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Tukacs V, Mittli D, Hunyadi-Gulyás É, Darula Z, Juhász G, Kardos J, Kékesi KA. Comparative analysis of hippocampal extracellular space uncovers widely altered peptidome upon epileptic seizure in urethane-anaesthetized rats. Fluids Barriers CNS 2024; 21:6. [PMID: 38212833 PMCID: PMC10782730 DOI: 10.1186/s12987-024-00508-w] [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: 08/24/2023] [Accepted: 10/31/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND The brain extracellular fluid (ECF), composed of secreted neurotransmitters, metabolites, peptides, and proteins, may reflect brain processes. Analysis of brain ECF may provide new potential markers for synaptic activity or brain damage and reveal additional information on pathological alterations. Epileptic seizure induction is an acute and harsh intervention in brain functions, and it can activate extra- and intracellular proteases, which implies an altered brain secretome. Thus, we applied a 4-aminopyridine (4-AP) epilepsy model to study the hippocampal ECF peptidome alterations upon treatment in rats. METHODS We performed in vivo microdialysis in the hippocampus for 3-3 h of control and 4-AP treatment phase in parallel with electrophysiology measurement. Then, we analyzed the microdialysate peptidome of control and treated samples from the same subject by liquid chromatography-coupled tandem mass spectrometry. We analyzed electrophysiological and peptidomic alterations upon epileptic seizure induction by two-tailed, paired t-test. RESULTS We detected 2540 peptides in microdialysate samples by mass spectrometry analysis; and 866 peptides-derived from 229 proteins-were found in more than half of the samples. In addition, the abundance of 322 peptides significantly altered upon epileptic seizure induction. Several proteins of significantly altered peptides are neuropeptides (Chgb) or have synapse- or brain-related functions such as the regulation of synaptic vesicle cycle (Atp6v1a, Napa), astrocyte morphology (Vim), and glutamate homeostasis (Slc3a2). CONCLUSIONS We have detected several consequences of epileptic seizures at the peptidomic level, as altered peptide abundances of proteins that regulate epilepsy-related cellular processes. Thus, our results indicate that analyzing brain ECF by in vivo microdialysis and omics techniques is useful for monitoring brain processes, and it can be an alternative method in the discovery and analysis of CNS disease markers besides peripheral fluid analysis.
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Affiliation(s)
- Vanda Tukacs
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Dániel Mittli
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Hungarian Research Network (HUN-REN), Temesvári Körút 62, Szeged, 6726, Hungary
| | - Zsuzsanna Darula
- Laboratory of Proteomics Research, Biological Research Centre, Hungarian Research Network (HUN-REN), Temesvári Körút 62, Szeged, 6726, Hungary
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine, Temesvári Körút 62, Szeged, 6726, Hungary
| | - Gábor Juhász
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- InnoScience Hungary Ltd., Bátori Út 9, Mátranovák, 3142, Hungary
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Katalin Adrienna Kékesi
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
- InnoScience Hungary Ltd., Bátori Út 9, Mátranovák, 3142, Hungary.
- Department of Physiology and Neurobiology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
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Nestor L, De Bundel D, Vander Heyden Y, Smolders I, Van Eeckhaut A. Unravelling the brain metabolome: A review of liquid chromatography - mass spectrometry strategies for extracellular brain metabolomics. J Chromatogr A 2023; 1712:464479. [PMID: 37952387 DOI: 10.1016/j.chroma.2023.464479] [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] [Received: 07/24/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
The analysis of the brain extracellular metabolome is of interest for numerous subdomains within neuroscience. Not only does it provide information about normal physiological functions, it is even more of interest for biomarker discovery and target discovery in disease. The extracellular analysis of the brain is particularly interesting as it provides information about the release of mediators in the brain extracellular fluid to look at cellular signaling and metabolic pathways through the release, diffusion and re-uptake of neurochemicals. In vivo samples are obtained through microdialysis, cerebral open-flow microperfusion or solid-phase microextraction. The analytes of potential interest are typically low in concentration and can have a wide range of physicochemical properties. Liquid chromatography coupled to mass spectrometry has proven its usefulness in brain metabolomics. It allows sensitive and specific analysis of low sample volumes, obtained through different approaches. Several strategies for the analysis of the extracellular fluid have been proposed. The most widely used approaches apply sample derivatization, specific stationary phases and/or hydrophilic interaction liquid chromatography. Miniaturization of these methods allows an even higher sensitivity. The development of chiral metabolomics is indispensable, as it allows to compare the enantiomeric ratio of compounds and provides even more challenges. Some limitations continue to exist for the previously developed methods and the development of new, more sensitive methods remains needed. This review provides an overview of the methods developed for sampling and liquid chromatography-mass spectrometry analysis of the extracellular metabolome.
