1
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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: 7] [Impact Index Per Article: 7.0] [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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2
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Hou Y, Gao Y, Guo S, Zhang Z, Chen R, Zhang X. Applications of spatially resolved omics in the field of endocrine tumors. Front Endocrinol (Lausanne) 2023; 13:993081. [PMID: 36704039 PMCID: PMC9873308 DOI: 10.3389/fendo.2022.993081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.
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Affiliation(s)
- Yinuo Hou
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Shudi Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Zhibin Zhang
- General Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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3
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Mallah K, Zibara K, Kerbaj C, Eid A, Khoshman N, Ousseily Z, Kobeissy A, Cardon T, Cizkova D, Kobeissy F, Fournier I, Salzet M. Neurotrauma investigation through spatial omics guided by mass spectrometry imaging: Target identification and clinical applications. MASS SPECTROMETRY REVIEWS 2023; 42:189-205. [PMID: 34323300 DOI: 10.1002/mas.21719] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/04/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Traumatic brain injury (TBI) represents one of the major public health concerns worldwide due to the increase in TBI incidence as a result of injuries from daily life accidents such as sports and motor vehicle transportation as well as military-related practices. This type of central nervous system trauma is known to predispose patients to several neurological disorders such as Parkinson's disease, Alzheimer's disease, chronic trauamatic encephalopathy, and age-related Dementia. Recently, several proteomic and lipidomic platforms have been applied on different TBI studies to investigate TBI-related mechanisms that have broadened our understanding of its distinct neuropathological complications. In this study, we provide an updated comprehensive overview of the current knowledge and novel perspectives of the spatially resolved microproteomics and microlipidomics approaches guided by mass spectrometry imaging used in TBI studies and its applications in the neurotrauma field. In this regard, we will discuss the use of the spatially resolved microproteomics and assess the different microproteomic sampling methods such as laser capture microdissection, parafilm assisted microdissection, and liquid microjunction extraction as accurate and precise techniques in the field of neuroproteomics. Additionally, we will highlight lipid profiling applications and their prospective potentials in characterizing molecular processes involved in the field of TBI. Specifically, we will discuss the phospholipid metabolism acting as a precursor for proinflammatory molecules such as eicosanoids. Finally, we will survey the current state of spatial neuroproteomics and microproteomics applications and present the various studies highlighting their findings in these fields.
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Affiliation(s)
- Khalil Mallah
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- PRASE, Lebanese University, Beirut, Lebanon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Coline Kerbaj
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Ali Eid
- Department of Basic Medical Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nour Khoshman
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Zahraa Ousseily
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Abir Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Dasa Cizkova
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Center for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
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4
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Duhamel M, Drelich L, Wisztorski M, Aboulouard S, Gimeno JP, Ogrinc N, Devos P, Cardon T, Weller M, Escande F, Zairi F, Maurage CA, Le Rhun É, Fournier I, Salzet M. Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun 2022; 13:6665. [PMID: 36333286 PMCID: PMC9636229 DOI: 10.1038/s41467-022-34208-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.
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Affiliation(s)
- Marie Duhamel
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
| | - Lauranne Drelich
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Maxence Wisztorski
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Jean-Pascal Gimeno
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Nina Ogrinc
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Patrick Devos
- Univ. Lille, CHU Lille, ULR 2694 - METRICS: Évaluation des technologies de santé et des pratiques médicales, F-59000, Lille, France
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Michael Weller
- Department of Neurology & Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Fabienne Escande
- CHU Lille, Service de biochimie et biologie moléculaire, CHU Lille, F-59000, Lille, France
| | - Fahed Zairi
- CHU Lille, Service de neurochirurgie, F-59000, Lille, France
| | - Claude-Alain Maurage
- CHU Lille, Service de biochimie et biologie moléculaire, CHU Lille, F-59000, Lille, France
| | - Émilie Le Rhun
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
- Department of Neurology & Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland.
- CHU Lille, Service de biochimie et biologie moléculaire, CHU Lille, F-59000, Lille, France.
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
- Institut Universitaire de France (IUF), 75000, Paris, France.
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
- Institut Universitaire de France (IUF), 75000, Paris, France.
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5
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Darie-Ion L, Whitham D, Jayathirtha M, Rai Y, Neagu AN, Darie CC, Petre BA. Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research. Molecules 2022; 27:6196. [PMID: 36234736 PMCID: PMC9570737 DOI: 10.3390/molecules27196196] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein-protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide "molecular pictures", which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.
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Affiliation(s)
- Laura Darie-Ion
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Yashveen Rai
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 22, 700505 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Brînduşa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
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6
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Kwon Y, Piehowski PD, Zhao R, Sontag RL, Moore RJ, Burnum-Johnson KE, Smith RD, Qian WJ, Kelly RT, Zhu Y. Hanging drop sample preparation improves sensitivity of spatial proteomics. LAB ON A CHIP 2022; 22:2869-2877. [PMID: 35838077 PMCID: PMC9320080 DOI: 10.1039/d2lc00384h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Spatial proteomics holds great promise for revealing tissue heterogeneity in both physiological and pathological conditions. However, one significant limitation of most spatial proteomics workflows is the requirement of large sample amounts that blurs cell-type-specific or microstructure-specific information. In this study, we developed an improved sample preparation approach for spatial proteomics and integrated it with our previously-established laser capture microdissection (LCM) and microfluidics sample processing platform. Specifically, we developed a hanging drop (HD) method to improve the sample recovery by positioning a nanowell chip upside-down during protein extraction and tryptic digestion steps. Compared with the commonly-used sitting-drop method, the HD method keeps the tissue pixel away from the container surface, and thus improves the accessibility of the extraction/digestion buffer to the tissue sample. The HD method can increase the MS signal by 7 fold, leading to a 66% increase in the number of identified proteins. An average of 721, 1489, and 2521 proteins can be quantitatively profiled from laser-dissected 10 μm-thick mouse liver tissue pixels with areas of 0.0025, 0.01, and 0.04 mm2, respectively. The improved system was further validated in the study of cell-type-specific proteomes of mouse uterine tissues.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Paul D Piehowski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Ryan L Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA.
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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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8
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Hajjaji N, Aboulouard S, Cardon T, Bertin D, Robin YM, Fournier I, Salzet M. Path to Clonal Theranostics in Luminal Breast Cancers. Front Oncol 2022; 11:802177. [PMID: 35096604 PMCID: PMC8793283 DOI: 10.3389/fonc.2021.802177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Integrating tumor heterogeneity in the drug discovery process is a key challenge to tackle breast cancer resistance. Identifying protein targets for functionally distinct tumor clones is particularly important to tailor therapy to the heterogeneous tumor subpopulations and achieve clonal theranostics. For this purpose, we performed an unsupervised, label-free, spatially resolved shotgun proteomics guided by MALDI mass spectrometry imaging (MSI) on 124 selected tumor clonal areas from early luminal breast cancers, tumor stroma, and breast cancer metastases. 2868 proteins were identified. The main protein classes found in the clonal proteome dataset were enzymes, cytoskeletal proteins, membrane-traffic, translational or scaffold proteins, or transporters. As a comparison, gene-specific transcriptional regulators, chromatin related proteins or transmembrane signal receptor were more abundant in the TCGA dataset. Moreover, 26 mutated proteins have been identified. Similarly, expanding the search to alternative proteins databases retrieved 126 alternative proteins in the clonal proteome dataset. Most of these alternative proteins were coded mainly from non-coding RNA. To fully understand the molecular information brought by our approach and its relevance to drug target discovery, the clonal proteomic dataset was further compared to the TCGA breast cancer database and two transcriptomic panels, BC360 (nanoString®) and CDx (Foundation One®). We retrieved 139 pathways in the clonal proteome dataset. Only 55% of these pathways were also present in the TCGA dataset, 68% in BC360 and 50% in CDx. Seven of these pathways have been suggested as candidate for drug targeting, 22 have been associated with breast cancer in experimental or clinical reports, the remaining 19 pathways have been understudied in breast cancer. Among the anticancer drugs, 35 drugs matched uniquely with the clonal proteome dataset, with only 7 of them already approved in breast cancer. The number of target and drug interactions with non-anticancer drugs (such as agents targeting the cardiovascular system, metabolism, the musculoskeletal or the nervous systems) was higher in the clonal proteome dataset (540 interactions) compared to TCGA (83 interactions), BC360 (419 interactions), or CDx (172 interactions). Many of the protein targets identified and drugs screened were clinically relevant to breast cancer and are in clinical trials. Thus, we described the non-redundant knowledge brought by this clone-tailored approach compared to TCGA or transcriptomic panels, the targetable proteins identified in the clonal proteome dataset, and the potential of this approach for drug discovery and repurposing through drug interactions with antineoplastic agents and non-anticancer drugs.
