1
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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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2
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Phipps WS, Kilgore MR, Kennedy JJ, Whiteaker JR, Hoofnagle AN, Paulovich AG. Clinical Proteomics for Solid Organ Tissues. Mol Cell Proteomics 2023; 22:100648. [PMID: 37730181 PMCID: PMC10692389 DOI: 10.1016/j.mcpro.2023.100648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023] Open
Abstract
The evaluation of biopsied solid organ tissue has long relied on visual examination using a microscope. Immunohistochemistry is critical in this process, labeling and detecting cell lineage markers and therapeutic targets. However, while the practice of immunohistochemistry has reshaped diagnostic pathology and facilitated improvements in cancer treatment, it has also been subject to pervasive challenges with respect to standardization and reproducibility. Efforts are ongoing to improve immunohistochemistry, but for some applications, the benefit of such initiatives could be impeded by its reliance on monospecific antibody-protein reagents and limited multiplexing capacity. This perspective surveys the relevant challenges facing traditional immunohistochemistry and describes how mass spectrometry, particularly liquid chromatography-tandem mass spectrometry, could help alleviate problems. In particular, targeted mass spectrometry assays could facilitate measurements of individual proteins or analyte panels, using internal standards for more robust quantification and improved interlaboratory reproducibility. Meanwhile, untargeted mass spectrometry, showcased to date clinically in the form of amyloid typing, is inherently multiplexed, facilitating the detection and crude quantification of 100s to 1000s of proteins in a single analysis. Further, data-independent acquisition has yet to be applied in clinical practice, but offers particular strengths that could appeal to clinical users. Finally, we discuss the guidance that is needed to facilitate broader utilization in clinical environments and achieve standardization.
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Affiliation(s)
- William S Phipps
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark R Kilgore
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jacob J Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA; Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.
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3
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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4
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Claes BR, Krestensen KK, Yagnik G, Grgic A, Kuik C, Lim MJ, Rothschild KJ, Vandenbosch M, Heeren RMA. MALDI-IHC-Guided In-Depth Spatial Proteomics: Targeted and Untargeted MSI Combined. Anal Chem 2023; 95:2329-2338. [PMID: 36638208 PMCID: PMC9893213 DOI: 10.1021/acs.analchem.2c04220] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Recently, a novel technology was published, utilizing the strengths of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) and immunohistochemistry (IHC), achieving highly multiplexed, targeted imaging of biomolecules in tissue. This new technique, called MALDI-IHC, opened up workflows to target molecules of interest using MALDI-MSI that are usually targeted by standard IHC. In this paper, the utility of targeted MALDI-IHC and its complementarity with untargeted on-tissue bottom-up spatial proteomics is explored using breast cancer tissue. Furthermore, the MALDI-2 effect was investigated and demonstrated to improve MALDI-IHC. Formalin-fixed paraffin-embedded (FFPE) human breast cancer tissue sections were stained for multiplex MALDI-IHC with six photocleavable mass-tagged (PC-MT) antibodies constituting a breast cancer antibody panel (CD20, actin-αSM, HER2, CD68, vimentin, and panCK). K-means spatial clusters were created based on the MALDI-IHC images and cut out using laser-capture microdissection (LMD) for further untargeted LC-MS-based bottom-up proteomics analyses. Numerous peptides could be tentatively assigned to multiple proteins, of which three proteins were also part of the antibody panel (vimentin, keratins, and actin). Post-ionization with MALDI-2 showed an increased intensity of the PC-MTs and suggests options for the development of new mass-tags. Although the on-tissue digestion covered a wider range of proteins, the MALDI-IHC allowed for easy and straightforward identification of proteins that were not detected in untargeted approaches. The combination of the multiplexed MALDI-IHC with image-guided proteomics showed great potential to further investigate diseases by providing complementary information from the same tissue section and without the need for customized instrumentation.
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Affiliation(s)
- Britt
S. R. Claes
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Kasper K. Krestensen
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Gargey Yagnik
- AmberGen,
Inc., 44 Manning Road, Billerica, Massachusetts 01821, United States
| | - Andrej Grgic
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Christel Kuik
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Mark J. Lim
- AmberGen,
Inc., 44 Manning Road, Billerica, Massachusetts 01821, United States
| | - Kenneth J. Rothschild
- AmberGen,
Inc., 44 Manning Road, Billerica, Massachusetts 01821, United States,Molecular
Biophysics Laboratory, Department of Physics and Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Michiel Vandenbosch
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Ron M. A. Heeren
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands,
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5
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Lim MJ, Yagnik G, Henkel C, Frost SF, Bien T, Rothschild KJ. MALDI HiPLEX-IHC: multiomic and multimodal imaging of targeted intact proteins in tissues. Front Chem 2023; 11:1182404. [PMID: 37201132 PMCID: PMC10187789 DOI: 10.3389/fchem.2023.1182404] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/14/2023] [Indexed: 05/20/2023] Open
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is one of the most widely used methods for imaging the spatial distribution of unlabeled small molecules such as metabolites, lipids and drugs in tissues. Recent progress has enabled many improvements including the ability to achieve single cell spatial resolution, 3D-tissue image reconstruction, and the precise identification of different isomeric and isobaric molecules. However, MALDI-MSI of high molecular weight intact proteins in biospecimens has thus far been difficult to achieve. Conventional methods normally require in situ proteolysis and peptide mass fingerprinting, have low spatial resolution, and typically detect only the most highly abundant proteins in an untargeted manner. In addition, MSI-based multiomic and multimodal workflows are needed which can image both small molecules and intact proteins from the same tissue. Such a capability can provide a more comprehensive understanding of the vast complexity of biological systems at the organ, tissue, and cellular levels of both normal and pathological function. A recently introduced top-down spatial imaging approach known as MALDI HiPLEX-IHC (MALDI-IHC for short) provides a basis for achieving this high-information content imaging of tissues and even individual cells. Based on novel photocleavable mass-tags conjugated to antibody probes, high-plex, multimodal and multiomic MALDI-based workflows have been developed to image both small molecules and intact proteins on the same tissue sample. Dual-labeled antibody probes enable multimodal mass spectrometry and fluorescent imaging of targeted intact proteins. A similar approach using the same photocleavable mass-tags can be applied to lectin and other probes. We detail here several examples of MALDI-IHC workflows designed to enable high-plex, multiomic and multimodal imaging of tissues at a spatial resolution as low as 5 µm. This approach is compared to other existing high-plex methods such as imaging mass cytometry, MIBI-TOF, GeoMx and CODEX. Finally, future applications of MALDI-IHC are discussed.
