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Purohit K, Reddy N, Sunna A. Exploring the Potential of Bioactive Peptides: From Natural Sources to Therapeutics. Int J Mol Sci 2024; 25:1391. [PMID: 38338676 PMCID: PMC10855437 DOI: 10.3390/ijms25031391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Bioactive peptides, specific protein fragments with positive health effects, are gaining traction in drug development for advantages like enhanced penetration, low toxicity, and rapid clearance. This comprehensive review navigates the intricate landscape of peptide science, covering discovery to functional characterization. Beginning with a peptidomic exploration of natural sources, the review emphasizes the search for novel peptides. Extraction approaches, including enzymatic hydrolysis, microbial fermentation, and specialized methods for disulfide-linked peptides, are extensively covered. Mass spectrometric analysis techniques for data acquisition and identification, such as liquid chromatography, capillary electrophoresis, untargeted peptide analysis, and bioinformatics, are thoroughly outlined. The exploration of peptide bioactivity incorporates various methodologies, from in vitro assays to in silico techniques, including advanced approaches like phage display and cell-based assays. The review also discusses the structure-activity relationship in the context of antimicrobial peptides (AMPs), ACE-inhibitory peptides (ACEs), and antioxidative peptides (AOPs). Concluding with key findings and future research directions, this interdisciplinary review serves as a comprehensive reference, offering a holistic understanding of peptides and their potential therapeutic applications.
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Affiliation(s)
- Kruttika Purohit
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
| | - Narsimha Reddy
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
- School of Science, Parramatta Campus, Western Sydney University, Penrith, NSW 2751, Australia
| | - Anwar Sunna
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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2
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Schrader M. Origins, Technological Advancement, and Applications of Peptidomics. Methods Mol Biol 2024; 2758:3-47. [PMID: 38549006 DOI: 10.1007/978-1-0716-3646-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.
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Affiliation(s)
- Michael Schrader
- Department of Bioengineering Sciences, Weihenstephan-Tr. University of Applied Sciences, Freising, Germany.
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3
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Zaikin VG, Borisov RS. Mass Spectrometry as a Crucial Analytical Basis for Omics Sciences. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [PMCID: PMC8693159 DOI: 10.1134/s1061934821140094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review is devoted to the consideration of mass spectrometric platforms as applied to omics sciences. The most significant attention is paid to omics related to life sciences (genomics, proteomics, meta-bolomics, lipidomics, glycomics, plantomics, etc.). Mass spectrometric approaches to solving the problems of petroleomics, polymeromics, foodomics, humeomics, and exosomics, related to inorganic sciences, are also discussed. The review comparatively presents the advantages of various principles of separation and mass spectral techniques, complementary derivatization, used to obtain large arrays of various structural and quantitative information in the mentioned omics sciences.
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Affiliation(s)
- V. G. Zaikin
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R. S. Borisov
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991 Moscow, Russia
- RUDN University, 117198 Moscow, Russia
- Core Facility Center “Arktika,” Northern (Arctic) Federal University, 163002 Arkhangelsk, Russia
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4
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McMillen JC, Gutierrez DB, Judd AM, Spraggins JM, Caprioli RM. Enhancement of Tryptic Peptide Signals from Tissue Sections Using MALDI IMS Postionization (MALDI-2). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2583-2591. [PMID: 34515472 DOI: 10.1021/jasms.1c00213] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for highly multiplexed, unlabeled mapping of analytes from tissue sections. However, further work is needed to improve the sensitivity and depth of coverage for protein and peptide IMS. We demonstrate signal enhancement of proteolytic peptides from thin tissue sections of human kidney by conventional MALDI (MALDI-1) augmented using a second ionizing laser (termed MALDI-2). Proteins were digested in situ using trypsin prior to IMS analysis. For tentative identification of peptides and proteins, a tissue homogenate from the same organ used for IMS was analyzed by LC-MS/MS, and data are available via ProteomeXchange with identifier PXD023877. These identified proteins were then digested in silico to generate a database of theoretical peptides to then match to MALDI IMS data sets. Peptides were tentatively identified by matching the MALDI peak list to the database peptide list based on mass accuracy (5 ppm mass error). This resulted in 1337 ± 96 (n = 3) peptides and 2076 ± 362 (n = 3) unique peptides matched to IMS peaks from MALDI-1 and MALDI-2, respectively. Protein identifications requiring two or more peptides per protein resulted in 276 ± 20 proteins with MALDI-1 and 401 ± 60 with MALDI-2. These results demonstrate that MALDI-2 provides enhanced sensitivity for the spatial mapping of tryptic peptides and significantly increases the number of proteins identified in IMS experiments.