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Affiliation(s)
- Liam Nestor
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Dimitri De Bundel
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Yvan Vander Heyden
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling (FABI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ilse Smolders
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ann Van Eeckhaut
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium.
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Abid MSR, Mousavi S, Checco JW. Identifying Receptors for Neuropeptides and Peptide Hormones: Challenges and Recent Progress. ACS Chem Biol 2021; 16:251-263. [PMID: 33539706 DOI: 10.1021/acschembio.0c00950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intercellular signaling events mediated by neuropeptides and peptide hormones represent important targets for both basic science and drug discovery. For many bioactive peptides, the protein receptors that transmit information across the receiving cell membrane are not known, severely limiting these signaling pathways as potential therapeutic targets. Identifying the receptor(s) for a given peptide of interest is complicated by several factors. Most notably, cell-cell signaling peptides are generated through dynamic biosynthetic pathways, can act on many different families of receptor proteins, and can participate in complex ligand-receptor interactions that extend beyond a simple one-to-one archetype. Here, we discuss recent methodological advances to identify signaling partners for bioactive peptides. Recent efforts have centered on methods to identify candidate receptors via transcript expression, methods to match peptide-receptor pairs through high throughput screening, and methods to capture direct ligand-receptor interactions using chemical probes. Future applications of the receptor identification approaches discussed here, as well as technical advancements to address their limitations, promise to lead to a greater understanding of how cells communicate to deliver complex physiologies. Importantly, such advancements will likely provide novel targets for the treatment of human diseases within the central nervous and endocrine systems.
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Affiliation(s)
- Md Shadman Ridwan Abid
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Somayeh Mousavi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - James W. Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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From Synapse to Function: A Perspective on the Role of Neuroproteomics in Elucidating Mechanisms of Drug Addiction. Proteomes 2018; 6:proteomes6040050. [PMID: 30544849 PMCID: PMC6315754 DOI: 10.3390/proteomes6040050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022] Open
Abstract
Drug addiction is a complex disorder driven by dysregulation in molecular signaling across several different brain regions. Limited therapeutic options currently exist for treating drug addiction and related psychiatric disorders in clinical populations, largely due to our incomplete understanding of the molecular pathways that influence addiction pathology. Recent work provides strong evidence that addiction-related behaviors emerge from the convergence of many subtle changes in molecular signaling networks that include neuropeptides (neuropeptidome), protein-protein interactions (interactome) and post-translational modifications such as protein phosphorylation (phosphoproteome). Advancements in mass spectrometry methodology are well positioned to identify these novel molecular underpinnings of addiction and further translate these findings into druggable targets for therapeutic development. In this review, we provide a general perspective of the utility of novel mass spectrometry-based approaches for addressing critical questions in addiction neuroscience, highlighting recent innovative studies that exemplify how functional assessments of the neuroproteome can provide insight into the mechanisms of drug addiction.
