/acs.analchem.1c00239] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
Carbohydrates, such as oligo- and polysaccharides, are highly abundant biopolymers that are involved in numerous processes. The study of their structure and functions is commonly based on a material that is isolated from complex natural sources. However, a more precise analysis requires pure compounds with well-defined structures that can be obtained from chemical or enzymatic syntheses. Novel synthetic strategies have increased the accessibility of larger monodisperse polysaccharides, posing a challenge to the analytical methods used for their molecular characterization. Here, we present wide mass range ultrahigh-resolution matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) as a powerful platform for the analysis of synthetic oligo- and polysaccharides. Synthetic carbohydrates 16-, 64-, 100-, and 151-mers were mass analyzed and characterized by MALDI in-source decay FT-ICR MS. Detection of fragment ions generated from glycosidic bond cleavage (or cross-ring cleavage) provided information of the monosaccharide content and the linkage type, allowing for the corroboration of the carbohydrate compositions and structures.
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Affiliation(s)
- Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - A. Abragam Joseph
- Department
of Biomolecular Systems, Max-Planck-Institute
of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Qian Zhu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhengnan Shen
- School
of Physical Science and Technology, ShanghaiTech
University, 393 Huaxia Middle Road, Shanghai 201210, China
| | - Alonso Pardo-Vargas
- Department
of Biomolecular Systems, Max-Planck-Institute
of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Fabrizio Chiodo
- Institute
of Biomolecular Chemistry (ICB), Italian
National Research Council (CNR), Via Campi Flegrei, 34, Pozzuoli, Napoli 80078, Italy
- Amsterdam
UMC-Locatie VUMC, Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
| | - Antonio Molinaro
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 4, Napoli 80126, Italy
| | - Alba Silipo
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 4, Napoli 80126, Italy
| | - Yuri E. M. van der Burgt
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Biao Yu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School
of Chemistry and Materials Science, Hangzhou Institute for Advanced
Study, University of Chinese Academy of
Sciences, 1 Sub-lane
Xiangshan, Hangzhou 310024, China
| | - Peter H. Seeberger
- Department
of Biomolecular Systems, Max-Planck-Institute
of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
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31
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Trimpin S, Marshall DD, Karki S, Madarshahian S, Hoang K, Meher AK, Pophristic M, Richards AL, Lietz CB, Fischer JL, Elia EA, Wang B, Pagnotti VS, Lutomski CA, El-Baba TJ, Lu IC, Wager-Miller J, Mackie K, McEwen CN, Inutan ED. An overview of biological applications and fundamentals of new inlet and vacuum ionization technologies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 1:e8829. [PMID: 32402102 DOI: 10.1002/rcm.8829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/01/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The developments of new ionization technologies based on processes previously unknown to mass spectrometry (MS) have gained significant momentum. Herein we address the importance of understanding these unique ionization processes, demonstrate the new capabilities currently unmet by other methods, and outline their considerable analytical potential. METHODS The inlet and vacuum ionization methods of solvent-assisted ionization (SAI), matrix-assisted ionization (MAI), and laserspray ionization can be used with commercial and dedicated ion sources producing ions from atmospheric or vacuum conditions for analyses of a variety of materials including drugs, lipids, and proteins introduced from well plates, pipet tips and plate surfaces with and without a laser using solid or solvent matrices. Mass spectrometers from various vendors are employed. RESULTS Results are presented highlighting strengths relative to ionization methods of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization. We demonstrate the utility of multi-ionization platforms encompassing MAI, SAI, and ESI and enabling detection of what otherwise is missed, especially when directly analyzing mixtures. Unmatched robustness is achieved with dedicated vacuum MAI sources with mechanical introduction of the sample to the sub-atmospheric pressure (vacuum MAI). Simplicity and use of a wide array of matrices are attained using a conduit (inlet ionization), preferably heated, with sample introduction from atmospheric pressure. Tissue, whole blood, urine (including mouse, chicken, and human origin), bacteria strains and chemical on-probe reactions are analyzed directly and, especially in the case of vacuum ionization, without concern of carryover or instrument contamination. CONCLUSIONS Examples are provided highlighting the exceptional analytical capabilities associated with the novel ionization processes in MS that reduce operational complexity while increasing speed and robustness, achieving mass spectra with low background for improved sensitivity, suggesting the potential of this simple ionization technology to drive MS into areas currently underserved, such as clinical and medical applications.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- MS™, LLC, Newark, DE, 19711, USA
