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Yang Q, Liu C, Qi K, Xiong Y, Pan Y, Tian C. Imaging and quantification of neuropeptides in mouse pituitary tissue by atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9755. [PMID: 38600731 DOI: 10.1002/rcm.9755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
Abstract
RATIONALE Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) mass spectrometry has enabled the untargeted analysis and imaging of neuropeptides and proteins in biological tissues under ambient conditions. Sensitivity in AP-MALDI can be improved by using sample-specific preparation methods. METHODS A comprehensive and detailed optimization strategy including instrument parameters, matrix spraying and sample tissue washing pretreatment was implemented to enhance the sensitivity and coverage of neuropeptides in mouse pituitary tissues by commercial AP-MALDI mass spectrometry imaging (MSI). RESULTS The sensitivity of a commercial AP-MALDI system for endogenous neuropeptides in mouse pituitary was enhanced by up to 15.2-fold by shortening the transmission gap from the sample plate to the inlet, attaching copper adhesive tape to an indium tin oxide-coated glass slide, optimizing the matrix spray solvent and using sample tissue washing pretreatment. Following careful optimization, the distributions of nine endogenous neuropeptides were successfully visualized in the pituitary. Furthermore, the quantitative capability of AP-MALDI for neuropeptides was evaluated and the concentrations of neuropeptides oxytocin and vasopressin in the pituitary posterior lobe were increased approximately twofold under hypertonic saline stress. CONCLUSION Mouse pituitary neuropeptides have emerged as important signaling molecules due to their role in stress response. This work indicates the potential of modified AP-MALDI as a promising AP MSI method for in situ visualization and quantification of neuropeptides in complex biological tissues.
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Affiliation(s)
- Qi Yang
- Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chengyuan Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Keke Qi
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, China
| | - Ying Xiong
- Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Changlin Tian
- Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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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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Wu W, Fields L, DeLaney K, Buchberger AR, Li L. An Updated Guide to the Identification, Quantitation, and Imaging of the Crustacean Neuropeptidome. Methods Mol Biol 2024; 2758:255-289. [PMID: 38549019 PMCID: PMC11071638 DOI: 10.1007/978-1-0716-3646-6_14] [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] [Indexed: 04/02/2024]
Abstract
Crustaceans serve as a useful, simplified model for studying peptides and neuromodulation, as they contain numerous neuropeptide homologs to mammals and enable electrophysiological studies at the single-cell and neural circuit levels. Crustaceans contain well-defined neural networks, including the stomatogastric ganglion, oesophageal ganglion, commissural ganglia, and several neuropeptide-rich organs such as the brain, pericardial organs, and sinus glands. As existing mass spectrometry (MS) methods are not readily amenable to neuropeptide studies, there is a great need for optimized sample preparation, data acquisition, and data analysis methods. Herein, we present a general workflow and detailed methods for MS-based neuropeptidomic analysis of crustacean tissue samples and circulating fluids. In conjunction with profiling, quantitation can also be performed with isotopic or isobaric labeling. Information regarding the localization patterns and changes of peptides can be studied via mass spectrometry imaging. Combining these sample preparation strategies and MS analytical techniques allows for a multi-faceted approach to obtaining deep knowledge of crustacean peptidergic signaling pathways.
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Affiliation(s)
- Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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Abid MSR, Qiu H, Checco JW. Label-Free Quantitation of Endogenous Peptides. Methods Mol Biol 2024; 2758:125-150. [PMID: 38549012 PMCID: PMC11027169 DOI: 10.1007/978-1-0716-3646-6_7] [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] [Indexed: 04/02/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.
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Affiliation(s)
| | - Haowen Qiu
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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5
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Cockx B, Van Bael S, Boelen R, Vandewyer E, Yang H, Le TA, Dalzell JJ, Beets I, Ludwig C, Lee J, Temmerman L. Mass Spectrometry-Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes. Mol Cell Proteomics 2023; 22:100479. [PMID: 36481452 PMCID: PMC9881375 DOI: 10.1016/j.mcpro.2022.100479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
Neuropeptides regulate animal physiology and behavior, making them widely studied targets of functional genetics research. While the field often relies on differential -omics approaches to build hypotheses, no such method exists for neuropeptidomics. It would nonetheless be valuable for studying behaviors suspected to be regulated by neuropeptides, especially when little information is otherwise available. This includes nictation, a phoretic strategy of Caenorhabditis elegans dauers that parallels host-finding strategies of infective juveniles of many pathogenic nematodes. We here developed a targeted peptidomics method for the model organism C. elegans and show that 161 quantified neuropeptides are more abundant in its dauer stage compared with L3 juveniles. Many of these have orthologs in the commercially relevant pathogenic nematode Steinernema carpocapsae, in whose infective juveniles, we identified 126 neuropeptides in total. Through further behavioral genetics experiments, we identify flp-7 and flp-11 as novel regulators of nictation. Our work advances knowledge on the genetics of nictation behavior and adds comparative neuropeptidomics as a tool to functional genetics workflows.
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Affiliation(s)
- Bram Cockx
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Sven Van Bael
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rose Boelen
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elke Vandewyer
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Tuan Anh Le
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Johnathan J Dalzell
- School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Isabel Beets
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Liesbet Temmerman
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium.
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Multiplexed quantitative neuropeptidomics via DiLeu isobaric tagging. Methods Enzymol 2022; 663:235-257. [DOI: 10.1016/bs.mie.2021.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Neuropeptides Involved in Facial Nerve Regeneration. Biomedicines 2021; 9:biomedicines9111575. [PMID: 34829804 PMCID: PMC8615594 DOI: 10.3390/biomedicines9111575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Neuropeptides and neurotransmitters act as intermediaries to transmit impulses from one neuron to another via a synapse. These neuropeptides are also related to nerve degeneration and regeneration during nerve damage. Although there are various neuropeptides, three are associated with neural regeneration in facial nerve damage: calcitonin gene-related peptide (CGRP), galanin, and pituitary adenylyl cyclase-activating peptide (PACAP). Alpha CGRP in facial motoneurons is a signaling factor involved in neuroglial and neuromuscular interactions during regeneration. Thus, it may be a marker for facial nerve regeneration. Galanin is a marker of injured axons rather than nerve regeneration. PACAP has various effects on nerve regeneration by regulating the surrounding cells and providing neurotrophic factors. Thus, it may also be used as a marker for facial nerve regeneration. However, the precise roles of these substances in nerve generation are not yet fully understood. Animal studies have demonstrated that they may act as neuromodulators to promote neurotrophic factors involved in nerve regeneration as they appear early, before changes in the injured cells and their environment. Therefore, they may be markers of nerve regeneration.
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