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Affiliation(s)
- Nawale Hajjaji
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Delphine Bertin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Yves-Marie Robin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut universitaire de France, Paris, France
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut universitaire de France, Paris, France
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9
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Malaker SA, Quanico J, Raffo-Romero A, Kobeissy F, Aboulouard S, Tierny D, Bertozzi CR, Fournier I, Salzet M. On-tissue spatially resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape. Cell Chem Biol 2022; 29:30-42.e4. [PMID: 34102146 PMCID: PMC8617081 DOI: 10.1016/j.chembiol.2021.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/06/2021] [Accepted: 05/10/2021] [Indexed: 01/22/2023]
Abstract
Here, we present an approach to identify N-linked glycoproteins and deduce their spatial localization using a combination of matrix-assisted laser desorption ionization (MALDI) N-glycan mass spectrometry imaging (MSI) and spatially resolved glycoproteomics. We subjected glioma biopsies to on-tissue PNGaseF digestion and MALDI-MSI and found that the glycan HexNAc4-Hex5-NeuAc2 was predominantly expressed in necrotic regions of high-grade canine gliomas. To determine the underlying sialo-glycoprotein, various regions in adjacent tissue sections were subjected to microdigestion and manual glycoproteomic analysis. Results identified haptoglobin as the protein associated with HexNAc4-Hex5-NeuAc2, thus directly linking glycan imaging with intact glycopeptide identification. In total, our spatially resolved glycoproteomics technique identified over 400 N-, O-, and S- glycopeptides from over 30 proteins, demonstrating the diverse array of glycosylation present on the tissue slices and the sensitivity of our technique. Ultimately, this proof-of-principle work demonstrates that spatially resolved glycoproteomics greatly complement MALDI-MSI in understanding dysregulated glycosylation.
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Affiliation(s)
- Stacy Alyse Malaker
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94035, USA,Present address: Department of Chemistry, Yale University, New Haven, CT 06511, USA,These authors contributed equally
| | - Jusal Quanico
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Present address: Center for Proteomics, Antwerp University,Campus Groenenborger, Groenenborgerlaan 171, 2020 Antwerp, Belgium,These authors contributed equally
| | - Antonella Raffo-Romero
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Soulaimane Aboulouard
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France
| | - Dominique Tierny
- OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 rue du Dr Yersin, 59120 Loos, France
| | - Carolyn Ruth Bertozzi
- Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94035, USA,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Correspondence: (I.F.), (M.S.)
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Lead contact,Correspondence: (I.F.), (M.S.)
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10
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Lawal RO, Richardson LT, Dong C, Donnarumma F, Solouki T, Murray KK. Deep-ultraviolet laser ablation sampling for proteomic analysis of tissue. Anal Chim Acta 2021; 1184:339021. [PMID: 34625253 DOI: 10.1016/j.aca.2021.339021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/29/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Deep-ultraviolet laser ablation with a pulsed 193 nm ArF excimer laser was used to remove localized regions from tissue sections from which proteins were extracted for spatially resolved proteomic analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). The ability to capture intact proteins by ablation at 193 nm wavelength was verified by matrix-assisted laser desorption ionization (MALDI) of the protein standard bovine serum albumin (BSA), which showed that BSA was ablated and captured without fragmentation. A Bradford assay of the ablated and captured proteins indicated 90% efficiency for transfer of the intact protein at a laser fluence of 3 kJ/m2. Rat brain tissue sections mounted on quartz microscope slides and ablated in transmission mode yielded 2 μg protein per mm2 as quantified by the Bradford assay. Tissue areas ranging from 0.06 mm2 to 1 mm2 were ablated and the ejected material was collected for proteomic analysis. Extracted proteins were digested and the resulting peptides were analyzed by LC-MS/MS. The proteins extracted from the ablated areas were identified and the average number of identified proteins ranged from 85 in the 0.06 mm2 area to 2400 in the 1 mm2 area of a 50 μm thick tissue. In comparison to infrared laser ablation of equivalent sampled areas, both the protein mass and number of proteins identified using DUV laser ablation sampling were approximately four times larger.
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Affiliation(s)
- Remilekun O Lawal
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Luke T Richardson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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11
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Drelich L, Aboulouard S, Franck J, Salzet M, Fournier I, Wisztorski M. Toward High Spatially Resolved Proteomics Using Expansion Microscopy. Anal Chem 2021; 93:12195-12203. [PMID: 34449217 DOI: 10.1021/acs.analchem.0c05372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Expansion microscopy (EM) is an emerging approach for morphological examination of biological specimens at nanoscale resolution using conventional optical microscopy. To achieve physical separation of cell structures, tissues are embedded in a swellable polymer and expanded several fold in an isotropic manner. This work shows the development and optimization of physical tissue expansion as a new method for spatially resolved large-scale proteomics. Herein we established a novel method to enlarge the tissue section to be compatible with manual microdissection on regions of interest and MS-based proteomic analysis. A major issue in expansion microscopy is the loss of protein information during the mechanical homogenization phase due to the use of proteinase K. For isotropic expansion, different homogenization agents were investigated, both to maximize protein identification and to minimize protein diffusion. Best results were obtained with SDS for homogenization. Using our modified protocol, we were able to enlarge a tissue section more than 3-fold and identified up to 655 proteins from 1 mm in size after expansion, equivalent to 330 μm in their real size corresponding thus to an average of 260 cells. This approach can be performed easily without any expensive sampling instrument. We demonstrated the compatibility of sample preparation for expansion microscopy and proteomic study in a spatial context.
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Affiliation(s)
- Lauranne Drelich
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Soulaimane Aboulouard
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Julien Franck
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France.,Institut Universitaire de France (IUF), Paris, 75000, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France.,Institut Universitaire de France (IUF), Paris, 75000, France
| | - Maxence Wisztorski
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
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12
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Pulukkody AC, Yung YP, Donnarumma F, Murray KK, Carlson RP, Hanley L. Spatially resolved analysis of Pseudomonas aeruginosa biofilm proteomes measured by laser ablation sample transfer. PLoS One 2021; 16:e0250911. [PMID: 34292966 PMCID: PMC8297752 DOI: 10.1371/journal.pone.0250911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
Heterogeneity in the distribution of nutrients and oxygen gradients during biofilm growth gives rise to changes in phenotype. There has been long term interest in identifying spatial differences during biofilm development including clues that identify chemical heterogeneity. Laser ablation sample transfer (LAST) allows site-specific sampling combined with label free proteomics to distinguish radially and axially resolved proteomes for Pseudomonas aeruginosa biofilms. Specifically, differential protein abundances on oxic vs. anoxic regions of a biofilm were observed by combining LAST with bottom up proteomics. This study reveals a more active metabolism in the anoxic region of the biofilm with respect to the oxic region for this clinical strain of P. aeruginosa, despite this organism being considered an aerobe by nature. Protein abundance data related to cellular acclimations to chemical gradients include identification of glucose catabolizing proteins, high abundance of proteins from arginine and polyamine metabolism, and proteins that could also support virulence and environmental stress mediation in the anoxic region. Finally, the LAST methodology requires only a few mm2 of biofilm area to identify hundreds of proteins.