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Affiliation(s)
- Josiah C McMillen
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Audra M Judd
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue S #3218, Nashville, Tennessee 37205, United States
| | - Richard M Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 1161 21st Avenue S, Nashville, Tennessee 37232, United States
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5
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Foreman RE, George AL, Reimann F, Gribble FM, Kay RG. Peptidomics: A Review of Clinical Applications and Methodologies. J Proteome Res 2021; 20:3782-3797. [PMID: 34270237 DOI: 10.1021/acs.jproteome.1c00295] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improvements in both liquid chromatography (LC) and mass spectrometry (MS) instrumentation have greatly enhanced proteomic and small molecule metabolomic analysis in recent years. Less focus has been on the improved capability to detect and quantify small bioactive peptides, even though the exact sequences of the peptide species produced can have important biological consequences. Endogenous bioactive peptide hormones, for example, are generated by the targeted and regulated cleavage of peptides from their prohormone sequence. This process may include organ specific variants, as proglucagon is converted to glucagon in the pancreas but glucagon-like peptide-1 (GLP-1) in the small intestine, with glucagon raising, whereas GLP-1, as an incretin, lowering blood glucose. Therefore, peptidomics workflows must preserve the structure of the processed peptide products to prevent the misidentification of ambiguous peptide species. The poor in vivo and in vitro stability of peptides in biological matrices is a major factor that needs to be considered when developing methods to study them. The bioinformatic analysis of peptidomics data sets requires the inclusion of specific post-translational modifications, which are critical for the function of many bioactive peptides. This review aims to discuss and contrast the various extraction, analytical, and bioinformatics approaches used for human peptidomics studies in a multitude of matrices.
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Affiliation(s)
- Rachel E Foreman
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Amy L George
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Frank Reimann
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Fiona M Gribble
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Richard G Kay
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
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Vu NQ, DeLaney K, Li L. Neuropeptidomics: Improvements in Mass Spectrometry Imaging Analysis and Recent Advancements. Curr Protein Pept Sci 2021; 22:158-169. [PMID: 33200705 PMCID: PMC8330971 DOI: 10.2174/1389203721666201116115708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022]
Abstract
Neuropeptides are an important class of endogenous peptides in the nervous system that regulate physiological functions such as feeding, glucose homeostasis, pain, memory, reproduction, and many others. In order to understand the functional role of neuropeptides in diseases or disorders, studies investigating their dysregulation in terms of changes in abundance and localization must be carried out. As multiple neuropeptides are believed to play a functional role in each physiological process, techniques capable of global profiling multiple neuropeptides simultaneously are desired. Mass spectrometry is well-suited for this goal due to its ability to perform untargeted measurements without prior comprehensive knowledge of the analytes of interest. Mass spectrometry imaging (MSI) is particularly useful because it has the capability to image a large variety of peptides in a single experiment without labeling. Like all analytical techniques, careful sample preparation is critical to successful MSI analysis. The first half of this review focuses on recent developments in MSI sample preparation and instrumentation for analyzing neuropeptides and other biomolecules in which the sample preparation technique may be directly applicable for neuropeptide analysis. The benefit offered by incorporating these techniques is shown as improvement in a number of observable neuropeptides, enhanced signal to noise, increased spatial resolution, or a combination of these aspects. The second half of this review focuses on recent biological discoveries about neuropeptides resulting from these improvements in MSI analysis. The recent progress in neuropeptide detection and analysis methods, including the incorporation of various tissue washes, matrices, instruments, ionization sources, and computation approaches combined with the advancements in understanding neuropeptide function in a variety of model organisms, indicates the potential for the utilization of MSI analysis of neuropeptides in clinical settings.