| | - Darrell D Marshall
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- MS™, LLC, Newark, DE, 19711, USA
| | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- MS™, LLC, Newark, DE, 19711, USA
| | | | - Khoa Hoang
- MS™, LLC, Newark, DE, 19711, USA
- University of the Sciences, Philadelphia, PA, 19104, USA
| | - Anil K Meher
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- MS™, LLC, Newark, DE, 19711, USA
| | - Milan Pophristic
- MS™, LLC, Newark, DE, 19711, USA
- University of the Sciences, Philadelphia, PA, 19104, USA
| | - Alicia L Richards
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | | | - Joshua L Fischer
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Efstathios A Elia
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Beixi Wang
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | | | - Corinne A Lutomski
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Tarick J El-Baba
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - I-Chung Lu
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - James Wager-Miller
- Gill Center for Biomolecular Science and Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 47405, USA
| | - Ken Mackie
- Gill Center for Biomolecular Science and Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, 47405, USA
| | - Charles N McEwen
- MS™, LLC, Newark, DE, 19711, USA
- University of the Sciences, Philadelphia, PA, 19104, USA
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- MS™, LLC, Newark, DE, 19711, USA
- Mindanao State University Iligan Institute of Technology, Iligan City, 9200, Philippines
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32
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Ivanova B, Spiteller M. Stochastic dynamic mass spectrometric quantification of steroids in mixture - Part II. Steroids 2020; 164:108750. [PMID: 33069721 DOI: 10.1016/j.steroids.2020.108750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/04/2020] [Indexed: 01/25/2023]
Abstract
This paper deals with quantification of the following steroids in mixture: hydrocortisone (1), deoxycorticosterone (2), progesterone (3) and methyltestosterone (4) by means of mass spectrometry and implementing our innovative stochatic dynamic functional relationship between the analyte concentration in solution and the experimental variable intensity. The mass spectrometric data are correlated independently using chromatography. Chemometric analysis is carried out.
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Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Nordrhein-Westfalen, Germany.
| | - Michael Spiteller
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Nordrhein-Westfalen, Germany
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33
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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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34
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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35
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36
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Bowman AP, Blakney GT, Hendrickson CL, Ellis SR, Heeren RMA, Smith DF. Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS. Anal Chem 2020; 92:3133-3142. [PMID: 31955581 PMCID: PMC7031845 DOI: 10.1021/acs.analchem.9b04768] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Detailed characterization
of complex biological surfaces by matrix-assisted
laser desorption/ionization (MALDI) mass spectrometry imaging (MSI)
requires instrumentation that is capable of high mass resolving power,
mass accuracy, and dynamic range. Fourier transform ion cyclotron
resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral
performance for MALDI MSI experiments, and often reveals molecular
features that are unresolved on lower performance instrumentation.
Higher magnetic field strength improves all performance characteristics
of FT-ICR; mass resolving power improves linearly, while mass accuracy
and dynamic range improve quadratically with magnetic field strength.
Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving
power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below
100 ppb, and dynamic range per pixel over 500:1 were obtained from
the direct analysis of biological tissue sections. Molecular features
with m/z differences as small as
1.79 mDa were resolved and identified with high mass accuracy. These
features allow for the separation and identification of lipids to
the underlying structures of tissues. The unique molecular detail,
accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR
MSI experiment enable researchers to visualize molecular structures
in complex tissues that have remained hidden until now. The instrument
described allows for future innovative, such as high-end studies to
unravel the complexity of biological, geological, and engineered organic
material surfaces with an unsurpassed detail.