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Affiliation(s)
- Mark J. Lim
- AmberGen, Inc., Billerica, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
| | | | | | | | - Tanja Bien
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Kenneth J. Rothschild
- AmberGen, Inc., Billerica, MA, United States
- Department of Physics and Photonics Center, Boston University, Boston, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
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6
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Liu M, Miao D, Qin S, Liu H, Bai Y. Mass tags-based mass spectrometric immunoassay and its bioanalysis applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Xu S, Liu H, Bai Y. Highly sensitive and multiplexed mass spectrometric immunoassay techniques and clinical applications. Anal Bioanal Chem 2022; 414:5121-5138. [PMID: 35165779 DOI: 10.1007/s00216-022-03945-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022]
Abstract
Immunoassay is one of the most important clinical techniques for disease/pathological diagnosis. Mass spectrometry (MS) has been a popular and powerful readout technique for immunoassays, generating the mass spectrometric immunoassays (MSIAs) with unbeatable channels for multiplexed detection. The sensitivity of MSIAs has been greatly improved with the development of mass labels from element labels to small-molecular labels. MSIAs are also expended from the representative element MS-based methods to the laser-based organic MS and latest ambient MS, improving in both technology and methodology. Various MSIAs present high potential for clinical applications, including the biomarker screening, the immunohistochemistry, and the advanced single-cell analysis. Here, we give an overall review of the development of MSIAs in recent years, highlighting the latest improvement of mass labels and MS techniques for clinical immunoassays.
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Affiliation(s)
- Shuting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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8
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Hu J, Liu F, Chen Y, Shangguan G, Ju H. Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules. ACS Sens 2021; 6:3517-3535. [PMID: 34529414 DOI: 10.1021/acssensors.1c01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.
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Affiliation(s)
- Junjie Hu
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Guoqiang Shangguan
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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9
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Stevens KG, McFarlane LO, Platts K, O'Brien-Simpson N, Li W, Blencowe A, Trim PJ, Pukala TL. Retro Diels-Alder Fragmentation of Fulvene-Maleimide Bioconjugates for Mass Spectrometric Detection of Biomolecules. Anal Chem 2021; 93:12204-12212. [PMID: 34461717 DOI: 10.1021/acs.analchem.1c00193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diels-Alder chemistry is a well-explored avenue for the synthesis of bioactive materials; however, its potential applications have recently expanded following the development of reactions that can be performed in buffered aqueous environments at low temperatures, including fulvene-maleimide [4 + 2] cycloadditions. In this study, we synthesized two novel amine-reactive fulvene linkers to demonstrate the application of this chemistry for generating mass spectrometry-cleavable labels ("mass tags"), which can be used for the labeling and detection of proteins. Successful conjugation of these linkers to maleimide-labeled peptides was observed at low temperatures in phosphate-buffered saline, allowing the non-destructive modification of proteins with such mass tags. The labile nature of fulvene-maleimide adducts in the gas phase also makes them suitable for both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometric analysis. Unlike previous examples of MALDI mass tags, we show that fulvene-maleimide cycloaddition adducts fragment predictably upon gas-phase activation without the need for bulky photocleavable groups. Further exploration of this chemistry could therefore lead to new approaches for mass spectrometry-based bioassays.
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Affiliation(s)
- Katherine G Stevens
- Department of Chemistry, Faculty of Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Lewis O McFarlane
- Department of Chemistry, Faculty of Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Kirsten Platts
- Applied Chemistry and Translational Biomaterials Group, Clinical and Health Sciences, The University of South Australia, Adelaide, South Australia 5000, Australia
| | - Neil O'Brien-Simpson
- Centre for Oral Health Research, The Melbourne Dental School and the Bio21 Institute, The University of Melbourne, 720 Swanston Street, Carlton, Melbourne, Victoria 3010, Australia
| | - Wenyi Li
- Centre for Oral Health Research, The Melbourne Dental School and the Bio21 Institute, The University of Melbourne, 720 Swanston Street, Carlton, Melbourne, Victoria 3010, Australia
| | - Anton Blencowe
- Applied Chemistry and Translational Biomaterials Group, Clinical and Health Sciences, The University of South Australia, Adelaide, South Australia 5000, Australia
| | - Paul J Trim
- Proteomics, Metabolomics and MS Imaging, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
| | - Tara L Pukala
- Department of Chemistry, Faculty of Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
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10
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Yagnik G, Liu Z, Rothschild KJ, Lim MJ. Highly Multiplexed Immunohistochemical MALDI-MS Imaging of Biomarkers in Tissues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:977-988. [PMID: 33631930 PMCID: PMC8033562 DOI: 10.1021/jasms.0c00473] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Immunohistochemistry (IHC) combined with fluorescence microscopy provides an important and widely used tool for researchers and pathologists to image multiple biomarkers in tissue specimens. However, multiplex IHC using standard fluorescence microscopy is generally limited to 3-5 different biomarkers, with hyperspectral or multispectral methods limited to 8. We report the development of a new technology based on novel photocleavable mass-tags (PC-MTs) for facile antibody labeling, which enables highly multiplexed IHC based on MALDI mass spectrometric imaging (MALDI-IHC). This approach significantly exceeds the multiplexity of both fluorescence- and previous cleavable mass-tag-based methods. Up to 12-plex MALDI-IHC was demonstrated on mouse brain, human tonsil, and breast cancer tissues specimens, reflecting the known molecular composition, anatomy, and pathology of the targeted biomarkers. Novel dual-labeled fluorescent PC-MT antibodies and label-free small-molecule mass spectrometric imaging greatly extend the capability of this new approach. MALDI-IHC shows promise for use in the fields of tissue pathology, tissue diagnostics, therapeutics, and precision medicine.