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Affiliation(s)
- Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Kellen DeLaney
- 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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7
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Vestal M, Li L, Dobrinskikh E, Shi Y, Wang B, Shi X, Li S, Vestal C, Parker K. Rapid MALDI-TOF molecular imaging: Instrument enhancements and their practical consequences. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4423. [PMID: 31314129 DOI: 10.1002/jms.4423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
A new high performance linear MALDI-TOF mass spectrometer provides both high spatial resolution and high speed. This instrument employs a new ion optics system with a grounded ion source and efficient transfer and detection of ions over a broad mass range. This provides very high sensitivity, precision, and an extended dynamic range for both positive and negative ion detection. Here we demonstrate the capabilities of this system by imaging pancreatic tissue samples from rats and mice.
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Affiliation(s)
- Marvin Vestal
- SimulTOF Systems, Virgin Instruments Corp, Marlborough, Massachusetts, 01752
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | | | - Yatao Shi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705
| | - Bowen Wang
- Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, 43210
| | - Xudong Shi
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705
| | - Sicheng Li
- SimulTOF Systems, Virgin Instruments Corp, Marlborough, Massachusetts, 01752
| | - Christina Vestal
- SimulTOF Systems, Virgin Instruments Corp, Marlborough, Massachusetts, 01752
| | - Kenneth Parker
- SimulTOF Systems, Virgin Instruments Corp, Marlborough, Massachusetts, 01752
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8
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Ščupáková K, Balluff B, Tressler C, Adelaja T, Heeren RM, Glunde K, Ertaylan G. Cellular resolution in clinical MALDI mass spectrometry imaging: the latest advancements and current challenges. Clin Chem Lab Med 2020; 58:914-929. [PMID: 31665113 PMCID: PMC9867918 DOI: 10.1515/cclm-2019-0858] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is the workhorse of metabolomics, proteomics and lipidomics. Mass spectrometry imaging (MSI), its extension to spatially resolved analysis of tissues, is a powerful tool for visualizing molecular information within the histological context of tissue. This review summarizes recent developments in MSI and highlights current challenges that remain to achieve molecular imaging at the cellular level of clinical specimens. We focus on matrix-assisted laser desorption/ionization (MALDI)-MSI. We discuss the current status of each of the analysis steps and remaining challenges to reach the desired level of cellular imaging. Currently, analyte delocalization and degradation, matrix crystal size, laser focus restrictions and detector sensitivity are factors that are limiting spatial resolution. New sample preparation devices and laser optic systems are being developed to push the boundaries of these limitations. Furthermore, we review the processing of cellular MSI data and images, and the systematic integration of these data in the light of available algorithms and databases. We discuss roadblocks in the data analysis pipeline and show how technology from other fields can be used to overcome these. Finally, we conclude with curative and community efforts that are needed to enable contextualization of the information obtained.
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Affiliation(s)
- Klára Ščupáková
- Maastricht MultiModal Molecular Imaging Institute (M4I), University of Maastricht, Maastricht, The Netherlands
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), University of Maastricht, Maastricht, The Netherlands
| | - Caitlin Tressler
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tobi Adelaja
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ron M.A. Heeren
- Corresponding author: Ron M.A. Heeren, Maastricht MultiModal Molecular Imaging Institute (M4I), University of Maastricht, Maastricht, The Netherlands,
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; and The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gökhan Ertaylan
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
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9
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Berghmans E, Jacobs J, Deben C, Hermans C, Broeckx G, Smits E, Maes E, Raskin J, Pauwels P, Baggerman G. Mass Spectrometry Imaging Reveals Neutrophil Defensins as Additional Biomarkers for Anti-PD-(L)1 Immunotherapy Response in NSCLC Patients. Cancers (Basel) 2020; 12:E863. [PMID: 32252405 PMCID: PMC7225984 DOI: 10.3390/cancers12040863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/17/2022] Open
Abstract
(1) Background: Therapeutic blocking of the interaction between programmed death-1 (PD-1) with its ligand PD-L1, an immune checkpoint, is a promising approach to restore the antitumor immune response. Improved clinical outcomes have been shown in different human cancers, including non-small cell lung cancer (NSCLC). Unfortunately, still a high number of NSCLC patients are treated with immunotherapy without obtaining any clinical benefit, due to the limitations of PD-L1 protein expression as the currently sole predictive biomarker for clinical use; (2) Methods: In this study, we applied mass spectrometry imaging (MSI) to discover new protein biomarkers, and to assess the possible correlation between candidate biomarkers and a positive immunotherapy response by matrix-assisted laser desorption/ionization (MALDI) MSI in 25 formalin-fixed paraffin-embedded (FFPE) pretreatment tumor biopsies (Biobank@UZA); (3) Results: Using MALDI MSI, we revealed that the addition of neutrophil defensin 1, 2 and 3 as pretreatment biomarkers may more accurately predict the outcome of immunotherapy treatment in NSCLC. These results were verified and confirmed with immunohistochemical analyses. In addition, we provide in-vitro evidence of the immune stimulatory effect of neutrophil defensins towards cancer cells; and (4) Conclusions: With proteomic approaches, we have discovered neutrophil defensins as additional prospective biomarkers for an anti-PD-(L)1 immunotherapy response. Thereby, we also demonstrated that the neutrophil defensins contribute in the activation of the immune response towards cancer cells, which could provide a new lead towards an anticancer therapy.