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Affiliation(s)
- Andrew P Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Greg T Blakney
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States.,Department of Chemistry and Biochemistry , Florida State University , 95 Chieftain Way , Tallahassee , Florida 32306 , United States
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Donald F Smith
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States
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37
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Piehowski PD, Zhu Y, Bramer LM, Stratton KG, Zhao R, Orton DJ, Moore RJ, Yuan J, Mitchell HD, Gao Y, Webb-Robertson BJM, Dey SK, Kelly RT, Burnum-Johnson KE. Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution. Nat Commun 2020; 11:8. [PMID: 31911630 PMCID: PMC6946663 DOI: 10.1038/s41467-019-13858-z] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/20/2019] [Indexed: 12/19/2022] Open
Abstract
Biological tissues exhibit complex spatial heterogeneity that directs the functions of multicellular organisms. Quantifying protein expression is essential for elucidating processes within complex biological assemblies. Imaging mass spectrometry (IMS) is a powerful emerging tool for mapping the spatial distribution of metabolites and lipids across tissue surfaces, but technical challenges have limited the application of IMS to the analysis of proteomes. Methods for probing the spatial distribution of the proteome have generally relied on the use of labels and/or antibodies, which limits multiplexing and requires a priori knowledge of protein targets. Past efforts to make spatially resolved proteome measurements across tissues have had limited spatial resolution and proteome coverage and have relied on manual workflows. Here, we demonstrate an automated approach to imaging that utilizes label-free nanoproteomics to analyze tissue voxels, generating quantitative cell-type-specific images for >2000 proteins with 100-µm spatial resolution across mouse uterine tissue sections preparing for blastocyst implantation. Imaging mass spectrometry is a powerful emerging tool for mapping the spatial distribution of biomolecules across tissue surfaces. Here the authors showcase an automated technology for deep proteome imaging that utilizes ultrasensitive microfluidics and a mass spectrometry workflow to analyze tissue voxels, generating quantitative cell-type-specific images.
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Affiliation(s)
- Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Zhu
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kelly G Stratton
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jia Yuan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Sudhansu K Dey
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ryan T Kelly
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA. .,Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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38
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Kaya I, Jennische E, Dunevall J, Lange S, Ewing AG, Malmberg P, Baykal AT, Fletcher JS. Spatial Lipidomics Reveals Region and Long Chain Base Specific Accumulations of Monosialogangliosides in Amyloid Plaques in Familial Alzheimer's Disease Mice (5xFAD) Brain. ACS Chem Neurosci 2020; 11:14-24. [PMID: 31774647 DOI: 10.1021/acschemneuro.9b00532] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ganglioside metabolism is significantly altered in Alzheimer's disease (AD), which is a progressive neurodegenerative disease prominently characterized by one of its pathological hallmarks, amyloid deposits or "senile plaques". While the plaques mainly consist of aggregated variants of amyloid-β protein (Aβ), recent studies have revealed a number of lipid species including gangliosides in amyloid plaques along with Aβ peptides. It has been widely suggested that long chain (sphingosine) base (LCBs), C18:1-LCB and C20:1-LCB, containing gangliosides might play different roles in neuronal function in vivo. In order to elucidate region-specific aspects of amyloid-plaque associated C18:1-LCB and C20:1-LCB ganglioside accumulations, high spatial resolution (10 μm per pixel) matrix assisted laser desorption ionization imaging mass spectrometry (MALDI-IMS) of gangliosides in amyloid plaques was performed in hippocampal and adjacent cortical regions of 12 month old 5xFAD mouse coronal brain sections from two different stereotaxic coordinates (bregma points, -2.2 and -2.7 mm). MALDI-IMS uncovered brain-region (2 and 3D) and/or LCB specific accumulations of monosialogangliosides (GMs): GM1, GM2, and GM3 in the hippocampal and cortical amyloid plaques. The results reveal monosialogangliosides to be an important component of amyloid plaques and the accumulation of different gangliosides is region and LCB specific in 12 month old 5xFAD mouse brain. This is discussed in relation to amyloid-associated AD pathogenesis such as lipid related immune changes in amyloid plaques, AD specific ganglioside metabolism, and, notably, AD-associated impaired neurogenesis in the subgranular zone.