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Affiliation(s)
- Aruni Chathurya Pulukkody
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yeni P. Yung
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Kermit K. Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ross P. Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Luke Hanley
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
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13
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Otsuka Y. Direct Liquid Extraction and Ionization Techniques for Understanding Multimolecular Environments in Biological Systems (Secondary Publication). Mass Spectrom (Tokyo) 2021; 10:A0095. [PMID: 34249586 PMCID: PMC8246329 DOI: 10.5702/massspectrometry.a0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/23/2022] Open
Abstract
A combination of direct liquid extraction using a small volume of solvent and electrospray ionization allows the rapid measurement of complex chemical components in biological samples and visualization of their distribution in tissue sections. This review describes the development of such techniques and their application to biological research since the first reports in the early 2000s. An overview of electrospray ionization, ion suppression in samples, and the acceleration of specific chemical reactions in charged droplets is also presented. Potential future applications for visualizing multimolecular environments in biological systems are discussed.
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Affiliation(s)
- Yoichi Otsuka
- Graduate School of Science, Osaka University, 1–1 Machikaneyama-cho, Toyonaka, Osaka 560–0043, Japan
- JST, PRESTO, 4–1–8 Honcho, Kawaguchi, Saitama 332–0012, Japan
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14
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Alexovič M, Sabo J, Longuespée R. Microproteomic sample preparation. Proteomics 2021; 21:e2000318. [PMID: 33547857 DOI: 10.1002/pmic.202000318] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/11/2022]
Abstract
Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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15
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Implementation of MALDI Mass Spectrometry Imaging in Cancer Proteomics Research: Applications and Challenges. J Pers Med 2020; 10:jpm10020054. [PMID: 32580362 PMCID: PMC7354689 DOI: 10.3390/jpm10020054] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Studying the proteome–the entire set of proteins in cells, tissues, organs and body fluids—is of great relevance in cancer research, as differential forms of proteins are expressed in response to specific intrinsic and extrinsic signals. Discovering protein signatures/pathways responsible for cancer transformation may lead to a better understanding of tumor biology and to a more effective diagnosis, prognosis, recurrence and response to therapy. Moreover, proteins can act as a biomarker or potential drug targets. Hence, it is of major importance to implement proteomic, particularly mass spectrometric, approaches in cancer research, to provide new crucial insights into tumor biology. Recently, mass spectrometry imaging (MSI) approaches were implemented in cancer research, to provide individual molecular characteristics of each individual tumor while retaining molecular spatial distribution, essential in the context of personalized disease management and medicine.
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16
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Wang K, Donnarumma F, Pettit ME, Szot CW, Solouki T, Murray KK. MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4475. [PMID: 31726477 DOI: 10.1002/jms.4475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
A multimodal workflow for mass spectrometry imaging was developed that combines MALDI imaging with protein identification and quantification by liquid chromatography tandem mass spectrometry (LC-MS/MS). Thin tissue sections were analyzed by MALDI imaging, and the regions of interest (ROI) were identified using a smoothing and edge detection procedure. A midinfrared laser at 3-μm wavelength was used to remove the ROI from the brain tissue section after MALDI mass spectrometry imaging (MALDI MSI). The captured material was processed using a single-pot solid-phase-enhanced sample preparation (SP3) method and analyzed by LC-MS/MS using ion mobility (IM) enhanced data independent acquisition (DIA) to identify and quantify proteins; more than 600 proteins were identified. Using a modified database that included isoform and the post-translational modifications chain, loss of the initial methionine, and acetylation, 14 MALDI MSI peaks were identified. Comparison of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the identified proteins was achieved through an evolutionary relationships classification system.
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Affiliation(s)
- Kelin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Michael E Pettit
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, United States
| | - Carson W Szot
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
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17
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18
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Ostromohov N, Rofman B, Bercovici M, Kaigala G. Electrokinetic Scanning Probe. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904268. [PMID: 31885215 DOI: 10.1002/smll.201904268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/25/2019] [Indexed: 06/10/2023]
Abstract
The theoretical analysis and experimental demonstration of a new concept are presented for a non-contact scanning probe, in which transport of fluid and molecules is controlled by electric fields. The electrokinetic scanning probe (ESP) enables local chemical and biochemical interactions with surfaces in liquid environments. The physical mechanism and design criteria for such a probe are presented, and its compatibility with a wide range of processing solutions and pH values are demonstrated. The applicability of the probe is shown for surface patterning in conjunction with localized heating and 250-fold analyte stacking.
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Affiliation(s)
- Nadya Ostromohov
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803, Rueschlikon, Switzerland
| | - Baruch Rofman
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Govind Kaigala
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803, Rueschlikon, Switzerland
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19
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Eveque-Mourroux MR, Rocha B, Barré FPY, Heeren RMA, Cillero-Pastor B. Spatially resolved proteomics in osteoarthritis: State of the art and new perspectives. J Proteomics 2020; 215:103637. [PMID: 31926309 DOI: 10.1016/j.jprot.2020.103637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/07/2019] [Accepted: 01/05/2020] [Indexed: 01/18/2023]
Abstract
Osteoarthritis (OA) is one of the most common diseases worldwide caused by chronic degeneration of the joints. Its high prevalence and the involvement of several tissues define OA as a highly heterogeneous disease. New biological markers to evaluate the progression of the pathology and improve its prognosis are needed. Among all the different -omic strategies applied to OA, solution phase bottom-up proteomics has made an extensive contribution to the field of biomarker research. However, new technologies for protein analysis should be considered for a better understanding of the disease. This review focuses on complementary proteomic methodologies and new technologies for translational research of OA and other rheumatic pathologies, especially mass spectrometry imaging and protein imaging methods not applied by the OA community yet.
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Affiliation(s)
- M R Eveque-Mourroux
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, the Netherlands
| | - B Rocha
- Proteomics Group-ProteoRed/ISCIII, Grupo de Investigación de Reumatología (GIR), INIBIC - Hospital Universitario de A Coruña, A Coruña, Spain
| | - F P Y Barré
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, the Netherlands
| | - R M A Heeren
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, the Netherlands
| | - B Cillero-Pastor
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, the Netherlands.
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20
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Claes BSR, Takeo E, Fukusaki E, Shimma S, Heeren RMA. Imaging Isomers on a Biological Surface: A Review. Mass Spectrom (Tokyo) 2019; 8:A0078. [PMID: 32158629 PMCID: PMC7035452 DOI: 10.5702/massspectrometry.a0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry imaging is an imaging technology that allows the localization and identification of molecules on (biological) sample surfaces. Obtaining the localization of a compound in tissue is of great value in biological research. Yet, the identification of compounds remains a challenge. Mass spectrometry alone, even with high-mass resolution, cannot always distinguish between the subtle structural differences of isomeric compounds. This review discusses recent advances in mass spectrometry imaging of lipids, steroid hormones, amino acids and proteins that allow imaging with isomeric resolution. These improvements in detailed identification can give new insights into the local biological activity of isomers.