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Affiliation(s)
- Gargey Yagnik
- AmberGen,
Inc., 313 Pleasant Street, Watertown, Massachusetts 02472, United States
| | - Ziying Liu
- AmberGen,
Inc., 313 Pleasant Street, Watertown, Massachusetts 02472, United States
| | - Kenneth J. Rothschild
- AmberGen,
Inc., 313 Pleasant Street, Watertown, Massachusetts 02472, United States
- Molecular
Biophysics Laboratory, Department of Physics and Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Mark J. Lim
- AmberGen,
Inc., 313 Pleasant Street, Watertown, Massachusetts 02472, United States
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11
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McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM. Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4663. [PMID: 33241625 DOI: 10.26434/chemrxiv.12494705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/14/2020] [Indexed: 05/18/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, untargeted detection of many hundreds of analytes from tissue. Recently, laser postionization (MALDI-2) has been developed for increased ion yield and sensitivity for lipid IMS. However, the dependence of MALDI-2 performance on the various lipid classes is largely unknown. To understand the effect of the applied matrix on MALDI-2 analysis of lipids, samples including an equimolar lipid standard mixture, various tissue homogenates, and intact rat kidney tissue sections were analyzed using the following matrices: α-cyano-4-hydroxycinnamic acid, 2',5'-dihydroxyacetophenone, 2',5'-dihydroxybenzoic acid (DHB), and norharmane (NOR). Lipid signal enhancement of protonated species using MALDI-2 technology varied based on the matrix used. Although signal improvements were observed for all matrices, the most dramatic effects using MALDI-2 were observed using NOR and DHB. For lipid standards analyzed by MALDI-2, NOR provided the broadest coverage, enabling the detection of all 13 protonated standards, including nonpolar lipids, whereas DHB gave less coverage but gave the highest signal increase for those lipids recorded. With respect to tissue homogenates and rat kidney tissue, mass spectra were compared and showed that the number and intensity of neutral lipids tentatively identified with MALDI-2 using NOR increased significantly (e.g., fivefold intensity increase for triacylglycerol). In the cases of DHB with MALDI-2, the number of protonated lipids identified from tissue homogenates doubled with 152 on average compared with 76 with MALDI alone. High spatial resolution imaging (~20 μm) of rat kidney tissue showed similar results using DHB with 125 lipids tentatively identified from MALDI-2 spectra versus just 72 using standard MALDI. From the four matrices tested, NOR provided the greatest increase in sensitivity for neutral lipids (triacylglycerol, diacylglycerol, monoacylglycerol, and cholesterol ester), and DHB provided the highest overall number of lipids detected using MALDI-2 technology.
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Affiliation(s)
- Josiah C McMillen
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
| | - Jarod A Fincher
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Dustin R Klein
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, 37232, USA
- Departments of Biochemistry, Pharmacology and Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
- Department of Pharmacology, Vanderbilt University
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, 37232, USA
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12
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McMillen JC, Fincher JA, Klein DR, Spraggins JM, Caprioli RM. Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4663. [PMID: 33241625 PMCID: PMC8099046 DOI: 10.1002/jms.4663] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/14/2020] [Indexed: 05/04/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, untargeted detection of many hundreds of analytes from tissue. Recently, laser postionization (MALDI-2) has been developed for increased ion yield and sensitivity for lipid IMS. However, the dependence of MALDI-2 performance on the various lipid classes is largely unknown. To understand the effect of the applied matrix on MALDI-2 analysis of lipids, samples including an equimolar lipid standard mixture, various tissue homogenates, and intact rat kidney tissue sections were analyzed using the following matrices: α-cyano-4-hydroxycinnamic acid, 2',5'-dihydroxyacetophenone, 2',5'-dihydroxybenzoic acid (DHB), and norharmane (NOR). Lipid signal enhancement of protonated species using MALDI-2 technology varied based on the matrix used. Although signal improvements were observed for all matrices, the most dramatic effects using MALDI-2 were observed using NOR and DHB. For lipid standards analyzed by MALDI-2, NOR provided the broadest coverage, enabling the detection of all 13 protonated standards, including nonpolar lipids, whereas DHB gave less coverage but gave the highest signal increase for those lipids recorded. With respect to tissue homogenates and rat kidney tissue, mass spectra were compared and showed that the number and intensity of neutral lipids tentatively identified with MALDI-2 using NOR increased significantly (e.g., fivefold intensity increase for triacylglycerol). In the cases of DHB with MALDI-2, the number of protonated lipids identified from tissue homogenates doubled with 152 on average compared with 76 with MALDI alone. High spatial resolution imaging (~20 μm) of rat kidney tissue showed similar results using DHB with 125 lipids tentatively identified from MALDI-2 spectra versus just 72 using standard MALDI. From the four matrices tested, NOR provided the greatest increase in sensitivity for neutral lipids (triacylglycerol, diacylglycerol, monoacylglycerol, and cholesterol ester), and DHB provided the highest overall number of lipids detected using MALDI-2 technology.
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Affiliation(s)
- Josiah C. McMillen
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jarod A. Fincher
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Dustin R. Klein
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Jeffrey M. Spraggins
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Mass Spectrometry Research Center, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Pharmacology, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN 37232
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13
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Abstract
Mass spectrometry imaging (MSI) is a label-free molecular imaging technique allowing an untargeted detection of a broad range of biomolecules and xenobiotics. MSI enables imaging of the spatial distribution of proteins, peptides, lipids and metabolites from a wide range of samples. To date, this technique is commonly applied to tissue sections in cancer diagnostics and biomarker development, but also molecular histology in general. Advances in the methodology and bioinformatics improved the resolution of MS images below the single cell level and increased the flexibility of the workflow. However, MSI-based research in virology is just starting to gain momentum and its full potential has not been exploited yet. In this review, we discuss the main applications of MSI in virology. We review important aspects of matrix-assisted laser desorption/ionization (MALDI) MSI, the most widely used MSI technique in virology. In addition, we summarize relevant literature on MSI studies that aim to unravel virus-host interactions and virus pathogenesis, to elucidate antiviral drug kinetics and to improve current viral disease diagnostics. Collectively, these studies strongly improve our general understanding of virus-induced changes in the proteome, metabolome and metabolite distribution in host tissues of humans, animals and plants upon infection. Furthermore, latest MSI research provided important insights into the drug distribution and distribution kinetics, especially in antiretroviral research. Finally, MSI-based investigations of oncogenic viruses greatly increased our knowledge on tumor mass signatures and facilitated the identification of cancer biomarkers.