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Affiliation(s)
- Ibrahim Kaya
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal 43180, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Platform, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
| | - Eva Jennische
- Institute of Biomedicine, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Johan Dunevall
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Stefan Lange
- Institute of Biomedicine, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Platform, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
| | - Per Malmberg
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - John S. Fletcher
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Platform, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
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39
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Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host. Proc Natl Acad Sci U S A 2019; 116:21980-21982. [PMID: 31611408 PMCID: PMC6825271 DOI: 10.1073/pnas.1913991116] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Siderophores, iron-scavenging small molecules, are fundamental to bacterial nutrient metal acquisition and enable pathogens to overcome challenges imposed by nutritional immunity. Multimodal imaging mass spectrometry allows visualization of host−pathogen iron competition, by mapping siderophores within infected tissue. We have observed heterogeneous distributions of Staphylococcus aureus siderophores across infectious foci, challenging the paradigm that the vertebrate host is a uniformly iron-depleted environment to invading microbes.
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40
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Cassat JE, Moore JL, Wilson KJ, Stark Z, Prentice BM, Van de Plas R, Perry WJ, Zhang Y, Virostko J, Colvin DC, Rose KL, Judd AM, Reyzer ML, Spraggins JM, Grunenwald CM, Gore JC, Caprioli RM, Skaar EP. Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions. Sci Transl Med 2019. [PMID: 29540616 DOI: 10.1126/scitranslmed.aan6361] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Diseases are characterized by distinct changes in tissue molecular distribution. Molecular analysis of intact tissues traditionally requires preexisting knowledge of, and reagents for, the targets of interest. Conversely, label-free discovery of disease-associated tissue analytes requires destructive processing for downstream identification platforms. Tissue-based analyses therefore sacrifice discovery to gain spatial distribution of known targets or sacrifice tissue architecture for discovery of unknown targets. To overcome these obstacles, we developed a multimodality imaging platform for discovery-based molecular histology. We apply this platform to a model of disseminated infection triggered by the pathogen Staphylococcus aureus, leading to the discovery of infection-associated alterations in the distribution and abundance of proteins and elements in tissue in mice. These data provide an unbiased, three-dimensional analysis of how disease affects the molecular architecture of complex tissues, enable culture-free diagnosis of infection through imaging-based detection of bacterial and host analytes, and reveal molecular heterogeneity at the host-pathogen interface.
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Affiliation(s)
- James E Cassat
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica L Moore
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Kevin J Wilson
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Zach Stark
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Boone M Prentice
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - William J Perry
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Yaofang Zhang
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - John Virostko
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel C Colvin
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristie L Rose
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Audra M Judd
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Michelle L Reyzer
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Caroline M Grunenwald
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John C Gore
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA.,Departments of Radiology and Radiologic Sciences, Biomedical Engineering, Molecular Physiology and Biophysics, and Physics and Astronomy, Vanderbilt University, Nashville, TN 37232, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA.,Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. .,U.S. Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, 37232, USA
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41
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Trimpin S. Novel ionization processes for use in mass spectrometry: 'Squeezing' nonvolatile analyte ions from crystals and droplets. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:96-120. [PMID: 30138957 DOI: 10.1002/rcm.8269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 05/25/2023]
Abstract