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Affiliation(s)
- Britt S. R. Claes
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University
| | - Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Ron M. A. Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University
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21
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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22
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Mallah K, Quanico J, Raffo-Romero A, Cardon T, Aboulouard S, Devos D, Kobeissy F, Zibara K, Salzet M, Fournier I. Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease. Mol Cell Proteomics 2019; 18:1669-1682. [PMID: 31204315 PMCID: PMC6683007 DOI: 10.1074/mcp.ra119.001604] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) represents a major health concerns with no clinically-approved FDA drug available for therapeutic intervention. Several genomics and neuroproteomics studies have been employed to decipher the underlying pathological mechanisms involved that can serve as potential neurotherapeutic targets and unveil a possible underlying relation of TBI to other secondary neurological disorders. In this work, we present a novel high throughput systems biology approach using a spatially resolved microproteomics platform conducted on different brain regions in an experimental rat model of moderate of controlled cortical injury (CCI) at a temporal pattern postinjury (1 day, 3 days, 7 days, and 10 days). Mapping the spatiotemporal landscape of signature markers in TBI revealed an overexpression of major protein families known to be implicated in Parkinson's disease (PD) such as GPR158, HGMB1, synaptotagmin and glutamate decarboxylase in the ipsilateral substantia nigra. In silico bioinformatics docking experiments indicated the potential correlation between TBI and PD through alpha-synuclein. In an in vitro model, stimulation with palmitoylcarnitine triggered an inflammatory response in macrophages and a regeneration processes in astrocytes which also further confirmed the in vivo TBI proteomics data. Taken together, this is the first study to assess the microproteomics landscape in TBI, mainly in the substantia nigra, thus revealing a potential predisposition for PD or Parkinsonism post-TBI.
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Affiliation(s)
- Khalil Mallah
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; §ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Jusal Quanico
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Antonella Raffo-Romero
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Tristan Cardon
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Soulaimane Aboulouard
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - David Devos
- ¶Department of Neurology, Expert center for Parkinson's disease, Department of Pharmacology, University of Lille, CHU LILLE, INSERM UMR_S 1171, LICEND, France
| | - Firas Kobeissy
- ‖Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Kazem Zibara
- §ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Michel Salzet
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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23
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Kocurek KI, May RC, Cooper HJ. Application of High-Field Asymmetric Waveform Ion Mobility Separation to LESA Mass Spectrometry of Bacteria. Anal Chem 2019; 91:4755-4761. [DOI: 10.1021/acs.analchem.9b00307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Pettit ME, Donnarumma F, Murray KK, Solouki T. Infrared laser ablation sampling coupled with data independent high resolution UPLC-IM-MS/MS for tissue analysis. Anal Chim Acta 2018; 1034:102-109. [DOI: 10.1016/j.aca.2018.06.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 12/30/2022]
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25
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Hayama T, Ohyama K. Recent development and trends in sample extraction and preparation for mass spectrometric analysis of nucleotides, nucleosides, and proteins. J Pharm Biomed Anal 2018; 161:51-60. [PMID: 30145449 DOI: 10.1016/j.jpba.2018.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
This review describes the recent developments in sample extraction and preparation techniques for mass spectrometric analysis of nucleotides, nucleosides, and proteins. Unique materials and techniques have been developed for highly selective extraction of nucleotides and nucleosides by solid-phase extraction strategies using various affinities. However, for proteins, the analysis of small-scale sections of diseased tissues (formalin-fixed, paraffin-embedded tissues) and the direct analysis of an exact lesion on the surface of diseased tissues (liquid extraction surface analysis) have become important advances in this field. In this review, we focus on the latest developments of these techniques and strategies.
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Affiliation(s)
- Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Kaname Ohyama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto-machi, Nagasaki 852-8588, Japan.
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26
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Huber K, Khamehgir-Silz P, Schramm T, Gorshkov V, Spengler B, Römpp A. Approaching cellular resolution and reliable identification in mass spectrometry imaging of tryptic peptides. Anal Bioanal Chem 2018; 410:5825-5837. [PMID: 30066193 PMCID: PMC6096711 DOI: 10.1007/s00216-018-1199-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/24/2018] [Accepted: 06/13/2018] [Indexed: 01/19/2023]
Abstract
On-tissue digestion has become the preferred method to identify proteins in mass spectrometry (MS) imaging. In this study, we report advances in data acquisition and protein identification for MS imaging after on-tissue digestion. Tryptic peptides in a coronal mouse brain section were measured at 50 μm pixel size and revealed detailed histological structures, e.g., the ependyma (consisting of one to two cell layers), which was confirmed by H&E staining. This demonstrates that MS imaging of tryptic peptides at or close to cellular resolution is within reach. We also describe a detailed identification workflow which resulted in the identification of 99 proteins (with 435 corresponding peptides), based on comparison with LC-MS/MS data and in silico digest. These results were obtained with stringent parameters, including high mass accuracy in imaging mode (RSME < 3 ppm) and at least two unique peptides per protein showing consistent spatial distribution. We identified almost 50% of proteins with at least four corresponding peptides. As there is no agreed approach for identification of proteins after on-tissue digestion yet, we discuss our workflow in detail and make the corresponding mass spectral data available as “open data” via ProteomeXchange (identifier PXD003172). With this, we would like to contribute to a more effective discussion and the development of new approaches for tryptic peptide identification in MS imaging. From an experimental point of view, we demonstrate the improvement due to the combination of high spatial resolution and high mass resolution/mass accuracy on a measurement at 25 μm pixel size in mouse cerebellum tissue. A whole body section of a mouse pub imaged at 50 μm pixel size (40 GB, 230,000 spectra) demonstrates the stability of our protocol. For this data set, we developed a workflow that is based on conversion to the common data format imzML and sequential application of freely available software tools. In combination, the presented results for spatial resolution, protein identification, and data processing constitute significant improvements for the field of on-tissue digestion. MS imaging of coronal mouse brain cerebellum with a pixel size of 25 μm: A Optical image, B myelin staining, C H&E staining, and D MS image overlay (RGB) of tryptic peptides m/z = 726.4045 ± 0.005, HGFLPR + H+ (red), m/z = 536.3173 ± 0.005, AKPAK + Na+ (green), and m/z = 994.5436 ± 0.005, WRQLIEK + Na+ (blue) ![]()
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Affiliation(s)
- Katharina Huber
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Pegah Khamehgir-Silz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Thorsten Schramm
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Vladimir Gorshkov
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany. .,Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitaetsstrasse 30, 95440, Bayreuth, Germany.
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27
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Zhu Y, Dou M, Piehowski PD, Liang Y, Wang F, Chu RK, Chrisler WB, Smith JN, Schwarz KC, Shen Y, Shukla AK, Moore RJ, Smith RD, Qian WJ, Kelly RT. Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets. Mol Cell Proteomics 2018; 17:1864-1874. [PMID: 29941660 DOI: 10.1074/mcp.tir118.000686] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution because of the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 μm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-μm-thick rat brain cortex tissue sections having diameters of 50, 100, and 200 μm, respectively. We also analyzed 100-μm-diameter sections corresponding to 10-18 cells from three different regions of rat brain and comparatively quantified ∼1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues.
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Affiliation(s)
- Ying Zhu
- From the ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Maowei Dou
- From the ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Paul D Piehowski
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Yiran Liang
- From the ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Fangjun Wang
- ¶CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Rosalie K Chu
- From the ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - William B Chrisler
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Jordan N Smith
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Kaitlynn C Schwarz
- From the ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Yufeng Shen
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Anil K Shukla
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Ronald J Moore
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Richard D Smith
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Wei-Jun Qian
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - Ryan T Kelly
- From the ‡Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354;
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28
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Veličković D, Chu RK, Carrell AA, Thomas M, Paša-Tolić L, Weston DJ, Anderton CR. Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS 2 Increases Confidence in Both Molecular Identification and Localization. Anal Chem 2017; 90:702-707. [PMID: 29210566 DOI: 10.1021/acs.analchem.7b04319] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC-MS2) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS2I, to confidently annotate and localize a broad range of metabolites involved in a tripartite symbiosis system of moss, cyanobacteria, and fungus. We found that the combination of these two imaging modalities generated very congruent ion images, providing the link between highly accurate structural information onfered by LESA and high spatial resolution attainable by MALDI. These results demonstrate how this combined methodology could be very useful in differentiating metabolite routes in complex systems.