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Wilson RE, Jaquins-Gerstl A, Weber SG. On-Column Dimethylation with Capillary Liquid Chromatography-Tandem Mass Spectrometry for Online Determination of Neuropeptides in Rat Brain Microdialysate. Anal Chem 2018; 90:4561-4568. [PMID: 29504751 PMCID: PMC6236683 DOI: 10.1021/acs.analchem.7b04965] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have developed a method for online collection and quantitation of neuropeptides in rat brain microdialysates using on-column dimethylation with capillary liquid chromatography-tandem mass spectrometry (cLC-MS2). This method addresses a number of the challenges of quantifying neuropeptides with cLC-MS. It is also a completely automated and robust method for the preparation of stable isotope labeled-peptide internal standards to correct for matrix effects and thus ensure accurate quantitation. Originally developed for tissue-derived proteomics samples ( Raijmakers et al. Mol. Cell. Proteomics 2008 , 7 , 1755 - 1762 ), the efficacy of on-column dimethylation for native peptides in microdialysate has not been demonstrated until now. We have modified the process to make it more amenable to the time scale of microdialysis sampling and to reduce the accumulation of nonvolatile contaminants on the column and, thus, loss of sensitivity. By decreasing labeling time, we have a temporal resolution of 1 h from sample loading to elution and our peptide detection limits are in the low pM range for 5 μL injections of microdialysate. We have demonstrated the effectiveness of this method by quantifying basal and potassium stimulated concentrations of the neuropeptides leu-enkephalin and met-enkephalin in the rat hippocampus. To our knowledge, this is the first report of quantitation of these peptides in the hippocampus using MS.
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Affiliation(s)
- Rachael E Wilson
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Andrea Jaquins-Gerstl
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Stephen G Weber
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
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6
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Zestos AG, Kennedy RT. Microdialysis Coupled with LC-MS/MS for In Vivo Neurochemical Monitoring. AAPS JOURNAL 2017; 19:1284-1293. [PMID: 28660399 DOI: 10.1208/s12248-017-0114-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/13/2017] [Indexed: 10/19/2022]
Abstract
Microdialysis is a powerful sampling technique used to monitor small molecules in vivo. Despite the many applications of microdialysis sampling, it is limited by the method of analyzing the resulting samples. An emerging technique for analysis of microdialysis samples is liquid chromatography-tandem mass spectrometry (LC-MS/MS). This technique is highly versatile, allowing multiplexed analysis of neurotransmitters, metabolites, and neuropeptides. Using LC-MS/MS for polar neurotransmitters is hampered by weak retention reverse phase LC columns. Several derivatization reagents have been utilized to enhance separation and resolution of neurochemicals in dialysate samples including benzoyl chloride (BzCl), dansyl chloride, formaldehyde, ethylchloroformate, and propionic anhydride. BzCl reacts with amine and phenol groups so that many neurotransmitters can be labeled. Besides improving separation on reverse phase columns, this reagent also increases sensitivity. It is available in a heavy form so that it can be used to make stable-isotope labeled internal standard for improved quantification. Using BzCl with LC-MS/MS has allowed for measuring as many as 70 neurochemicals in a single assay. With slightly different conditions, LC-MS/MS has also been used for monitoring endocannabinoids. LC-MS/MS is also useful for neuropeptide assay because it allows for highly sensitive, sequence specific measurement of most peptides. These advances have allowed for multiplexed neurotransmitter measurements in behavioral, circuit analysis, and drug effect studies.
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Affiliation(s)
- Alexander G Zestos
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan, 48109-1055, USA.,Department of Pharmacology, University of Michigan, 2301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, Michigan, 48109-1055, USA.,Department of Chemistry, American University, 4400 Massachusetts Avenue, NW, Washington, District of Columbia, 20016, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan, 48109-1055, USA. .,Department of Pharmacology, University of Michigan, 2301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, Michigan, 48109-1055, USA.