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Affiliation(s)
- Eline Berghmans
- Centre for Proteomics, University of Antwerp, 2020 Antwerpen, Belgium;
- Health Unit, VITO, 2400 Mol, Belgium
| | - Julie Jacobs
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Christophe Deben
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Christophe Hermans
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Glenn Broeckx
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Evelien Smits
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., Lincoln 7674, New Zealand;
| | - Jo Raskin
- Thoracic Oncology Department, Antwerp University Hospital, 2650 Edegem, Belgium;
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp, 2610 Wilrijk, Belgium; (J.J.); (C.D.); (C.H.); (G.B.); (E.S.); (P.P.)
- Pathology Department, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, 2020 Antwerpen, Belgium;
- Health Unit, VITO, 2400 Mol, Belgium
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Prentice BM, Hart NJ, Phillips N, Haliyur R, Judd A, Armandala R, Spraggins JM, Lowe CL, Boyd KL, Stein RW, Wright CV, Norris JL, Powers AC, Brissova M, Caprioli RM. Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. Diabetologia 2019; 62:1036-1047. [PMID: 30955045 PMCID: PMC6553460 DOI: 10.1007/s00125-019-4855-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/20/2019] [Indexed: 12/20/2022]
Abstract
AIMS/HYPOTHESIS The molecular response and function of pancreatic islet cells during metabolic stress is a complex process. The anatomical location and small size of pancreatic islets coupled with current methodological limitations have prevented the achievement of a complete, coherent picture of the role that lipids and proteins play in cellular processes under normal conditions and in diseased states. Herein, we describe the development of untargeted tissue imaging mass spectrometry (IMS) technologies for the study of in situ protein and, more specifically, lipid distributions in murine and human pancreases. METHODS We developed matrix-assisted laser desorption/ionisation (MALDI) IMS protocols to study metabolite, lipid and protein distributions in mouse (wild-type and ob/ob mouse models) and human pancreases. IMS allows for the facile discrimination of chemically similar lipid and metabolite isoforms that cannot be distinguished using standard immunohistochemical techniques. Co-registration of MS images with immunofluorescence images acquired from serial tissue sections allowed accurate cross-registration of cell types. By acquiring immunofluorescence images first, this serial section approach guides targeted high spatial resolution IMS analyses (down to 15 μm) of regions of interest and leads to reduced time requirements for data acquisition. RESULTS MALDI IMS enabled the molecular identification of specific phospholipid and glycolipid isoforms in pancreatic islets with intra-islet spatial resolution. This technology shows that subtle differences in the chemical structure of phospholipids can dramatically affect their distribution patterns and, presumably, cellular function within the islet and exocrine compartments of the pancreas (e.g. 18:1 vs 18:2 fatty acyl groups in phosphatidylcholine lipids). We also observed the localisation of specific GM3 ganglioside lipids [GM3(d34:1), GM3(d36:1), GM3(d38:1) and GM3(d40:1)] within murine islet cells that were correlated with a higher level of GM3 synthase as verified by immunostaining. However, in human pancreas, GM3 gangliosides were equally distributed in both the endocrine and exocrine tissue, with only one GM3 isoform showing islet-specific localisation. CONCLUSIONS/INTERPRETATION The development of more complete molecular profiles of pancreatic tissue will provide important insight into the molecular state of the pancreas during islet development, normal function, and diseased states. For example, this study demonstrates that these results can provide novel insight into the potential signalling mechanisms involving phospholipids and glycolipids that would be difficult to detect by targeted methods, and can help raise new hypotheses about the types of physiological control exerted on endocrine hormone-producing cells in islets. Importantly, the in situ measurements afforded by IMS do not require a priori knowledge of molecules of interest and are not susceptible to the limitations of immunohistochemistry, providing the opportunity for novel biomarker discovery. Notably, the presence of multiple GM3 isoforms in mouse islets and the differential localisation of lipids in human tissue underscore the important role these molecules play in regulating insulin modulation and suggest species, organ, and cell specificity. This approach demonstrates the importance of both high spatial resolution and high molecular specificity to accurately survey the molecular composition of complex, multi-functional tissues such as the pancreas.