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Affiliation(s)
- Luca D Bertzbach
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | | | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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14
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Stevens KG, Pukala TL. Conjugating immunoassays to mass spectrometry: Solutions to contemporary challenges in clinical diagnostics. Trends Analyt Chem 2020; 132:116064. [PMID: 33046944 PMCID: PMC7539833 DOI: 10.1016/j.trac.2020.116064] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Developments in immunoassays and mass spectrometry have independently influenced diagnostic technology. However, both techniques possess unique strengths and limitations, which define their ability to meet evolving requirements for faster, more affordable and more accurate clinical tests. In response, hybrid techniques, which combine the accessibility and ease-of-use of immunoassays with the sensitivity, high throughput and multiplexing capabilities of mass spectrometry are continually being explored. Developments in antibody conjugation methodology have expanded the role of these biomolecules to applications outside of conventional colorimetric assays and histology. Furthermore, the range of different mass spectrometry ionisation and analysis technologies has enabled its successful adaptation as a detection method for numerous clinically relevant immunological assays. Several recent examples of combined mass spectrometry-immunoassay techniques demonstrate the potential of these methods as improved diagnostic tests for several important human diseases. The present challenges are to continue technological advancements in mass spectrometry instrumentation and develop improved bioconjugation methods, which can overcome their existing limitations and demonstrate the clinical significance of these hybrid approaches.
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15
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Han J, Sun J, Song S, Beljaars L, Groothuis GMM, Permentier H, Bischoff R, Halmos GB, Verhoeven CJ, Amstalden van Hove ER, Horvatovich P, Casini A. Targeted imaging of integrins in cancer tissues using photocleavable Ru(ii) polypyridine complexes as mass-tags. Chem Commun (Camb) 2020; 56:5941-5944. [PMID: 32347235 DOI: 10.1039/d0cc00774a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Targeted epitope-based mass spectrometry imaging (MSI) utilizes laser cleavable mass-tags bound to targeting moieties for detecting proteins in tissue sections. Our work constitutes the first proof-of-concept of a novel laser desorption ionization (LDI)-MSI strategy using photocleavable Ru(ii) polypyridine complexes as mass-tags for imaging of integrins αvβ3 in human cancer tissues.
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Affiliation(s)
- Jiaying Han
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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16
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Ahmed M, Broeckx G, Baggerman G, Schildermans K, Pauwels P, Van Craenenbroeck AH, Dendooven A. Next-generation protein analysis in the pathology department. J Clin Pathol 2019; 73:1-6. [DOI: 10.1136/jclinpath-2019-205864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/12/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
Abstract
Traditionally, immunohistochemistry (IHC) is used by pathologists to localise specific proteins or peptides in tissue slides. In the era of personalised medicine, however, molecular tissue analysis becomes indispensable for correct diagnosis, prognosis and therapeutic decision, not only on the DNA or mRNA level but also on the protein level. Combining molecular information with imaging presents many advantages. Therefore, matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) is a promising technique to be added to the armamentarium of the pathologist. Here, we focus on the workflow, advantages and drawbacks of both MALDI IMS and IHC. We also briefly discuss a few other protein imaging modalities and give examples of applications.
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17
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Han J, Permentier H, Bischoff R, Groothuis G, Casini A, Horvatovich P. Imaging of protein distribution in tissues using mass spectrometry: An interdisciplinary challenge. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Xu S, Ma W, Bai Y, Liu H. Ultrasensitive Ambient Mass Spectrometry Immunoassays: Multiplexed Detection of Proteins in Serum and on Cell Surfaces. J Am Chem Soc 2018; 141:72-75. [DOI: 10.1021/jacs.8b10853] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shuting Xu
- Beijing National Laboratory for Molecular Sciences,
Key Laboratory of Bioorganic Chemistry and Molecular Engineering of
Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Wen Ma
- Beijing National Laboratory for Molecular Sciences,
Key Laboratory of Bioorganic Chemistry and Molecular Engineering of
Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences,
Key Laboratory of Bioorganic Chemistry and Molecular Engineering of
Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences,
Key Laboratory of Bioorganic Chemistry and Molecular Engineering of
Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
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19
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Li H, Popp R, Borchers CH. Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Abstract
Over the last decade mass spectrometry imaging (MSI) has been integrated in to many areas of drug discovery and development. It can have significant impact in oncology drug discovery as it allows efficacy and safety of compounds to be assessed against the backdrop of the complex tumour microenvironment. We will discuss the roles of MSI in investigating compound and metabolite biodistribution and defining pharmacokinetic -pharmacodynamic relationships, analysis that is applicable to all drug discovery projects. We will then look more specifically at how MSI can be used to understand tumour metabolism and other applications specific to oncology research. This will all be described alongside the challenges of applying MSI to industry research with increased use of metrology for MSI.