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7
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Enzyme-linked DNA dendrimer nanosensors for acetylcholine. Sci Rep 2015; 5:14832. [PMID: 26442999 PMCID: PMC4595838 DOI: 10.1038/srep14832] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/07/2015] [Indexed: 12/17/2022] Open
Abstract
It is currently difficult to measure small dynamics of molecules in the brain with high spatial and temporal resolution while connecting them to the bigger picture of brain function. A step towards understanding the underlying neural networks of the brain is the ability to sense discrete changes of acetylcholine within a synapse. Here we show an efficient method for generating acetylcholine-detecting nanosensors based on DNA dendrimer scaffolds that incorporate butyrylcholinesterase and fluorescein in a nanoscale arrangement. These nanosensors are selective for acetylcholine and reversibly respond to levels of acetylcholine in the neurophysiological range. This DNA dendrimer architecture has the potential to overcome current obstacles to sensing in the synaptic environment, including the nanoscale size constraints of the synapse and the ability to quantify the spatio-temporal fluctuations of neurotransmitter release. By combining the control of nanosensor architecture with the strategic placement of fluorescent reporters and enzymes, this novel nanosensor platform can facilitate the development of new selective imaging tools for neuroscience.
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8
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Morales JM, Skipwith CG, Clark HA. Quadruplex Integrated DNA (QuID) Nanosensors for Monitoring Dopamine. SENSORS 2015; 15:19912-24. [PMID: 26287196 PMCID: PMC4570402 DOI: 10.3390/s150819912] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 12/25/2022]
Abstract
Dopamine is widely innervated throughout the brain and critical for many cognitive and motor functions. Imbalances or loss in dopamine transmission underlie various psychiatric disorders and degenerative diseases. Research involving cellular studies and disease states would benefit from a tool for measuring dopamine transmission. Here we show a Quadruplex Integrated DNA (QuID) nanosensor platform for selective and dynamic detection of dopamine. This nanosensor exploits DNA technology and enzyme recognition systems to optically image dopamine levels. The DNA quadruplex architecture is designed to be compatible in physically constrained environments (110 nm) with high flexibility, homogeneity, and a lower detection limit of 110 µM.
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Affiliation(s)
- Jennifer M Morales
- Department of Pharmaceutical Sciences, Northeastern University, 206 The Fenway, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - Christopher G Skipwith
- Department of Pharmaceutical Sciences, Northeastern University, 206 The Fenway, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - Heather A Clark
- Department of Pharmaceutical Sciences, Northeastern University, 206 The Fenway, 360 Huntington Avenue, Boston, MA 02115, USA.
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9
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Murphy NP. Dynamic measurement of extracellular opioid activity: status quo, challenges, and significance in rewarded behaviors. ACS Chem Neurosci 2015; 6:94-107. [PMID: 25585132 DOI: 10.1021/cn500295q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Opioid peptides are the endogenous ligands of opioid receptors, which are also the molecular target of naturally occurring and synthetic opiates, such as morphine and heroin. Since their discovery in the 1970s, opioid peptides, which are found widely throughout the central nervous system and the periphery, have been intensely studied because of their involvement in pain and pleasure. Over the years, our understanding of opioid peptides has widened to cover a multitude of functions, including learning and memory, affective state, gastrointestinal transit, feeding, immune function, and metabolism. Unsurprisingly, aberrant opioid activity is implicated in numerous pathologies, including drug addiction, overeating, pain, depression, and obesity. To date, virtually all preclinical and clinical studies aimed at understanding the function of endogenous opioids have relied upon manipulating endogenous opioid fluxes using opioid receptor ligands or genetic manipulations of opioid receptors and endogenous opioids. Difficulties in directly monitoring endogenous opioid fluxes, particularly in the central nervous system, have presented a major obstacle to fully understanding endogenous opioid function. This review summarizes these challenges and offers suggestions for future goals while focusing on the neurobiology of reward, specifically drawing attention to studies that have succeeded in dynamically measuring opioid peptides.