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Affiliation(s)
- Boone M Prentice
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Nathaniel J Hart
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil Phillips
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachana Haliyur
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Audra Judd
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Radhika Armandala
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey M Spraggins
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Cindy L Lowe
- Translational Pathology Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelli L Boyd
- Translational Pathology Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roland W Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Christopher V Wright
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Jeremy L Norris
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Marcela Brissova
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Richard M Caprioli
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN, USA.
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Berghmans E, Van Raemdonck G, Schildermans K, Willems H, Boonen K, Maes E, Mertens I, Pauwels P, Baggerman G. MALDI Mass Spectrometry Imaging Linked with Top-Down Proteomics as a Tool to Study the Non-Small-Cell Lung Cancer Tumor Microenvironment. Methods Protoc 2019; 2:mps2020044. [PMID: 31164623 PMCID: PMC6632162 DOI: 10.3390/mps2020044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Advanced non-small-cell lung cancer (NSCLC) is generally linked with a poor prognosis and is one of the leading causes of cancer-related deaths worldwide. Since only a minority of the patients respond well to chemotherapy and/or targeted therapies, immunotherapy might be a valid alternative in the lung cancer treatment field, as immunotherapy attempts to strengthen the body’s own immune response to recognize and eliminate malignant tumor cells. However, positive response patterns to immunotherapy remain unclear. In this study, we demonstrate how immune-related factors could be visualized from single NSCLC tissue sections (Biobank@UZA) while retaining their spatial information by using matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), in order to unravel the molecular profile of NSCLC patients. In this way, different regions in lung cancerous tissues could be discriminated based on the molecular composition. In addition, we linked visualization (MALDI MSI) and identification (based on liquid chromatography higher resolution mass spectrometry) of the molecules of interest for the correct biological interpretation of the observed molecular differences within the area in which these molecules are detected. This is of major importance to fully understand the underlying molecular profile of the NSCLC tumor microenvironment.
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Affiliation(s)
- Eline Berghmans
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Geert Van Raemdonck
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
| | - Karin Schildermans
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Hanny Willems
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., 8140 Christchurch, New Zealand.
| | - Inge Mertens
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
| | - Patrick Pauwels
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Belgium.
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
- Health Unit, VITO, Boeretang 200, 2400 Mol, Belgium.
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12
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Pan F, He X, Feng J, Cui W, Gao L, Li M, Yang H, Wang C, Hu Y. Peptidome analysis reveals the involvement of endogenous peptides in mouse pancreatic dysfunction with aging. J Cell Physiol 2019; 234:14090-14099. [PMID: 30618084 DOI: 10.1002/jcp.28098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/13/2018] [Indexed: 01/15/2023]
Abstract
Type 2 diabetes (T2D) is a glucose regulation disorder that has significantly enhanced mortality and the global disease burden. The prevalence of T2D has increased worldwide and is higher in the elderly. The function of pancreatic islets decreases with age, which is one important reason for the occurrence of diabetes in the elderly. Recently, peptidome analysis has attracted attention. However, the role of age-related peptides in pancreatic dysfunction has not been investigated extensively. Here, we conducted a comparison of endogenous peptides between pancreas from adult and aging mice by liquid chromatography tandem mass spectrometry (LC-MS/MS). A total of 2,089 peptides originating from 1,280 protein precursors were identified, of which 232 were upregulated and 183 were downregulated in the aging mice (fold change ≥ 2 and p < 0.05), suggesting that the expression of pancreatic peptides in mice varied with age. The molecular weight of most peptides was <3.0 kDa, and the isoelectric point distribution had a bimodal characteristic. Further analysis of cleavage site patterns indicated that proteases cleaved pancreatic proteins according to their rules. Moreover, Gene Ontology and pathway analyses showed that the differentially expressed peptides potentially had specific effects on pancreatic dysfunction. Some differential peptides were located within the domains of precursor proteins that were closely associated with the development of diabetes. We believe that our research may advance the current understanding of pancreas-derived peptides and that certain peptides may be involved in the etiology of diabetes.