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Affiliation(s)
| | | | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | | | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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29
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Delcourt V, Franck J, Quanico J, Gimeno JP, Wisztorski M, Raffo-Romero A, Kobeissy F, Roucou X, Salzet M, Fournier I. Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions. Mol Cell Proteomics 2017; 17:357-372. [PMID: 29122912 PMCID: PMC5795397 DOI: 10.1074/mcp.m116.065755] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
Tissue spatially-resolved proteomics was performed on 3 brain regions, leading to the characterization of 123 reference proteins. Moreover, 8 alternative proteins from alternative open reading frames (AltORF) were identified. Some proteins display specific post-translational modification profiles or truncation linked to the brain regions and their functions. Systems biology analysis performed on the proteome identified in each region allowed to associate sub-networks with the functional physiology of each brain region. Back correlation of the proteins identified by spatially-resolved proteomics at a given tissue localization with the MALDI MS imaging data, was then performed. As an example, mapping of the distribution of the matrix metallopeptidase 3-cleaved C-terminal fragment of α-synuclein (aa 95–140) identified its specific distribution along the hippocampal dentate gyrus. Taken together, we established the molecular physiome of 3 rat brain regions through reference and hidden proteome characterization.
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Affiliation(s)
- Vivian Delcourt
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France.,§Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Julien Franck
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Jusal Quanico
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Jean-Pascal Gimeno
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Maxence Wisztorski
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Antonella Raffo-Romero
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Firas Kobeissy
- ¶Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Xavier Roucou
- §Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Michel Salzet
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France;
| | - Isabelle Fournier
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France;
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30
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Lamont L, Baumert M, Ogrinc Potočnik N, Allen M, Vreeken R, Heeren RMA, Porta T. Integration of Ion Mobility MS E after Fully Automated, Online, High-Resolution Liquid Extraction Surface Analysis Micro-Liquid Chromatography. Anal Chem 2017; 89:11143-11150. [PMID: 28945354 PMCID: PMC5677252 DOI: 10.1021/acs.analchem.7b03512] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Direct
analysis by mass spectrometry (imaging) has become increasingly
deployed in preclinical and clinical research due to its rapid and
accurate readouts. However, when it comes to biomarker discovery or
histopathological diagnostics, more sensitive and in-depth profiling
from localized areas is required. We developed a comprehensive, fully
automated online platform for high-resolution liquid extraction surface
analysis (HR-LESA) followed by micro–liquid chromatography
(LC) separation and a data-independent acquisition strategy for untargeted
and low abundant analyte identification directly from tissue sections.
Applied to tissue sections of rat pituitary, the platform demonstrated
improved spatial resolution, allowing sample areas as small as 400
μm to be studied, a major advantage over conventional LESA.
The platform integrates an online buffer exchange and washing step
for removal of salts and other endogenous contamination that originates
from local tissue extraction. Our carry over–free platform
showed high reproducibility, with an interextraction variability below
30%. Another strength of the platform is the additional selectivity
provided by a postsampling gas-phase ion mobility separation. This
allowed distinguishing coeluted isobaric compounds without requiring
additional separation time. Furthermore, we identified untargeted
and low-abundance analytes, including neuropeptides deriving from
the pro-opiomelanocortin precursor protein and localized a specific
area of the pituitary gland (i.e., adenohypophysis) known to secrete
neuropeptides and other small metabolites related to development,
growth, and metabolism. This platform can thus be applied for the
in-depth study of small samples of complex tissues with histologic
features of ∼400 μm or more, including potential neuropeptide
markers involved in many diseases such as neurodegenerative diseases,
obesity, bulimia, and anorexia nervosa.
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Affiliation(s)
- Lieke Lamont
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| | | | - Nina Ogrinc Potočnik
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| | - Mark Allen
- Advion , Harlow CM20 2NQ, United Kingdom
| | - Rob Vreeken
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands.,Janssen Pharmaceutica , Beerse, Belgium
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
| | - Tiffany Porta
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University , Maastricht, The Netherlands
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31
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Kocurek KI, Stones L, Bunch J, May RC, Cooper HJ. Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2066-2077. [PMID: 28681361 PMCID: PMC5594050 DOI: 10.1007/s13361-017-1718-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/21/2023]
Abstract
We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus (Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS. A range of the proteins detected were selected for top-down LESA MS/MS. Thirty-nine proteins were identified by top-down LESA MS/MS, including 16 proteins that have not previously been observed by any other technique. The potential of LESA MS for classification and characterization of novel species is illustrated by the de novo sequencing of a new protein from the unknown species of Staphylococcus. Graphical Abstract ᅟ.
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Affiliation(s)
- Klaudia I Kocurek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Leanne Stones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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32
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Quanico J, Franck J, Cardon T, Leblanc E, Wisztorski M, Salzet M, Fournier I. NanoLC-MS coupling of liquid microjunction microextraction for on-tissue proteomic analysis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2017; 1865:891-900. [PMID: 27836619 DOI: 10.1016/j.bbapap.2016.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/26/2022]
Abstract
Mass spectrometry (MS)-based microproteomics on localized regions of tissue sections was achieved by direct coupling of liquid microjunction microextraction with a nanoscale liquid chromatography-tandem MS, resulting in the identification of >500 protein groups from a region as small as 250μm in diameter representing only a few hundred of cells. The method was applied on the examination of benign and tumor regions initially defined by imaging mass spectrometry (IMS) analysis of a consecutive high grade serous ovarian tumor tissue section. Results identified the higher abundance of eukaryotic translation initiation factors eIF4A, its isoform eIF4A2, and eIF5A and its isoform eIF5A2, and lower abundance of actin-binding proteins OBSCN, TAGLN and CNN3 on tumor regions, concomitant with previous findings. This demonstrates the use of the method for downstream characterization of distinct regions identified by IMS. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Jusal Quanico
- Université de Lille 1, Inserm U-1192, Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Julien Franck
- Université de Lille 1, Inserm U-1192, Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Tristan Cardon
- Université de Lille 1, Inserm U-1192, Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Eric Leblanc
- Université de Lille 1, Inserm U-1192, Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Department of Gynecology Oncology, Oscar Lambret Center, Lille, France.
| | - Maxence Wisztorski
- Université de Lille 1, Inserm U-1192, Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Michel Salzet
- Université de Lille 1, Inserm U-1192, Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Université de Lille 1, Inserm U-1192, Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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33
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Delcourt V, Franck J, Leblanc E, Narducci F, Robin YM, Gimeno JP, Quanico J, Wisztorski M, Kobeissy F, Jacques JF, Roucou X, Salzet M, Fournier I. Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine 2017; 21:55-64. [PMID: 28629911 PMCID: PMC5514399 DOI: 10.1016/j.ebiom.2017.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Recently, it was demonstrated that proteins can be translated from alternative open reading frames (altORFs), increasing the size of the actual proteome. Top-down mass spectrometry-based proteomics allows the identification of intact proteins containing post-translational modifications (PTMs) as well as truncated forms translated from reference ORFs or altORFs. METHODS Top-down tissue microproteomics was applied on benign, tumor and necrotic-fibrotic regions of serous ovarian cancer biopsies, identifying proteins exhibiting region-specific cellular localization and PTMs. The regions of interest (ROIs) were determined by MALDI mass spectrometry imaging and spatial segmentation. FINDINGS Analysis with a customized protein sequence database containing reference and alternative proteins (altprots) identified 15 altprots, including alternative G protein nucleolar 1 (AltGNL1) found in the tumor, and translated from an altORF nested within the GNL1 canonical coding sequence. Co-expression of GNL1 and altGNL1 was validated by transfection in HEK293 and HeLa cells with an expression plasmid containing a GNL1-FLAG(V5) construct. Western blot and immunofluorescence experiments confirmed constitutive co-expression of altGNL1-V5 with GNL1-FLAG. CONCLUSIONS Taken together, our approach provides means to evaluate protein changes in the case of serous ovarian cancer, allowing the detection of potential markers that have never been considered.