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Affiliation(s)
- Niall P. Murphy
- Department of Psychiatry
and Biobehavioral Sciences, Univesity of California, Los Angeles, 2579 MacDonald
Research Laboratories, 675 Charles E. Young Drive
South Los Angeles, California 90095, United States
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10
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Schmerberg CM, Li L. Mass spectrometric detection of neuropeptides using affinity-enhanced microdialysis with antibody-coated magnetic nanoparticles. Anal Chem 2013; 85:915-22. [PMID: 23249250 DOI: 10.1021/ac302403e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microdialysis (MD) is a useful sampling tool for many applications due to its ability to permit sampling from an animal concurrent with normal activity. MD is of particular importance in the field of neuroscience, in which it is used to sample neurotransmitters (NTs) while the animal is behaving in order to correlate dynamic changes in NTs with behavior. One important class of signaling molecules, the neuropeptides (NPs), however, presented significant challenges when studied with MD, due to the low relative recovery (RR) of NPs by this technique. Affinity-enhanced microdialysis (AE-MD) has previously been used to improve recovery of NPs and similar molecules. For AE-MD, an affinity agent (AA), such as an antibody-coated particle or free antibody, is added to the liquid perfusing the MD probe. This AA provides an additional mass transport driving force for analyte to pass through the dialysis membrane and thus increases the RR. In this work, a variety of AAs have been investigated for AE-MD of NPs in vitro and in vivo, including particles with C18 surface functionality and antibody-coated particles. Antibody-coated magnetic nanoparticles (AbMnP) provided the best RR enhancement in vitro, with statistically significant (p < 0.05) enhancements for 4 out of 6 NP standards tested, and RR increases up to 41-fold. These particles were then used for in vivo MD in the Jonah crab, Cancer borealis, during a feeding study, with mass spectrometric (MS) detection. 31 NPs were detected in a 30 min collection sample, compared to 17 when no AA was used. The use of AbMnP also increased the temporal resolution from 4 to 18 h in previous studies to just 30 min in this study. The levels of NPs detected were also sufficient for reliable quantitation with the MS system in use, permitting quantitative analysis of the concentration changes for 7 identified NPs on a 30 min time course during feeding.
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Affiliation(s)
- Claire M Schmerberg
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, USA
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Clough GF, Stenken JA, Church MK. High Molecular Weight Targets and Treatments Using Microdialysis. MICRODIALYSIS IN DRUG DEVELOPMENT 2013. [DOI: 10.1007/978-1-4614-4815-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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Direct cellular peptidomics of hypothalamic neurons. Front Neuroendocrinol 2011; 32:377-86. [PMID: 21334363 PMCID: PMC3165142 DOI: 10.1016/j.yfrne.2011.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 02/10/2011] [Accepted: 02/14/2011] [Indexed: 11/23/2022]
Abstract
The chemical complexity of cell-to-cell communication has emerged as a fundamental challenge to understanding brain systems. This is certainly true for the hypothalamus, where neuropeptide signals are heterogeneous, localized and dynamic. Thus far, most hypothalamic peptidomic studies have centered on the entire structure; however, recent advances in collection strategies and analytical technologies have enabled direct, high-resolution peptidomic profiles focused on two regions of interest, the suprachiasmatic and supraoptic nuclei, including their sub-regions and individual cells. Suites of peptides now can be identified and probed for function. High spatial and analytical sensitivities reveal that discrete hypothalamic nuclei have distinct peptidomic signatures. Peptidomic discovery not only reveals unanticipated complexity, but also peptides previously unknown that act as key circuit components. Analysis of tissue releasates identifies peptides secreted into the extracellular environment and available for transmitting intercellular signals. Direct sampling techniques define peptide-releasate profiles in spatial, temporal and event-dependent patterns. These approaches are providing remarkable new insights into the complexity of neuropeptidergic cell-to-cell signaling central to neuroendocrine physiology.
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The absolute quantification of endogenous levels of brain neuropeptides in vivo using LC-MS/MS. Bioanalysis 2011; 3:1271-85. [PMID: 21649502 DOI: 10.4155/bio.11.91] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Neuropeptides seem to play an important role when the CNS is challenged. In order to obtain better insights into the central peptidergic effects, it is essential to monitor their concentration in the brain. Quantification of neuropeptides in dialysates is challenging due to their low extracellular concentrations (low pM range), their low microdialysis efficiencies, the need for acceptable temporal resolution, the small sample volumes, the complexity of the matrix and the tendency of peptides to stick to glass and polymeric materials. The quantification of neuropeptides in dialysates therefore necessitates the use of very sensitive nano-LC-MS/MS methods. A number of LC-MS/MS and microdialysis parameters need to be optimized to achieve maximal sensitivity. The optimized and validated methods can be used to investigate the in vivo neuropeptide release during pathological conditions, in this way initiating new and immense challenges for the development of new drugs.