Together with my group and collaborators, I have been fortunate to have had a key role in the discovery of new ionization processes that we developed into new flexible, sensitive, rapid, reliable, and robust ionization technologies and methods for use in mass spectrometry (MS). Our current research is focused on how best to understand, improve, and use these novel ionization processes which convert volatile and nonvolatile compounds from solids or liquids into gas-phase ions for analysis by MS using e.g. mass-selected fragmentation and ion mobility spectrometry to provide reproducible, accurate, and improved mass and drift time resolution. In my view, the apex was the discovery of vacuum matrix-assisted ionization (vMAI) in 2012 on an intermediate pressure matrix-assisted laser desorption/ionization (MALDI) source without the use of a laser, high voltages, or any other added energy. Only exposure of the matrix:analyte to the sub-atmospheric pressure of the mass spectrometer was necessary to initiate ionization. These findings were initially rejected by three different scientific journals, with comments related to 'how can this work?', 'where do the charges come from?', and 'it is not analytically useful'. Meanwhile, we and others have demonstrated analytical utility without a complete understanding of the mechanism. In reality, MALDI and electrospray ionization are widely used in science and their mechanisms are still controversially discussed despite use and optimization of now 30 years. This Perspective covers the applications and mechanistic aspects of the novel ionization processes for use in MS that guided us in instrument developments, and provides our perspective on how they relate to traditional ionization processes.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- MSTM, LLC, Newark, DE, 19711, USA
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42
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Berghmans E, Van Raemdonck G, Schildermans K, Willems H, Boonen K, Maes E, Mertens I, Pauwels P, Baggerman G. MALDI Mass Spectrometry Imaging Linked with Top-Down Proteomics as a Tool to Study the Non-Small-Cell Lung Cancer Tumor Microenvironment. Methods Protoc 2019; 2:mps2020044. [PMID: 31164623 PMCID: PMC6632162 DOI: 10.3390/mps2020044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Advanced non-small-cell lung cancer (NSCLC) is generally linked with a poor prognosis and is one of the leading causes of cancer-related deaths worldwide. Since only a minority of the patients respond well to chemotherapy and/or targeted therapies, immunotherapy might be a valid alternative in the lung cancer treatment field, as immunotherapy attempts to strengthen the body’s own immune response to recognize and eliminate malignant tumor cells. However, positive response patterns to immunotherapy remain unclear. In this study, we demonstrate how immune-related factors could be visualized from single NSCLC tissue sections (Biobank@UZA) while retaining their spatial information by using matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), in order to unravel the molecular profile of NSCLC patients. In this way, different regions in lung cancerous tissues could be discriminated based on the molecular composition. In addition, we linked visualization (MALDI MSI) and identification (based on liquid chromatography higher resolution mass spectrometry) of the molecules of interest for the correct biological interpretation of the observed molecular differences within the area in which these molecules are detected. This is of major importance to fully understand the underlying molecular profile of the NSCLC tumor microenvironment.
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Affiliation(s)
- Eline Berghmans
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Geert Van Raemdonck
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
| | - Karin Schildermans
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Hanny Willems
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., 8140 Christchurch, New Zealand.
| | - Inge Mertens
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Patrick Pauwels
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
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43
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Stopka SA, Samarah LZ, Shaw JB, Liyu AV, Veličković D, Agtuca BJ, Kukolj C, Koppenaal DW, Stacey G, Paša-Tolić L, Anderton CR, Vertes A. Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry. Anal Chem 2019; 91:5028-5035. [PMID: 30821434 DOI: 10.1021/acs.analchem.8b05084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is an indispensable analytical tool to capture the array of metabolites within complex biological systems. However, conventional MS-based metabolomic workflows require extensive sample processing and separation resulting in limited throughput and potential alteration of the native molecular states in these systems. Ambient ionization methods, capable of sampling directly from tissues, circumvent some of these issues but require high-performance MS to resolve the molecular complexity within these samples. Here, we demonstrate a unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 tesla Fourier transform ion cyclotron resonance (21T-FTICR) for direct MS analysis and imaging applications. This analytical platform provides isotopic fine structure information directly from biological tissues, enabling the rapid assignment of molecular formulas and delivering a higher degree of confidence for molecular identification.