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21
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Kang N, Lee JM, Jeon A, Oh HB, Moon B. Design and synthesis of new mass tags for matrix-free laser desorption ionization mass spectrometry (LDI-MS) based on 6,11-dihydrothiochromeno[4,3-b]indole. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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22
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23
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Wang H, DeGnore JP, Kelly BD, True J, Garsha K, Bieniarz C. A technique for relative quantitation of cancer biomarkers in formalin-fixed, paraffin-embedded (FFPE) tissue using stable-isotope-label based mass spectrometry imaging (SILMSI). JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:1088-1095. [PMID: 28338251 DOI: 10.1002/jms.3623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/08/2015] [Accepted: 05/16/2015] [Indexed: 06/06/2023]
Abstract
We developed a novel technique for the relative quantitation of pairs of cancer biomarkers in formalin-fixed paraffin-embedded (FFPE) tissue. The method utilizes stable isotope labeled (SIL) chromogens deposited during the standard immunohistochemistry (IHC) tissue staining process. The labeled chromogens are precipitated on tissue enzymatically using the standard IHC protocols. The tissue is then imaged with matrix-free laser desorption ionization time-of-flight mass spectrometry, and peak intensities of reporter ions are used to estimate the relative quantitation of protein biomarkers across the tissue. The relative abundance of two breast cancer biomarkers, estrogen receptor (ER) and progesterone receptor (PgR), were quantitated using their ratio of expression in xenograft models, and the ratios were found to be reproducible both within and across serial sections. The relative quantification of multiple biomarkers in situ across a single tissue section adds an additional dimension in cancer histological evaluation by allowing a visual and statistical assessment of tumor heterogeneity. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Hong Wang
- Clinical Cancer Prevention, MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX, 77030, USA
| | - Jon P DeGnore
- Ventana Medical Systems, Inc., 1910 E. Innovation Park Drive, Tucson, AZ, 85755, USA
| | - Brian D Kelly
- Ventana Medical Systems, Inc., 1910 E. Innovation Park Drive, Tucson, AZ, 85755, USA
| | - Jan True
- Ventana Medical Systems, Inc., 1910 E. Innovation Park Drive, Tucson, AZ, 85755, USA
| | - Karl Garsha
- Ventana Medical Systems, Inc., 1910 E. Innovation Park Drive, Tucson, AZ, 85755, USA
| | - Christopher Bieniarz
- Ventana Medical Systems, Inc., 1910 E. Innovation Park Drive, Tucson, AZ, 85755, USA
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24
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Lorey M, Adler B, Yan H, Soliymani R, Ekström S, Yli-Kauhaluoma J, Laurell T, Baumann M. Mass-Tag Enhanced Immuno-Laser Desorption/Ionization Mass Spectrometry for Sensitive Detection of Intact Protein Antigens. Anal Chem 2015; 87:5255-62. [DOI: 10.1021/acs.analchem.5b00304] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Martina Lorey
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
- Institute
of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FI-00014, Finland
- Unit
of Systems Toxicology, Finnish Institute of Occupational Health, Topeliuksenkatu 41 b, FI-00250 Helsinki, Finland
| | - Belinda Adler
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Hong Yan
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Rabah Soliymani
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
| | - Simon Ekström
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Jari Yli-Kauhaluoma
- Division
of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 University of Helsinki, Finland
| | - Thomas Laurell
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
- Department
of Biomedical Engineering, Dongguk University, 202 Science Building Phildong 3ga. Joong-Gu Seoul, Republic of Korea
| | - Marc Baumann
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
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25
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Abstract
Enriched by a decade of remarkable developments, matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has witnessed a phenomenal expansion. Initially introduced for the mapping of peptides and intact proteins from mammalian tissue sections, MALDI IMS applications now extend to a wide range of molecules including peptides, lipids, metabolites and xenobiotics. Technology and methodology are quickly evolving to push the limits of the technique forward. Within a short period of time, numerous protocols and concepts have been developed and introduced in tissue section preparation, nonexhaustively including in situ tissue chemistries and solvent-free matrix depositions. Considering the past progress and current capabilities, this Review aims to cover the different aspects and challenges of tissue section preparation for MALDI IMS.
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26
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Fournaise E, Chaurand P. Increasing specificity in imaging mass spectrometry: high spatial fidelity transfer of proteins from tissue sections to functionalized surfaces. Anal Bioanal Chem 2014; 407:2159-66. [DOI: 10.1007/s00216-014-8300-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 01/05/2023]
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27
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Ball RJ, Green PS, Gale N, Langley GJ, Brown T. Peptide nucleic acid probes with charged photocleavable mass markers: Towards PNA-based MALDI-TOF MS genetic analysis. ARTIFICIAL DNA, PNA & XNA 2014; 1:27-35. [PMID: 21687524 DOI: 10.4161/adna.1.1.12199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 04/06/2010] [Accepted: 04/30/2010] [Indexed: 01/18/2023]
Abstract
Halogen-labelled peptide organic acid (HPOA) monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid (PNA) probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA.
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Affiliation(s)
- Rachel J Ball
- School of Chemistry; University of Southampton; Southampton, UK
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28
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Kopp C, Wisztorski M, Revel J, Mehiri M, Dani V, Capron L, Carette D, Fournier I, Massi L, Mouajjah D, Pagnotta S, Priouzeau F, Salzet M, Meibom A, Sabourault C. MALDI-MS and NanoSIMS imaging techniques to study cnidarian-dinoflagellate symbioses. ZOOLOGY 2014; 118:125-31. [PMID: 25447219 DOI: 10.1016/j.zool.2014.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/29/2014] [Accepted: 06/30/2014] [Indexed: 12/22/2022]
Abstract
Cnidarian-dinoflagellate photosynthetic symbioses are fundamental to biologically diverse and productive coral reef ecosystems. The hallmark of this symbiotic relationship is the ability of dinoflagellate symbionts to supply their cnidarian host with a wide range of nutrients. Many aspects of this association nevertheless remain poorly characterized, including the exact identity of the transferred metabolic compounds, the mechanisms that control their exchange across the host-symbiont interface, and the precise subcellular fate of the translocated materials in cnidarian tissues. This lack of knowledge is mainly attributed to difficulties in investigating such metabolic interactions both in situ, i.e. on intact symbiotic associations, and at high spatial resolution. To address these issues, we illustrate the application of two in situ and high spatial resolution molecular and ion imaging techniques-matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and the nano-scale secondary-ion mass spectrometry (NanoSIMS) ion microprobe. These imaging techniques provide important new opportunities for the detailed investigation of many aspects of cnidarian-dinoflagellate associations, including the dynamics of cellular interactions.
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Affiliation(s)
- C Kopp
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - M Wisztorski
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - J Revel
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France
| | - M Mehiri
- UMR7272 University of Nice-Sophia Antipolis, CNRS, Institut de Chimie de Nice, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - V Dani
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France
| | - L Capron
- UMR7272 University of Nice-Sophia Antipolis, CNRS, Institut de Chimie de Nice, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - D Carette
- CCMA, University of Nice-Sophia Antipolis, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - I Fournier
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - L Massi
- UMR7272 University of Nice-Sophia Antipolis, CNRS, Institut de Chimie de Nice, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - D Mouajjah
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - S Pagnotta
- CCMA, University of Nice-Sophia Antipolis, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France
| | - F Priouzeau
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France
| | - M Salzet
- PRISM, University of Lille 1, EA 4550 - FRE3637 CNRS, Bat SN3, F-59655 Villeneuve d'Ascq Cedex, France
| | - A Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - C Sabourault
- UMR7138 University of Nice-Sophia Antipolis, CNRS, Faculty of Science, 28 Avenue Valrose, BP 71, F-06108 Nice Cedex 2, France; UMR7138 Sorbonne University Paris 6, CNRS, Institut de Biologie Paris-Seine, 7 quai Saint Bernard, 75005 Paris, France.