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Hanrieder J, Ljungdahl A, Fälth M, Mammo SE, Bergquist J, Andersson M. L-DOPA-induced dyskinesia is associated with regional increase of striatal dynorphin peptides as elucidated by imaging mass spectrometry. Mol Cell Proteomics 2011; 10:M111.009308. [PMID: 21737418 PMCID: PMC3205869 DOI: 10.1074/mcp.m111.009308] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Opioid peptides are involved in various pathophysiological processes, including algesia, epilepsy, and drug dependence. A strong association between L-DOPA-induced dyskinesia (LID) and elevated prodynorphin mRNA levels has been established in both patients and in animal models of Parkinson's disease, but to date the endogenous prodynorphin peptide products have not been determined. Here, matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) was used for characterization, localization, and relative quantification of striatal neuropeptides in a rat model of LID in Parkinson's disease. MALDI IMS has the unique advantage of high sensitivity and high molecular specificity, allowing comprehensive detection of multiple molecular species in a single tissue section. Indeed, several dynorphins and enkephalins could be detected in the present study, including dynorphin A(1-8), dynorphin B, α-neoendorphin, MetEnkRF, MetEnkRGL, PEnk (198-209, 219-229). IMS analysis revealed elevated levels of dynorphin B, α-neoendorphin, substance P, and PEnk (220-229) in the dorsolateral striatum of high-dyskinetic animals compared with low-dyskinetic and lesion-only control rats. Furthermore, the peak-intensities of the prodynorphin derived peptides, dynorphin B and α-neoendorphin, were strongly and positively correlated with LID severity. Interestingly, these LID associated dynorphin peptides are not those with high affinity to κ opioid receptors, but are known to bind and activate also μ- and Δ-opioid receptors. In addition, the peak intensities of a novel endogenous metabolite of α-neoendorphin lacking the N-terminal tyrosine correlated positively with dyskinesia severity. MALDI IMS of striatal sections from Pdyn knockout mice verified the identity of fully processed dynorphin peptides and the presence of endogenous des-tyrosine α-neoendorphin. Des-tyrosine dynorphins display reduced opioid receptor binding and this points to possible novel nonopioid receptor mediated changes in the striatum of dyskinetic rats. Because des-tyrosine dynorphins can only be detected by mass spectrometry, as no antibodies are available, these findings highlight the importance of MALDI IMS analysis for the study of molecular dynamics in neurological diseases.
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Affiliation(s)
- Jörg Hanrieder
- Department of Pharmaceutical Biosciences, Drug Safety and Toxicology, Uppsala University, Uppsala, Sweden
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Medina-Casanellas S, Benavente F, Barbosa J, Sanz-Nebot V. Transient isotachophoresis in on-line solid phase extraction capillary electrophoresis time-of-flight-mass spectrometry for peptide analysis in human plasma. Electrophoresis 2011; 32:1750-9. [DOI: 10.1002/elps.201100017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Philippova MM, Khachin DP, Sazonova OV, Blishchenko EY, Yatskin ON, Nazimov IV, Karelin AA, Ivanov VT, Rasstrigin NA, Pivnik AV. Fragments of functional proteins in a primary culture of human erythrocytes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011. [DOI: 10.1134/s1068162008020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Xu H, Guy Y, Hamsher A, Shi G, Sandberg M, Weber SG. Electroosmotic sampling. Application to determination of ectopeptidase activity in organotypic hippocampal slice cultures. Anal Chem 2010; 82:6377-83. [PMID: 20669992 PMCID: PMC2920223 DOI: 10.1021/ac1012706] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We hypothesize that peptide-containing solutions pulled through tissue should reveal the presence and activity of peptidases in the tissue. Using the natural zeta-potential in the organotypic hippocampal slice culture (OHSC), physiological fluids can be pulled through the tissue with an electric field. The hydrolysis of the peptides present in the fluid drawn through the tissue can be determined using capillary HPLC with electrochemical detection of the biuret complexes of the peptides following a postcolumn reaction. We have characterized this new sampling method by measuring the flow rate, examining the use of internal standards, and examining cell death caused by sampling. The sampling flow rate ranges from 60 to 150 nL/min with a 150 microm (ID) sampling capillary with an electric field (at the tip of the capillary) from 30 to 60 V/cm. Cell death can be negligible with controlled sampling conditions. Using this sampling approach, we have electroosmotically pulled Leu-enkephalin through OHSCs to identify ectopeptidase activity in the CA3 region. These studies show that a bestatin-sensitive aminopeptidase may be critical for the hydrolysis of exogenous Leu-enkephalin, a neuropeptide present in the CA3 region of OHSCs.