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Affiliation(s)
- Vivian Delcourt
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Julien Franck
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Eric Leblanc
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Fabrice Narducci
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Yves-Marie Robin
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Jean-Pascal Gimeno
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; ONCOLille, Maison Régionale de la Recherche Clinique, Lille, France
| | - Jusal Quanico
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Jean-François Jacques
- Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Integrated mass spectrometry imaging and omics workflows on the same tissue section using grid-aided, parafilm-assisted microdissection. Biochim Biophys Acta Gen Subj 2017; 1861:1702-1714. [PMID: 28300637 DOI: 10.1016/j.bbagen.2017.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND In spite of the number of applications describing the use of MALDI MSI, one of its major drawbacks is the limited capability of identifying multiple compound classes directly on the same tissue section. METHODS We demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting acid dye 25 using a piezoelectric microspotter, and this grid was used as a guide to locate regions of interest and as an aid during manual microdissection. Subjecting the dissected pieces to the modified Folch method allows to separate the metabolites from proteins. The proteins can then be subjected to digestion under controlled conditions to improve protein identification yields. RESULTS The proof of concept experiment on rat brain generated 162 and 140 metabolite assignments from three ROIs (cerebellum, hippocampus and midbrain/hypothalamus) in positive and negative modes, respectively, and 890, 1303 and 1059 unique proteins. Integrated metabolite and protein overrepresentation analysis identified pathways associated with the biological functions of each ROI, most of which were not identified when looking at the protein and metabolite lists individually. CONCLUSIONS This combined MALDI MS imaging and multi-omics approach further extends the amount of information that can be generated from single tissue sections. GENERAL SIGNIFICANCE To the best of our knowledge, this is the first report combining both imaging and multi-omics analyses in the same workflow and on the same tissue section.
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Affiliation(s)
- Jusal Quanico
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Julien Franck
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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Rizzo DG, Prentice BM, Moore JL, Norris JL, Caprioli RM. Enhanced Spatially Resolved Proteomics Using On-Tissue Hydrogel-Mediated Protein Digestion. Anal Chem 2017; 89:2948-2955. [DOI: 10.1021/acs.analchem.6b04395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David G. Rizzo
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boone M. Prentice
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jessica L. Moore
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jeremy L. Norris
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M. Caprioli
- Department
of Chemistry, ‡Department of Biochemistry, §Mass Spectrometry Research Center, and ∥Departments
of Pharmacology and Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
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Wisztorski M, Quanico J, Franck J, Fatou B, Salzet M, Fournier I. Droplet-Based Liquid Extraction for Spatially-Resolved Microproteomics Analysis of Tissue Sections. Methods Mol Biol 2017; 1618:49-63. [PMID: 28523499 DOI: 10.1007/978-1-4939-7051-3_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Obtaining information on protein content while keeping their localization on tissue or organ is of importance in different domains to understand pathophysiological processes. There is increasing interest in studying the microenvironment and heterogeneity of tumors, which currently is difficult with existing proteomics techniques. The advent of new techniques, like MALDI Mass Spectrometry Imaging, made a significant progress in the last decade but is characterized by a number of inherent drawbacks. One of these is the limited identification of proteins. New alternative approaches such as spatially-resolved liquid microextraction have recently been proposed to overcome this limitation. In this chapter, we describe strategies using liquid microjunction to perform extraction of previously digested peptides or of intact proteins from tissue section in a localized manner.
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Affiliation(s)
- Maxence Wisztorski
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France.
| | - Jusal Quanico
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Julien Franck
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Benoit Fatou
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Michel Salzet
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Bat SN3, 1er étage, 59650, Villeneuve d'Ascq, France
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Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Combined MALDI Mass Spectrometry Imaging and Parafilm-Assisted Microdissection-Based LC-MS/MS Workflows in the Study of the Brain. Methods Mol Biol 2017; 1598:269-283. [PMID: 28508367 DOI: 10.1007/978-1-4939-6952-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins and other biomolecules such as lipids are significant players in the central nervous system and are implicated in various neurological disorders. Their identification, quantification, and distribution are thus important not only in understanding the disease but also in developing treatments. A combined workflow allowing the localized microextraction of discrete regions identified by a matrix-assisted laser desorption/ionization mass spectrometry (MSI) imaging experiment for proteomics analysis by liquid chromatography/tandem mass spectrometry (LC MS/MS) is described in this chapter. MSI was initially used to map lipid distributions allowing for the identification of regions of interest (ROIs) that are then subjected to microextraction in a consecutive tissue section. Mounting of consecutive tissue on parafilm allows microdissection of the ROIs, where proteins can then be recovered for processing and LC MS/MS analysis. The PAM method provides a fast and cheap means to perform further downstream analysis after an MSI experiment.
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Affiliation(s)
- Jusal Quanico
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Julien Franck
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
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Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Progress and Potential of Imaging Mass Spectrometry Applied to Biomarker Discovery. Methods Mol Biol 2017; 1598:21-43. [PMID: 28508356 DOI: 10.1007/978-1-4939-6952-4_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mapping provides a direct means to assess the impact of protein biomarkers and puts into context their relevance in the type of cancer being examined. To this end, mass spectrometry imaging (MSI) was developed to provide the needed spatial information which is missing in traditional liquid-based mass spectrometric proteomics approaches. Aptly described as a "molecular histology" technique, MSI gives an additional dimension in characterizing tumor biopsies, allowing for mapping of hundreds of molecules in a single analysis. A decade of developments focused on improving and standardizing MSI so that the technique can be translated into the clinical setting. This review describes the progress made in addressing the technological development that allows to bridge local protein detection by MSI to its identification and to illustrate its potential in studying various aspects of cancer biomarker discovery.
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Affiliation(s)
- Jusal Quanico
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Julien Franck
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000, Lille, France.
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Le Rhun E, Duhamel M, Wisztorski M, Gimeno JP, Zairi F, Escande F, Reyns N, Kobeissy F, Maurage CA, Salzet M, Fournier I. Evaluation of non-supervised MALDI mass spectrometry imaging combined with microproteomics for glioma grade III classification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:875-890. [PMID: 27890679 DOI: 10.1016/j.bbapap.2016.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 10/20/2022]
Abstract
An integrated diagnosis using molecular features is recommended in the 2016 World Health Organization (WHO) classification. Our aim was to explore non-targeted molecular classification using MALDI mass spectrometry imaging (MALDI MSI) associated to microproteomics in order to classify anaplastic glioma by integration of clinical data. We used fresh-frozen tissue sections to perform MALDI MSI of proteins based on their digestion peptides after in-situ trypsin digestion of the tissue sections and matrix deposition by micro-spraying. The generated 70μm spatial resolution image datasets were further processed by individual or global segmentation in order to cluster the tissues according to their molecular protein signature. The clustering gives 3 main distinct groups. Within the tissues the ROIs (regions of interest) defined by these groups were used for microproteomics by micro-extraction of the tryptic peptides after on-tissue enzymatic digestion. More than 2500 proteins including 22 alternative proteins (AltProt) are identified by the Shotgun microproteomics. Statistical analysis on the basis of the label free quantification of the proteins shows a similar classification to the MALDI MSI segmentation into 3 groups. Functional analysis performed on each group reveals sub-networks related to neoplasia for group 1, glioma with inflammation for group 2 and neurogenesis for group 3. This demonstrates the interest on these new non-targeted large molecular data combining both MALDI MSI and microproteomics data, for tumor classification. This analysis provides new insights into grade III glioma organization. This specific information could allow a more accurate classification of the biopsies according to the prognosis and the identification of potential new targeted therapeutic options. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Emilie Le Rhun
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Lille University Hospital, Neuro-Oncology, Department of Neurosurgery, F-59000 Lille, France; Breast Unit, Department of Medical Oncology, Oscar Lambret Center, Lille, France.
| | - Marie Duhamel
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Maxence Wisztorski
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Jean-Pascal Gimeno
- ONCOLille, Maison Régionale de la Recherche Clinique, F-59000 Lille, France.
| | - Fahed Zairi
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Lille University Hospital, Department of Neurosurgery, F-59000 Lille, France.
| | - Fabienne Escande
- Lille University Hospital, Pôle Pathologie Biologique, Service Anatomie Pathologique, F-59000 Lille, France.
| | - Nicolas Reyns
- Lille University Hospital, Department of Neurosurgery, F-59000 Lille, France.