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29
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Longuespée R, Boyon C, Desmons A, Kerdraon O, Leblanc E, Farré I, Vinatier D, Day R, Fournier I, Salzet M. Spectroimmunohistochemistry: A Novel Form of MALDI Mass Spectrometry Imaging Coupled to Immunohistochemistry for Tracking Antibodies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:132-41. [DOI: 10.1089/omi.2013.0075] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rémi Longuespée
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Institut de Pharmacologie de Sherbrooke, Département de Chirurgie/Urologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Charlotte Boyon
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Hôpital Jeanne de Flandre, Service de Chirurgie Gynécologique, Lille Cedex, France
| | - Annie Desmons
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
| | - Olivier Kerdraon
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Laboratoire d'Anatomie et de Cytologie Pathologiques, CHRU Lille, Lille Cedex, France
| | - Eric Leblanc
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Centre Oscar-Lambret, Département de Cancérologie Gynécologique, Lille Cedex, France
| | - Isabelle Farré
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Centre Oscar-Lambret, Département de Cancérologie Gynécologique, Lille Cedex, France
| | - Denis Vinatier
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
- Hôpital Jeanne de Flandre, Service de Chirurgie Gynécologique, Lille Cedex, France
| | - Robert Day
- Laboratoire d'Anatomie et de Cytologie Pathologiques, CHRU Lille, Lille Cedex, France
| | - Isabelle Fournier
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
| | - Michel Salzet
- Laboratoire PRISM : Protéomique, Réponse Inflammatoire, Spectrométrie de Masse, Cité Scientifique, Villeneuve D'Ascq, Lille Cedex, France
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30
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Hong R, True J, Bieniarz C. Enzymatically Amplified Mass Tags for Tissue Mass Spectrometry Imaging. Anal Chem 2014; 86:1459-67. [DOI: 10.1021/ac402718f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rui Hong
- Ventana Medical Systems, Inc., Technology and Applied Research, 1910 E. Innovation Park Drive, Oro Valley, Arizona 85755, United States
| | - Jan True
- Ventana Medical Systems, Inc., Technology and Applied Research, 1910 E. Innovation Park Drive, Oro Valley, Arizona 85755, United States
| | - Christopher Bieniarz
- Ventana Medical Systems, Inc., Technology and Applied Research, 1910 E. Innovation Park Drive, Oro Valley, Arizona 85755, United States
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31
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Applications of organoboron compounds in carbohydrate chemistry and glycobiology: analysis, separation, protection, and activation. Carbohydr Res 2013; 381:112-22. [DOI: 10.1016/j.carres.2013.09.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 01/05/2023]
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Abstract
Lectins are proteins of non-immune origin that bind specific carbohydrates without chemical modification. Coupled with the emerging biological and pathological significance of carbohydrates, lectins have become extensively used as research tools in glycobiology. However, lectin-based drug development has been impeded by high manufacturing costs, low chemical stability, and the potential risk of initiating an unfavorable immune response. As alternatives to lectins, non-protein small molecules having carbohydrate-binding properties (lectin mimics) are currently attracting a great deal of attention because of their ease of preparation and chemical modification. Lectin mimics of synthetic origin are divided roughly into two groups, boronic acid-dependent and boronic acid-independent lectin mimics. This article outlines their representative architectures and carbohydrate-binding properties, and discusses their therapeutic potential by reviewing recent attempts to develop antiviral and antimicrobial agents using their architectures. We also focus on the naturally occurring lectin mimics, pradimicins and benanomicins. They are the only class of non-protein natural products having a C-type lectin-like ability to recognize d-mannopyranosides in the presence of Ca2 + ions. Their molecular basis of carbohydrate recognition and therapeutic potential are also discussed.
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Affiliation(s)
- Yu Nakagawa
- Synthetic Cellular Chemistry Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
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33
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TARGETED MASS spectrometry Imaging: Specific Targeting Mass Spectrometry imaging technologies from history to perspective. ACTA ACUST UNITED AC 2012; 47:133-74. [DOI: 10.1016/j.proghi.2012.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2012] [Indexed: 12/28/2022]
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34
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Mass spectrometry imaging is moving toward drug protein co-localization. Trends Biotechnol 2012; 30:466-74. [DOI: 10.1016/j.tibtech.2012.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/23/2012] [Accepted: 05/24/2012] [Indexed: 12/20/2022]
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35
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Probe-based chemical modulations of tissues for IMS. J Proteomics 2012; 75:4921-4930. [PMID: 22634403 DOI: 10.1016/j.jprot.2012.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/14/2012] [Accepted: 05/17/2012] [Indexed: 12/20/2022]
Abstract
Chemical modulation imaging over a tissue is gaining momentum in the field of mass spectrometry. Some endogenous or exogenous compounds present in a tissue can be visualized by imaging mass spectrometry after chemical derivatization. This approach gives researchers the possibility to elude chemical interferences in components of the tissues, such as lipids or salts, as well as interferences caused by the matrix. The use of primary and secondary antibodies, the chemical derivatization of peptides and small molecules, and the use of (18)O labeling are various examples reviewed in this article to demonstrate the importance and potential of this emerging aspect of imaging mass spectrometry.