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Affiliation(s)
- Fenghui Pan
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xuan He
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Feng
- Department of Laboratory and Inspection Center, Jiangsu Institute of Planned Parenthood Research, Nanjing, Jiangsu, China
| | - Wenxia Cui
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Gao
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Man Li
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Haiyan Yang
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chun Wang
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun Hu
- Division of Geriatrics, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Chemistry, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
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13
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Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
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Aerts J, Laeremans A, Minerva L, Boonen K, Harshavardhan B, D'hooge R, Valkenborg D, Baggerman G, Arckens L. MS imaging and mass spectrometric synaptosome profiling identify PEP-19/pcp4 as a synaptic molecule involved in spatial learning in mice. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:936-945. [PMID: 27760390 DOI: 10.1016/j.bbapap.2016.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/07/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
The Morris water maze (MWM) spatial learning task has been demonstrated to involve a cognitive switch of action control to serve the transition from an early towards a late learning phase. However, the molecular mechanisms governing this switch are largely unknown. We employed MALDI MS imaging (MSI) to screen for changes in expression of small proteins in brain structures implicated in the different learning phases. We compared mice trained for 3days and 30days in the MWM, reflecting an early and a late learning phase in relation to the acquisition of a spatial learning task. An ion with m/z of 6724, identified as PEP-19/pcp4 by top-down tandem MS, was detected at higher intensity in the dorsal striatum of the late learning phase group compared with the early learning phase group. In addition, mass spectrometric analysis of synaptosomes confirmed the presence of PEP-19/pcp4 at the synapse. PEP-19/pcp4 has previously been identified as a critical determinant of synaptic plasticity in locomotor learning. Our findings extend PEP-19/pcp4 function to spatial learning in the forebrain and put MSI forward as a valid and unbiased research strategy for the discovery and identification of the molecular machinery involved in learning, memory and synaptic plasticity. 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)
- Jeroen Aerts
- KU Leuven, Department of Biology, Laboratory of Neuroplasticity and Neuroproteomics, Naamsestraat 59, 3000 Leuven, Belgium
| | - Annelies Laeremans
- KU Leuven, Department of Biology, Laboratory of Neuroplasticity and Neuroproteomics, Naamsestraat 59, 3000 Leuven, Belgium
| | - Laurens Minerva
- KU Leuven, Department of Biology, Laboratory of Neuroplasticity and Neuroproteomics, Naamsestraat 59, 3000 Leuven, Belgium
| | - Kurt Boonen
- KU Leuven, Department of Biology, Laboratory of Functional Genomics and Proteomics, Naamsestraat 59, 3000 Leuven, Belgium
| | | | - Rudi D'hooge
- KU Leuven, Laboratory of Biological Psychology, Tiensestraat 102, 3000 Leuven, Belgium
| | - Dirk Valkenborg
- Center for Proteomics, UAntwerp, Antwerp, Belgium; Unit Environmental Risk & Health, VITO, Mol, Belgium
| | - Geert Baggerman
- Center for Proteomics, UAntwerp, Antwerp, Belgium; Unit Environmental Risk & Health, VITO, Mol, Belgium
| | - Lutgarde Arckens
- KU Leuven, Department of Biology, Laboratory of Neuroplasticity and Neuroproteomics, Naamsestraat 59, 3000 Leuven, Belgium.