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Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Laith Z Samarah
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Caroline Kukolj
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Akos Vertes
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
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44
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Ryan DJ, Spraggins JM, Caprioli RM. Protein identification strategies in MALDI imaging mass spectrometry: a brief review. Curr Opin Chem Biol 2019; 48:64-72. [PMID: 30476689 PMCID: PMC6382520 DOI: 10.1016/j.cbpa.2018.10.023] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/26/2018] [Accepted: 10/26/2018] [Indexed: 01/21/2023]
Abstract
Matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful technology used to investigate the spatial distributions of thousands of molecules throughout a tissue section from a single experiment. As proteins represent an important group of functional molecules in tissue and cells, the imaging of proteins has been an important point of focus in the development of IMS technologies and methods. Protein identification is crucial for the biological contextualization of molecular imaging data. However, gas-phase fragmentation efficiency of MALDI generated proteins presents significant challenges, making protein identification directly from tissue difficult. This review highlights methods and technologies specifically related to protein identification that have been developed to overcome these challenges in MALDI IMS experiments.
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Affiliation(s)
- Daniel J. Ryan
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Department of Pharmacology, Vanderbilt University, 442 Robinson Research Building, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave #9160, Nashville, TN 37235, USA
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45
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Stephan JR, Yu F, Costello RM, Bleier BS, Nolan EM. Oxidative Post-translational Modifications Accelerate Proteolytic Degradation of Calprotectin. J Am Chem Soc 2018; 140:17444-17455. [PMID: 30380834 PMCID: PMC6534964 DOI: 10.1021/jacs.8b06354] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oxidative post-translational modifications affect the structure and function of many biomolecules. Herein we examine the biophysical and functional consequences of oxidative post-translational modifications to human calprotectin (CP, S100A8/S100A9 oligomer, MRP8/MRP14 oligomer, calgranulins A/B oligomer). This abundant metal-sequestering protein contributes to innate immunity by starving invading microbial pathogens of transition metal nutrients in the extracellular space. It also participates in the inflammatory response. Despite many decades of study, little is known about the fate of CP at sites of infection and inflammation. We present compelling evidence for methionine oxidation of CP in vivo, supported by using 15N-labeled CP-Ser (S100A8(C42S)/S100A9(C3S)) to monitor for adventitious oxidation following human sample collection. To elucidate the biochemical and functional consequences of oxidative post-translational modifications, we examine recombinant CP-Ser with methionine sulfoxide modifications generated by exposing the protein to hydrogen peroxide. These oxidized species coordinate transition metal ions and exert antibacterial activity. Nevertheless, oxidation of M81 in the S100A9 subunit disrupts Ca(II)-induced tetramerization and, in the absence of a transition metal ion bound at the His6 site, accelerates proteolytic degradation of CP. We demonstrate that native CP, which contains one Cys residue in each full-length subunit, forms disulfide bonds within and between S100A8/S100A9 heterodimers when exposed to hydrogen peroxide. Remarkably, disulfide bond formation accelerates proteolytic degradation of CP. We propose a new extension to the working model for extracellular CP where post-translational oxidation by reactive oxygen species generated during the neutrophil oxidative burst modulates its lifetime in the extracellular space.
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Affiliation(s)
- Jules R Stephan
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Fangting Yu
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Rebekah M Costello
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Benjamin S Bleier
- Department of Otolaryngology , Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Elizabeth M Nolan
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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46
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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: 138] [Impact Index Per Article: 23.0] [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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47
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Dilillo M, de Graaf EL, Yadav A, Belov ME, McDonnell LA. Ultraviolet Photodissociation of ESI- and MALDI-Generated Protein Ions on a Q-Exactive Mass Spectrometer. J Proteome Res 2018; 18:557-564. [PMID: 30484663 DOI: 10.1021/acs.jproteome.8b00896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The identification of molecular ions produced by MALDI or ESI strongly relies on their fragmentation to structurally informative fragments. The widely diffused fragmentation techniques for ESI multiply charged ions are either incompatible (ECD and ETD) or show lower efficiency (CID, HCD), with the predominantly singly charged peptide and protein ions formed by MALDI. In-source decay has been successfully adopted to sequence MALDI-generated ions, but it further increases spectral complexity, and it is not compatible with mass-spectrometry imaging. Excellent UVPD performances, in terms of number of fragment ions and sequence coverage, has been demonstrated for electrospray ionization for multiple proteomics applications. UVPD showed a much lower charge-state dependence, and so protein ions produced by MALDI may exhibit equal propensity to fragment. Here we report UVPD implementation on an Orbitrap Q-Exactive Plus mass spectrometer equipped with an ESI/EP-MALDI. UVPD of MALDI-generated ions was benchmarked against MALDI-ISD, MALDI-HCD, and ESI-UVPD. MALDI-UVPD outperformed MALDI-HCD and ISD, efficiently sequencing small proteins ions. Moreover, the singly charged nature of MALDI-UVPD avoids the bioinformatics challenges associated with highly congested ESI-UVPD mass spectra. Our results demonstrate the ability of UVPD to further improve tandem mass spectrometry capabilities for MALDI-generated protein ions. Data are available via ProteomeXchange with identifier PXD011526.