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36
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Yang J, Chaurand P, Norris JL, Porter NA, Caprioli RM. Activity-based probes linked with laser-cleavable mass tags for signal amplification in imaging mass spectrometry: analysis of serine hydrolase enzymes in mammalian tissue. Anal Chem 2012; 84:3689-95. [PMID: 22424244 PMCID: PMC3328658 DOI: 10.1021/ac300203v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A novel functional imaging mass spectrometry technology is described that utilizes activity-based probes for imaging enzyme active sites in tissue sections. We demonstrate this technology using an activity-based probe (fluorophosphate) that is specific for serine hydrolases. A dendrimer containing multiple mass tags that is attached to the activity-based probe is used to analyze the binding sites of the probe through release and measurement of the mass tags on laser irradiation. A generation 8 poly(amido amine) dendrimer with 1024 amino groups was labeled with an azide group, and then, more than 900 mass tags were attached in order to achieve signal amplification of nearly 3 orders of magnitude. The experimental protocol first involves binding of the activity-based probe containing an alkyne group to serine hydrolases in the tissue section followed by attachment of the dendrimer labeled with mass tags to the bound probe by Click chemistry. On irradiation of the labeled tissue by the laser beam in a raster pattern, the mass tags are liberated and recorded by the mass analyzer; consequently, the ion image of the mass tag reveals the distribution of serine hydrolases in the tissue. This process was shown using rat brain and mouse embryo sections. Targeted imaging has the advantage of providing high spatial resolution and high sensitivity through the use of signal amplification chemistry with high target specificity through the use of an enzyme activity probe.
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Affiliation(s)
- Junhai Yang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Pierre Chaurand
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - Jeremy L. Norris
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Ned A. Porter
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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37
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Le PAIR-gynécologie : recherche multi/interdisciplinaire en cancérologie gynécologique. Les problèmes à résoudre en 2012. Bull Cancer 2012; 99:479-98. [DOI: 10.1684/bdc.2012.1558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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38
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Lagarrigue M, Lavigne R, Guével B, Com E, Chaurand P, Pineau C. Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry: A Promising Technique for Reproductive Research1. Biol Reprod 2012; 86:74. [DOI: 10.1095/biolreprod.111.094896] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Santos HM, Kouvonen P, Capelo JL, Corthals GL. Isotopic labelling of peptides in tissues enhances mass spectrometric profiling. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:254-262. [PMID: 22223310 DOI: 10.1002/rcm.5325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE There is a need in imaging mass spectrometry to use the acquired isotope distribution to unequivocally determine the identity of a peptide ion. A way of achieving unambiguous differentiation of ions from protonated peptides from other [M + H](+) ions in a tissue would be via the direct on-tissue incorporation of (18)O into peptides. METHODS Tissues were first digested with trypsin for 3 h at 37 °C in a humidified chamber. For the (18)O-labelling of digested peptides 1 μL of H(2)(18)O/50 mM ammonium acetate (at pH 6.75) was added to the array of tryptic spots and incubated at room temperature for 20 min. α-Cyano-4-hydroxycinnamic acid was used as a matrix modifier. The mass spectral analysis of tissue sections was carried out using a matrix-assisted laser desorption/ionisation tandem time-of-flight (MALDI-TOF-TOF) instrument. RESULTS On-tissue incorporation of (18)O into peptides cannot be carried out during the digestion step inside a humidified chamber. After tissue digestion for 3 h at 37 °C in an humidified chamber, (18)O labelling was carried out for 20 min at room temperature (no humidified chamber). No trypsin was needed to enhance the labelling. CONCLUSIONS For first time the feasibility of (18)O-labelling of peptides in situ for tissues has been demonstrated. The method decouples protein digestion from peptide labelling and is performed in sequential steps. Furthermore, we observed that (18)O incorporation produces characteristic isotopic peptide distributions, thus making facile distinguishing peptides from other tissue molecular components that ionise in the MALDI ion source.
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Affiliation(s)
- Hugo M Santos
- REQUIMTE-CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
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40
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Cleavable linkers in chemical biology. Bioorg Med Chem 2012; 20:571-82. [DOI: 10.1016/j.bmc.2011.07.048] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/08/2011] [Accepted: 07/23/2011] [Indexed: 01/11/2023]
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41
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Dai C, Cazares LH, Wang L, Chu Y, Wang SL, Troyer DA, Semmes OJ, Drake RR, Wang B. Using boronolectin in MALDI-MS imaging for the histological analysis of cancer tissue expressing the sialyl Lewis X antigen. Chem Commun (Camb) 2011; 47:10338-40. [PMID: 21853197 DOI: 10.1039/c1cc11814e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Certain carbohydrate-based biomarkers are known to correlate with cancer formation and progression. By targeting sialyl Lewis X, we have developed the first boronolectin-MS tag conjugate, which allows for MALDI-based imaging of cancer based on its cell surface carbohydrate.
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Affiliation(s)
- Chaofeng Dai
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-4098, USA
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42
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MALDI imaging mass spectrometry for direct tissue analysis: technological advancements and recent applications. Histochem Cell Biol 2011; 136:227-44. [PMID: 21805154 DOI: 10.1007/s00418-011-0843-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2011] [Indexed: 12/29/2022]
Abstract
Matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a method that allows the investigation of the molecular content of tissues within its morphological context. Since it is able to measure the distribution of hundreds of analytes at once, while being label free, this method has great potential which has been increasingly recognized in the field of tissue-based research. In the last few years, MALDI-IMS has been successfully used for the molecular assessment of tissue samples mainly in biomedical research and also in other scientific fields. The present article will give an update on the application of MALDI-IMS in clinical and preclinical research. It will also give an overview of the multitude of technical advancements of this method in recent years. This includes developments in instrumentation, sample preparation, computational data analysis and protein identification. It will also highlight a number of emerging fields for application of MALDI-IMS like drug imaging where MALDI-IMS is used for studying the spatial distribution of drugs in tissues.
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Cazares LH, Troyer DA, Wang B, Drake RR, Semmes OJ. MALDI tissue imaging: from biomarker discovery to clinical applications. Anal Bioanal Chem 2011; 401:17-27. [PMID: 21541816 PMCID: PMC6037172 DOI: 10.1007/s00216-011-5003-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/31/2011] [Accepted: 04/08/2011] [Indexed: 11/26/2022]
Abstract
Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for the generation of multidimensional spatial expression maps of biomolecules directly from a tissue section. From a clinical proteomics perspective, this method correlates molecular detail to histopathological changes found in patient-derived tissues, enhancing the ability to identify candidates for disease biomarkers. The unbiased analysis and spatial mapping of a variety of molecules directly from clinical tissue sections can be achieved through this method. Conversely, targeted IMS, by the incorporation of laser-reactive molecular tags onto antibodies, aptamers, and other affinity molecules, enables analysis of specific molecules or a class of molecules. In addition to exploring tissue during biomarker discovery, the integration of MALDI-IMS methods into existing clinical pathology laboratory practices could prove beneficial to diagnostics. Querying tissue for the expression of specific biomarkers in a biopsy is a critical component in clinical decision-making and such markers are a major goal of translational research. An important challenge in cancer diagnostics will be to assay multiple parameters in a single slide when tissue quantities are limited. The development of multiplexed assays that maximize the yield of information from a small biopsy will help meet a critical challenge to current biomarker research. This review focuses on the use of MALDI-IMS in biomarker discovery and its potential as a clinical diagnostic tool with specific reference to our application of this technology to prostate cancer.