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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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16
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Buchberger A, Yu Q, Li L. Advances in Mass Spectrometric Tools for Probing Neuropeptides. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:485-509. [PMID: 26070718 PMCID: PMC6314846 DOI: 10.1146/annurev-anchem-071114-040210] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Neuropeptides are important mediators in the functionality of the brain and other neurological organs. Because neuropeptides exist in a wide range of concentrations, appropriate characterization methods are needed to provide dynamic, chemical, and spatial information. Mass spectrometry and compatible tools have been a popular choice in analyzing neuropeptides. There have been several advances and challenges, both of which are the focus of this review. Discussions range from sample collection to bioinformatic tools, although avenues such as quantitation and imaging are included. Further development of the presented methods for neuropeptidomic mass spectrometric analysis is inevitable, which will lead to a further understanding of the complex interplay of neuropeptides and other signaling molecules in the nervous system.
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Affiliation(s)
- Amanda Buchberger
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1322;
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222;
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1322;
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222;
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17
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Spraggins JM, Rizzo DG, Moore JL, Rose KL, Hammer ND, Skaar EP, Caprioli RM. MALDI FTICR IMS of Intact Proteins: Using Mass Accuracy to Link Protein Images with Proteomics Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:974-85. [PMID: 25904064 PMCID: PMC4442642 DOI: 10.1007/s13361-015-1147-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 05/11/2023]
Abstract
MALDI imaging mass spectrometry is a highly sensitive and selective tool used to visualize biomolecules in tissue. However, identification of detected proteins remains a difficult task. Indirect identification strategies have been limited by insufficient mass accuracy to confidently link ion images to proteomics data. Here, we demonstrate the capabilities of MALDI FTICR MS for imaging intact proteins. MALDI FTICR IMS provides an unprecedented combination of mass resolving power (~75,000 at m/z 5000) and accuracy (<5ppm) for proteins up to ~12kDa, enabling identification based on correlation with LC-MS/MS proteomics data. Analysis of rat brain tissue was performed as a proof-of-concept highlighting the capabilities of this approach by imaging and identifying a number of proteins including N-terminally acetylated thymosin β(4) (m/z 4,963.502, 0.6ppm) and ATP synthase subunit ε (m/z 5,636.074, -2.3ppm). MALDI FTICR IMS was also used to differentiate a series of oxidation products of S100A8 (m/z 10,164.03, -2.1ppm), a subunit of the heterodimer calprotectin, in kidney tissue from mice infected with Staphylococcus aureus. S100A8 - M37O/C42O(3) (m/z 10228.00, -2.6ppm) was found to co-localize with bacterial microcolonies at the center of infectious foci. The ability of MALDI FTICR IMS to distinguish S100A8 modifications is critical to understanding calprotectin's roll in nutritional immunity.
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Affiliation(s)
- Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37205, USA,
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18
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Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
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Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
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19
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Crecelius AC, Schubert US, von Eggeling F. MALDI mass spectrometric imaging meets “omics”: recent advances in the fruitful marriage. Analyst 2015; 140:5806-20. [DOI: 10.1039/c5an00990a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) is a method that allows the investigation of the molecular content of surfaces, in particular, tissues, within its morphological context.
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Affiliation(s)
- A. C. Crecelius
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - U. S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - F. von Eggeling
- Jena Center for Soft Matter (JCSM)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Institute of Physical Chemistry
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20
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Schrader M, Schulz-Knappe P, Fricker LD. Historical perspective of peptidomics. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Minerva L, Ceulemans A, Baggerman G, Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin Appl 2014; 6:581-95. [PMID: 23090913 DOI: 10.1002/prca.201200033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/12/2022]
Abstract
MALDI MS imaging (MSI) is an analytical tool capable of providing spatial distribution and relative abundance of biomolecules directly in tissue. After 15 years of intense efforts to improve the acquisition and quality of molecular images, MSI has matured into an asset of the proteomic toolbox. The power of MSI lies in the ability to differentiate tissue regions that are not histologically distinct but are characterized by different MS profiles. Recently, MSI has been gaining momentum in biomedical research and has found applications in disease diagnosis and prognosis, biomarker discovery, and drug therapy. Although the technology holds great promise, MSI is still faced with a set of methodological challenges presented by the clinical setting. There is a growing awareness regarding this topic and efforts are being taken to develop clear and practical standards to overcome these challenges. This review presents an overview of MALDI MSI as a biomarker discovery tool and recent methodological progress in the field.