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Affiliation(s)
- Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy
| | - Erik L de Graaf
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy
| | - Avinash Yadav
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy.,Scuola Normale Superiore di Pisa , 56126 Pisa , Italy
| | - Mikhail E Belov
- Spectroglyph LLC , Kennewick , Washington 99338 , United States
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS , 56107 San Giuliano Terme, Pisa , Italy.,Center for Proteomics and Metabolomics , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
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48
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Himmel LE, Hackett TA, Moore JL, Adams WR, Thomas G, Novitskaya T, Caprioli RM, Zijlstra A, Mahadevan-Jansen A, Boyd KL. Beyond the H&E: Advanced Technologies for in situ Tissue Biomarker Imaging. ILAR J 2018; 59:51-65. [PMID: 30462242 PMCID: PMC6645175 DOI: 10.1093/ilar/ily004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/27/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023] Open
Abstract
For decades, histopathology with routine hematoxylin and eosin staining has been and remains the gold standard for reaching a morphologic diagnosis in tissue samples from humans and veterinary species. However, within the past decade, there has been exponential growth in advanced techniques for in situ tissue biomarker imaging that bridge the divide between anatomic and molecular pathology. It is now possible to simultaneously observe localization and expression magnitude of multiple protein, nucleic acid, and molecular targets in tissue sections and apply machine learning to synthesize vast, image-derived datasets. As these technologies become more sophisticated and widely available, a team-science approach involving subspecialists with medical, engineering, and physics backgrounds is critical to upholding quality and validity in studies generating these data. The purpose of this manuscript is to detail the scientific premise, tools and training, quality control, and data collection and analysis considerations needed for the most prominent advanced imaging technologies currently applied in tissue sections: immunofluorescence, in situ hybridization, laser capture microdissection, matrix-assisted laser desorption ionization imaging mass spectrometry, and spectroscopic/optical methods. We conclude with a brief overview of future directions for ex vivo and in vivo imaging techniques.