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon; Department of Psychiatry, Center of Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
| | - Claude-Alain Maurage
- Lille University Hospital, Pôle Pathologie Biologique, Service Anatomie Pathologique, F-59000 Lille, France.
| | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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A Proof of Concept to Bridge the Gap between Mass Spectrometry Imaging, Protein Identification and Relative Quantitation: MSI~LC-MS/MS-LF. Proteomes 2016; 4:proteomes4040032. [PMID: 28248242 PMCID: PMC5260965 DOI: 10.3390/proteomes4040032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section. Then, we did a back-correlation of the m/z of the proteins detected by MALDI-MSI to those identified by label-free quantitation. This allowed us to compare the label-free quantitation of proteins obtained in LC-MS/MS with the peak intensities observed in MALDI-MSI. We managed to link identification to nine peaks observed by MALDI-MSI. The results showed that the MSI~LC-MS/MS-LF workflow (i) allowed us to study a representative muscle proteome compared to a classical bottom-up workflow; and (ii) was sparsely impacted by matrix deposition and laser ablation. This workflow, performed as a proof-of-concept, suggests that a single tissue section can be used to perform MALDI-MSI and protein extraction, identification, and relative quantitation.
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Rocha B, Cillero-Pastor B, Blanco FJ, Ruiz-Romero C. MALDI mass spectrometry imaging in rheumatic diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:784-794. [PMID: 27742553 DOI: 10.1016/j.bbapap.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/29/2016] [Accepted: 10/04/2016] [Indexed: 01/15/2023]
Abstract
Mass spectrometry imaging (MSI) is a technique used to visualize the spatial distribution of biomolecules such as peptides, proteins, lipids or other organic compounds by their molecular masses. Among the different MSI strategies, MALDI-MSI provides a sensitive and label-free approach for imaging of a wide variety of protein or peptide biomarkers from the surface of tissue sections, being currently used in an increasing number of biomedical applications such as biomarker discovery and tissue classification. In the field of rheumatology, MALDI-MSI has been applied to date for the analysis of joint tissues such as synovial membrane or cartilage. This review summarizes the studies and key achievements obtained using MALDI-MSI to increase understanding on rheumatic pathologies and to describe potential diagnostic or prognostic biomarkers of these diseases. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Beatriz Rocha
- Proteomics Unit-ProteoRed/ISCIII, Rheumatology Group, INIBIC - Hospital Universitario de A Coruña, SERGAS, A Coruña, Spain
| | | | - Francisco J Blanco
- Proteomics Unit-ProteoRed/ISCIII, Rheumatology Group, INIBIC - Hospital Universitario de A Coruña, SERGAS, A Coruña, Spain; RIER-RED de Inflamación y Enfermedades Reumáticas, INIBIC-CHUAC, A Coruña, Spain.
| | - Cristina Ruiz-Romero
- Proteomics Unit-ProteoRed/ISCIII, Rheumatology Group, INIBIC - Hospital Universitario de A Coruña, SERGAS, A Coruña, Spain; CIBER-BBN Instituto de Salud Carlos III, INIBIC-CHUAC, A Coruña, Spain.
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Randall EC, Race AM, Cooper HJ, Bunch J. MALDI Imaging of Liquid Extraction Surface Analysis Sampled Tissue. Anal Chem 2016; 88:8433-40. [PMID: 27447021 DOI: 10.1021/acs.analchem.5b04281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Combined mass spectrometry imaging methods in which two different techniques are executed on the same sample have recently been reported for a number of sample types. Such an approach can be used to examine the sampling effects of the first technique with a second, higher resolution method and also combines the advantages of each technique for a more complete analysis. In this work matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) was used to study the effects of liquid extraction surface analysis (LESA) sampling on mouse brain tissue. Complementary multivariate analysis techniques including principal component analysis, non-negative matrix factorization, and t-distributed stochastic neighbor embedding were applied to MALDI MS images acquired from tissue which had been sampled by LESA to gain a better understanding of localized tissue washing in LESA sampling. It was found that MALDI MS images could be used to visualize regions sampled by LESA. The variability in sampling area, spatial precision, and delocalization of analytes in tissue induced by LESA were assessed using both single-ion images and images provided by multivariate analysis.
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Affiliation(s)
- Elizabeth C Randall
- National Physical Laboratory , Hampton Road, Teddington, Middlesex, TW11 0LW, United Kingdom
| | - Alan M Race
- National Physical Laboratory , Hampton Road, Teddington, Middlesex, TW11 0LW, United Kingdom
| | | | - Josephine Bunch
- National Physical Laboratory , Hampton Road, Teddington, Middlesex, TW11 0LW, United Kingdom.,School of Pharmacy, University of Nottingham , University Park, Nottingham, NG7 2RD, United Kingdom
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Wisztorski M, Desmons A, Quanico J, Fatou B, Gimeno JP, Franck J, Salzet M, Fournier I. Spatially-resolved protein surface microsampling from tissue sections using liquid extraction surface analysis. Proteomics 2016; 16:1622-32. [DOI: 10.1002/pmic.201500508] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/29/2016] [Accepted: 02/24/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Maxence Wisztorski
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Annie Desmons
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Jusal Quanico
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Benoit Fatou
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Jean-Pascal Gimeno
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
- ONCOLille; Maison Régionale de la Recherche Clinique; Lille France
| | - Julien Franck
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Michel Salzet
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Isabelle Fournier
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
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Donnarumma F, Murray KK. Laser ablation sample transfer for localized LC-MS/MS proteomic analysis of tissue. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:261-8. [PMID: 27041656 DOI: 10.1002/jms.3744] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 05/25/2023]
Abstract
We have developed a mid-infrared laser ablation sampling technique for nano-flow liquid chromatography coupled with tandem mass spectrometry proteomic profiling of discrete regions from biological samples. Laser ablation performed in transmission geometry was used to transfer material from 50-µm thick tissue sections mounted on a glass microscope slide to a capturing solvent. Captured samples were processed using filter-aided sample preparation and enzymatically digested to produce tryptic peptides for data-dependent analysis with an ion trap mass spectrometer. Comparison with ultraviolet laser capture microdissection from neighboring regions on the same tissue section revealed that infrared laser ablation transfer has higher reproducibility between samples from different consecutive sections. Both techniques allowed for proteomics investigation of different organelles without the addition of surfactants.