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Affiliation(s)
- Laurens Minerva
- Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Leuven, Belgium
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22
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Škrášková K, Heeren RM. A review of complementary separation methods and matrix assisted laser desorption ionization-mass spectrometry imaging: Lowering sample complexity. J Chromatogr A 2013; 1319:1-13. [DOI: 10.1016/j.chroma.2013.10.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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23
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Ghosh S, Sengupta A, Sharma S, Sonawat HM. Metabolic perturbations of kidney and spleen in murine cerebral malaria: (1)H NMR-based metabolomic study. PLoS One 2013; 8:e73113. [PMID: 24039868 PMCID: PMC3765208 DOI: 10.1371/journal.pone.0073113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/18/2013] [Indexed: 02/02/2023] Open
Abstract
A significant fraction of global population is under the threat of malaria. Majority of annual death is due to the more complicated form of the infection i.e. the cerebral form, also known as Cerebral Malaria (CM). Host parasite interaction is known to cause a cascade of events in various tissues like brain, liver, kidney, and spleen. We have employed (1)H NMR based metabolomics to understand the specific perturbations of various tissues in CM. In our previous paper we have delineated the differences between CM vis-a-vis non-cerebral malaria (NCM) mice in serum, liver and brain. In this paper we focus on their differences of metabolic profile in kidney and spleen as kidney dysfunction and splenomegaly are known to be associated to neurological outcome of the disease. Moreover we have also looked into how the biological compartments (kidney, spleen and serum) interact with each other. The various metabolites involved in such interactions and their correlational aspects across the compartments have been studied in CM, NCM and control mice. The idea was to find out the specific pathways that are altered in CM mice. Our results demonstrate that both the kidney as well as spleen metabolism are differentially perturbed in CM with respect to NCM. The results point out that glutamate levels are decreased in CM mice with respect to NCM mice both in case of spleen and kidney while creatine, myo-inositol and betaine levels are increased in kidney of CM mice with respect to NCM mice. From the analysis of Multiway Principal Component Analysis (MPCA) we see that lipid metabolism and TCA cycle is altered in kidney and spleen.
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Affiliation(s)
- Soumita Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Arjun Sengupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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24
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Gustafsson OJR, Eddes JS, Meding S, McColl SR, Oehler MK, Hoffmann P. Matrix-assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin-fixed tissue. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:655-670. [PMID: 23418145 DOI: 10.1002/rcm.6488] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/07/2012] [Accepted: 12/10/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the means to map the in situ distribution of tryptic peptides in formalin-fixed clinical tissue samples. The ability to analyze clinical samples is of great importance to further developments in the imaging field. However, there is a requirement in this field of research for additional methods describing the characterization of tryptic peptides by MALDI imaging. METHODS AND RESULTS This protocol gives highly detailed instructions, with examples, for (1) successfully performing tryptic peptide MALDI imaging on formalin-fixed cancer tissue using a MALDI-TOF/TOF MS instrument, (2) tentatively generating identifications through nLC/MS/MS, and (3) validating these identifications by in situ MS/MS of peptides of interest. CONCLUSIONS This protocol provides a detailed and straightforward description of the methods required for groups new to MALDI imaging to begin analysis of formalin-fixed clinical samples.
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Affiliation(s)
- Ove J R Gustafsson
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia, 5005
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25
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Quanico J, Franck J, Dauly C, Strupat K, Dupuy J, Day R, Salzet M, Fournier I, Wisztorski M. Development of liquid microjunction extraction strategy for improving protein identification from tissue sections. J Proteomics 2013; 79:200-18. [DOI: 10.1016/j.jprot.2012.11.025] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/20/2012] [Accepted: 11/30/2012] [Indexed: 12/22/2022]
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26
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27
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Gustafsson JO, Eddes JS, Meding S, Koudelka T, Oehler MK, McColl SR, Hoffmann P. Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS. J Proteomics 2012; 75:5093-5105. [DOI: 10.1016/j.jprot.2012.04.054] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/20/2012] [Accepted: 04/21/2012] [Indexed: 11/16/2022]
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