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Affiliation(s)
- Lauren E Himmel
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Troy A Hackett
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Jessica L Moore
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Wilson R Adams
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Giju Thomas
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Tatiana Novitskaya
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Richard M Caprioli
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Andries Zijlstra
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Anita Mahadevan-Jansen
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Kelli L Boyd
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
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49
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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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50
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Kaya I, Brülls SM, Dunevall J, Jennische E, Lange S, Mårtensson J, Ewing AG, Malmberg P, Fletcher JS. On-Tissue Chemical Derivatization of Catecholamines Using 4-( N-Methyl)pyridinium Boronic Acid for ToF-SIMS and LDI-ToF Mass Spectrometry Imaging. Anal Chem 2018; 90:13580-13590. [PMID: 30346141 DOI: 10.1021/acs.analchem.8b03746] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The analysis of small polar compounds with ToF-SIMS and MALDI-ToF-MS have been generally hindered by low detection sensitivity, poor ionization efficiency, ion suppression, analyte in-source fragmentation, and background spectral interferences from either a MALDI matrix and/or endogenous tissue components. Chemical derivatization has been a well-established strategy for improved mass spectrometric detection of many small molecular weight endogenous compounds in tissues. Here, we present a devised strategy to selectively derivatize and sensitively detect catecholamines with both secondary ion ejection and laser desorption ionization strategies, which are used in many imaging mass spectrometry (IMS) experiments. Chemical derivatization of catecholamines was performed by a reaction with a synthesized permanent pyridinium-cation-containing boronic acid molecule, 4-( N-methyl)pyridinium boronic acid, through boronate ester formation (boronic acid-diol reaction). The derivatization facilitates their sensitive detection with ToF-SIMS and LDI-ToF mass spectrometric techniques. 4-( N-Methyl)pyridinium boronic acid worked as a reactive matrix for catecholamines with LDI and improved the sensitivity of detection for both SIMS and LDI, while the isotopic abundances of the boron atom reflect a unique isotopic pattern for derivatized catecholamines in MS analysis. Finally, the devised strategy was applied, as a proof of concept, for on-tissue chemical derivatization and GCIB-ToF-SIMS (down to 3 μm per pixel spatial resolution) and LDI-ToF mass spectrometry imaging of dopamine, epinephrine, and norepinephrine in porcine adrenal gland tissue sections. MS/MS using collision-induced dissociation (CID)-ToF-ToF-SIMS was subsequently employed on the same tissue sections after SIMS and LDI mass spectrometry imaging experiments, which provided tandem MS information for the validation of the derivatized catecholamines in situ. This methodology can be a powerful approach for the selective and sensitive ionization/detection and spatial localization of diol-containing molecules such as aminols, vic-diols, saccharides, and glycans along with catecholamines in tissue sections with both SIMS and LDI/MALDI-MS techniques.
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Affiliation(s)
- Ibrahim Kaya
- Department of Chemistry and Molecular Biology , University of Gothenburg , Kemivägen 10 , 405 30 Gothenburg , Sweden.,Department of Psychiatry and Neurochemistry , Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital , House V3, 43180 Mölndal , Sweden.,The Gothenburg Imaging Mass Spectrometry (Go: IMS) Laboratory , University of Gothenburg and Chalmers University of Technology , Gothenburg 412 96 , Sweden
| | - Steffen M Brülls
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , 412 96 Gothenburg , Sweden
| | - Johan Dunevall
- Department of Chemistry and Molecular Biology , University of Gothenburg , Kemivägen 10 , 405 30 Gothenburg , Sweden.,The Gothenburg Imaging Mass Spectrometry (Go: IMS) Laboratory , University of Gothenburg and Chalmers University of Technology , Gothenburg 412 96 , Sweden
| | - Eva Jennische
- Institute of Biomedicine , University of Gothenburg , Gothenburg 413 90 , Sweden
| | - Stefan Lange
- Institute of Biomedicine , University of Gothenburg , Gothenburg 413 90 , Sweden
| | - Jerker Mårtensson
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , 412 96 Gothenburg , Sweden
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology , University of Gothenburg , Kemivägen 10 , 405 30 Gothenburg , Sweden.,The Gothenburg Imaging Mass Spectrometry (Go: IMS) Laboratory , University of Gothenburg and Chalmers University of Technology , Gothenburg 412 96 , Sweden
| | - Per Malmberg
- The Gothenburg Imaging Mass Spectrometry (Go: IMS) Laboratory , University of Gothenburg and Chalmers University of Technology , Gothenburg 412 96 , Sweden.,Department of Chemistry and Chemical Engineering , Chalmers University of Technology , 412 96 Gothenburg , Sweden
| | - John S Fletcher
- Department of Chemistry and Molecular Biology , University of Gothenburg , Kemivägen 10 , 405 30 Gothenburg , Sweden.,The Gothenburg Imaging Mass Spectrometry (Go: IMS) Laboratory , University of Gothenburg and Chalmers University of Technology , Gothenburg 412 96 , Sweden
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