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Affiliation(s)
- Lisa H Cazares
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
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44
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Qiu F, Gu K, Yang B, Ding Y, Jiang D, Wu Y, Huang LL. DNA assay based on monolayer-barcoded nanoparticles for mass spectrometry in combination with magnetic microprobes. Talanta 2011; 85:1698-702. [PMID: 21807242 DOI: 10.1016/j.talanta.2011.06.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) based methodology offers simple, fast and sensitive diagnosis. While it has become the predominate approach in biomolecular analysis, it has not been suitable for analyzing nucleic acid due to its low ionization efficiency. We report herein on a DNA assay based on monolayer-barcoded nanoparticles that were encoded with reporter mass molecules, which act as surrogate molecules for the matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF MS) identification of target DNA through mass spectrometry in combination with magnetic microprobes. This assay demonstrated high MS sensitivity, with the ability to detect target DNA at femtomolar (10(-15) M) levels. This inaugural effort using combined techniques is significant because it showed an extraordinary analytical capability for differentiating the single nucleotide polymorphism (SNP), which comprises the most abundant source of genetic variation in the human genome. We also report herein the feasibility of MS detection of two target DNAs that have the same mass but different nucleotide base composition, which classic MS methodology is inherently unable to differentiate.
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Affiliation(s)
- Fei Qiu
- Institute of Molecular Medicine, Huaqiao University, Quanzhou, PR China
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45
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Abstract
Previously, MS was often used to analyze the composition and structure of biological molecules present in solutions. Today, technology developments enable the application of MS for the analysis of localized biomolecules on biological tissue surfaces. This technique is called MS imaging. MALDI imaging MS is a technique whereby thousands of compounds present in a tissue section are detected simultaneously without labeling. Although initially used for the detection of biomolecules such as peptides and proteins, this technology is also used today for drug detection. These characteristics make MS imaging an ideal technology that is perfectly adapted for ADME (absorption, distribution, metabolism and excretion) studies. In fact, this technology facilitates the tracking of one or several administered drugs, as well as the metabolites that result from their assimilations. In this article, we will present the various possibilities that MALDI imaging MS approaches have to offer for the study of drugs and their metabolites using MS, MS/MS, FAST-SRM and MRM modes. In this context, we investigate two studies: the distribution of olanzapine in the kidney and the overall distribution of BDM31343 in mouse whole-body section.
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46
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Urban PL, Amantonico A, Zenobi R. Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. MASS SPECTROMETRY REVIEWS 2011; 30:435-478. [PMID: 21254192 DOI: 10.1002/mas.20288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
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Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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47
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Yang L, Tang X, Weisbrod CR, Munske GR, Eng JK, von Haller PD, Kaiser NK, Bruce JE. A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies. Anal Chem 2010; 82:3556-66. [PMID: 20373789 DOI: 10.1021/ac902615g] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we present the results of proof-of-concept experiments using a novel photocleavable and mass spectrometry identifiable cross-linker pcPIR (photocleavable protein interaction reporter). pcPIR can be dissociated under UV irradiation either off- or online before the introduction to the mass spectrometers. Photo dissociation of cross-linkers is different from either the gas phase or the chemical cleavage of cross-linkers. Different types of cross-links can be identified using the pcPIR mass relationships, where the mass of cross-linked precursor equals the sum of the masses of the released products and reporter. Since pcPIR is cleaved prior to the entrance to the mass spectrometer, the released peptides are available to be sequenced with routine collision-induced dissociation (CID) MS/MS experiments and database search algorithms. In this report, the pcPIR strategy of identifying the cross-linked peptides with on- and off-line photocleavage coupled with novel targeted data dependent LC-MS/MS is demonstrated with the use of standard peptides, bovine serum albumin (BSA), and human hemoglobin tetramer protein complex.
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Affiliation(s)
- Li Yang
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
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48
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Zhang C. Proteomic Studies on the Development of the Central Nervous System and Beyond. Neurochem Res 2010; 35:1487-500. [DOI: 10.1007/s11064-010-0218-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2010] [Indexed: 11/27/2022]
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49
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McDonnell LA, Corthals GL, Willems SM, van Remoortere A, van Zeijl RJM, Deelder AM. Peptide and protein imaging mass spectrometry in cancer research. J Proteomics 2010; 73:1921-44. [PMID: 20510389 DOI: 10.1016/j.jprot.2010.05.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 04/28/2010] [Accepted: 05/16/2010] [Indexed: 12/12/2022]
Abstract
MALDI mass spectrometry is able to acquire protein profiles directly from tissue that can describe the levels of hundreds of distinct proteins. MALDI imaging MS can simultaneously reveal how each of these proteins varies in heterogeneous tissues. Numerous studies have now demonstrated how MALDI imaging MS can generate different protein profiles from the different cell types in a tumor, which can act as biomarker profiles or enable specific candidate protein biomarkers to be identified. MALDI imaging MS can be directly applied to patient samples where its utility is to accomplish untargeted multiplex analysis of the tissue's protein content, enabling the different regions of the tissue to be differentiated on the basis of previously unknown protein profiles/biomarkers. The technique continues to rapidly develop and is now approaching the cusp whereby its potential to provide new diagnostic/prognostic tools for cancer patients can be routinely investigated. Here the latest methodological developments are summarized and its application to a range of tumors is reported in detail. The prospects of MALDI imaging MS are then described from the perspectives of modern pathological practice and MS-based proteomics, to ensure the outlook addresses real clinical needs and reflects the real capabilities of MS-based proteomics of complex tissue samples.
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Affiliation(s)
- Liam A McDonnell
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands.
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50
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Affiliation(s)
- Kamila Chughtai
- FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ron M.A. Heeren
- FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands
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