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Affiliation(s)
- Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
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Affiliation(s)
- Julia Laskin
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, WA 99352
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Box 599, 751 24 Uppsala, Sweden
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Donnarumma F, Cao F, Murray KK. Laser Ablation with Vacuum Capture for MALDI Mass Spectrometry of Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:108-116. [PMID: 26374229 DOI: 10.1007/s13361-015-1249-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/04/2015] [Accepted: 08/08/2015] [Indexed: 06/05/2023]
Abstract
We have developed a laser ablation sampling technique for matrix-assisted laser desorption ionization (MALDI) mass spectrometry and tandem mass spectrometry (MS/MS) analyses of in-situ digested tissue proteins. Infrared laser ablation was used to remove biomolecules from tissue sections for collection by vacuum capture and analysis by MALDI. Ablation and transfer of compounds from tissue removes biomolecules from the tissue and allows further analysis of the collected material to facilitate their identification. Laser ablated material was captured in a vacuum aspirated pipette-tip packed with C18 stationary phase and the captured material was dissolved, eluted, and analyzed by MALDI. Rat brain and lung tissue sections 10 μm thick were processed by in-situ trypsin digestion after lipid and salt removal. The tryptic peptides were ablated with a focused mid-infrared laser, vacuum captured, and eluted with an acetonitrile/water mixture. Eluted components were deposited on a MALDI target and mixed with matrix for mass spectrometry analysis. Initial experiments were conducted with peptide and protein standards for evaluation of transfer efficiency: a transfer efficiency of 16% was obtained using seven different standards. Laser ablation vacuum capture was applied to freshly digested tissue sections and compared with sections processed with conventional MALDI imaging. A greater signal intensity and lower background was observed in comparison with the conventional MALDI analysis. Tandem time-of-flight MALDI mass spectrometry was used for compound identification in the tissue.
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Affiliation(s)
- Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fan Cao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Rao W, Pan N, Tian X, Yang Z. High-Resolution Ambient MS Imaging of Negative Ions in Positive Ion Mode: Using Dicationic Reagents with the Single-Probe. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:124-134. [PMID: 26489411 PMCID: PMC4924531 DOI: 10.1007/s13361-015-1287-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 05/30/2023]
Abstract
We have used the Single-probe, a miniaturized sampling device utilizing in-situ surface microextraction for ambient mass spectrometry (MS) analysis, for the high resolution MS imaging (MSI) of negatively charged species in the positive ionization mode. Two dicationic compounds, 1,5-pentanediyl-bis(1-butylpyrrolidinium) difluoride [C5(bpyr)2F2] and 1,3-propanediyl-bis(tripropylphosphonium) difluoride [C3(triprp)2F2], were added into the sampling solvent to form 1+ charged adducts with the negatively charged species extracted from tissues. We were able to detect 526 and 322 negatively charged species this way using [C5(bpyr)2F2] and [C3(triprp)2F2], respectively, including oleic acid, arachidonic acid, and several species of phosphatidic acid, phosphoethanolamine, phosphatidylserine, phosphatidylglycerol, phosphatidylinositol, and others. In conjunction with the identification of the non-adduct cations, we have tentatively identified a total number of 1200 and 828 metabolites from mouse brain sections using [C5(bpyr)2F2] and [C3(triprp)2F2], respectively, through high mass accuracy measurements (mass error <5 ppm); MS/MS analyses were also performed to verify the identity of selected species. In addition to the high mass accuracy measurement, we were able to generate high spatial resolution (~17 μm) MS images of mouse brain sections. Our study demonstrated that utilization of dicationic compounds in the surface microextraction with the Single-probe device can perform high mass and spatial resolution ambient MSI measurements of broader types of compounds in tissues. Other reagents can be potentially used with the Single-probe device for a variety of reactive MSI studies to enable the analysis of species that are previously intractable.
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48
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Fatou B, Wisztorski M, Focsa C, Salzet M, Ziskind M, Fournier I. Substrate-Mediated Laser Ablation under Ambient Conditions for Spatially-Resolved Tissue Proteomics. Sci Rep 2015; 5:18135. [PMID: 26674367 PMCID: PMC4682183 DOI: 10.1038/srep18135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/13/2015] [Indexed: 01/06/2023] Open
Abstract
Numerous applications of ambient Mass Spectrometry (MS) have been demonstrated over the past decade. They promoted the emergence of various micro-sampling techniques such as Laser Ablation/Droplet Capture (LADC). LADC consists in the ablation of analytes from a surface and their subsequent capture in a solvent droplet which can then be analyzed by MS. LADC is thus generally performed in the UV or IR range, using a wavelength at which analytes or the matrix absorb. In this work, we explore the potential of visible range LADC (532 nm) as a micro-sampling technology for large-scale proteomics analyses. We demonstrate that biomolecule analyses using 532 nm LADC are possible, despite the low absorbance of biomolecules at this wavelength. This is due to the preponderance of an indirect substrate-mediated ablation mechanism at low laser energy which contrasts with the conventional direct ablation driven by sample absorption. Using our custom LADC system and taking advantage of this substrate-mediated ablation mechanism, we were able to perform large-scale proteomic analyses of micro-sampled tissue sections and demonstrated the possible identification of proteins with relevant biological functions. Consequently, the 532 nm LADC technique offers a new tool for biological and clinical applications.
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Affiliation(s)
- Benoit Fatou
- Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France.,Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Maxence Wisztorski
- Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Cristian Focsa
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Michel Salzet
- Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Michael Ziskind
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Isabelle Fournier
- Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
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49
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Addie RD, Balluff B, Bovée JVMG, Morreau H, McDonnell LA. Current State and Future Challenges of Mass Spectrometry Imaging for Clinical Research. Anal Chem 2015; 87:6426-33. [DOI: 10.1021/acs.analchem.5b00416] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ruben D. Addie
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Liam A. McDonnell
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
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Li C, Zang T, Wrobel K, Huang JTJ, Nabi G. Quantitative urinary proteomics using stable isotope labelling by peptide dimethylation in patients with prostate cancer. Anal Bioanal Chem 2015; 407:3393-404. [PMID: 25724369 DOI: 10.1007/s00216-015-8569-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/30/2015] [Accepted: 02/16/2015] [Indexed: 01/14/2023]
Abstract
Prostate cancer (PCa) is the most commonly diagnosed malignancy in men. The current prevalent diagnosis method, prostate-specific antigen (PSA) screening test, has low sensitivity, specificity and is poor at predicting the grade of disease. Thus, new biomarkers are urgently needed to improve the PCa diagnosis and staging for the management of patients. The aim of this study is to investigate the first voided urinary sample after massage for biomarker discovery for PCa. In this work, untargeted metabolomic profiling of the first voided urinary sample after massage from 28 confirmed prostate cancer patients, 20 benign enlarged prostate patients and 6 healthy volunteers was performed using liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS). Single and multiple peptide protein and cross-linking molecules were identified using PEAKS software. Analytical and diagnostic performance was tested using the Student's t test, Benjamini Hochberg correction and the receiver operating characteristic (ROC) curves. Using differential display analysis to compare peptides and cross-linking molecules of urinary samples between patients with benign, enlarged prostate and malignant cancer, we identified multiple peptides derived from osteopontin (SPP1) and prothrombin (F2) that are lower in PCa patients than in benign and enlarged prostate. The diagnosis accuracies of SPP1 and F2 peptides are 0.65-0.77 and 0.68-0.72, respectively. In addition to this, there are significant differences between PCa and benign/enlarged prostate patients in pyridinoline (PYD) and deoxypyridinoline (DPD) (p value = 0.001). Differences also, as shown in the excretion of these molecules for different stages of PCa (p value = 0.04) as the level of DPD and DPD/PYD ratio, were high in patients with locally advanced tumours. The study underscores the importance of proteomics analysis, and our results demonstrate that a urinary-based in depth proteomic approach allows the potential identification of dysregulated pathways and diagnostic biomarkers.
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Affiliation(s)
- Chunhui Li
- Academic Section of Urology, Division of Imaging Technology, University of Dundee, Ninewells Hospital, Dundee, DD1 9SY, UK
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