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Affiliation(s)
- Hongjuan Xu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260
| | - Yifat Guy
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260
| | - Amy Hamsher
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260
| | - Guoyue Shi
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260
| | - Mats Sandberg
- Institute of Biomedicine, Gothenburg University, Gothenburg, Sweden
| | - Stephen G. Weber
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260
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18
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Lee JE, Atkins N, Hatcher NG, Zamdborg L, Gillette MU, Sweedler JV, Kelleher NL. Endogenous peptide discovery of the rat circadian clock: a focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry. Mol Cell Proteomics 2009; 9:285-97. [PMID: 19955084 DOI: 10.1074/mcp.m900362-mcp200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Understanding how a small brain region, the suprachiasmatic nucleus (SCN), can synchronize the body's circadian rhythms is an ongoing research area. This important time-keeping system requires a complex suite of peptide hormones and transmitters that remain incompletely characterized. Here, capillary liquid chromatography and FTMS have been coupled with tailored software for the analysis of endogenous peptides present in the SCN of the rat brain. After ex vivo processing of brain slices, peptide extraction, identification, and characterization from tandem FTMS data with <5-ppm mass accuracy produced a hyperconfident list of 102 endogenous peptides, including 33 previously unidentified peptides, and 12 peptides that were post-translationally modified with amidation, phosphorylation, pyroglutamylation, or acetylation. This characterization of endogenous peptides from the SCN will aid in understanding the molecular mechanisms that mediate rhythmic behaviors in mammals.
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Affiliation(s)
- Ji Eun Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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19
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Zhang X, Rauch A, Xiao H, Rainer G, Logothetis NK. Mass spectrometry-based neurochemical analysis: perspectives for primate research. Expert Rev Proteomics 2009; 5:641-52. [PMID: 18937555 DOI: 10.1586/14789450.5.5.641] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The analysis of neurochemicals from the brain represents a challenge for current analytical techniques due to a variety of factors, such as compositional complexity, limited amounts of sample and endogenous inferences. Advances in mass spectrometry (MS) provide great opportunities for the sensitive measurement of neurochemicals, offering benefits including simple sample preparation, broad capability for analysis of diverse compounds and rich structural information of analytes. Until recently, however, limited numbers of studies have reported on the analysis of small molecular neurochemicals, such as classical neurotransmitters, in part due to the difficulties in separation of polar molecules by using current chromatography techniques with MS-compatible conditions. By contrast, MS has become an indispensable tool for neuropeptide analysis , offering tremendous potential in the discovery of novel signaling peptides and biomarkers. This review covers recent advances in MS-based neurochemical analysis , including a comparison with related detection techniques, chromatographic separation and neuropeptide discovery. Issues relating to in vivo sample collection and sample preparation are discussed. To provide a wider view of the capability of MS in basic neuroscience and clinical research, we discuss MS-based neurochemical analysis conducted in different animal models and humans. We specifically highlight perspectives for the use of MS for brain functional studies and drug discovery in nonhuman primates.
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Affiliation(s)
- Xiaozhe Zhang
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tubingen, 72076, Germany.
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20
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Bernay B, Gaillard MC, Guryca V, Emadali A, Kuhn L, Bertrand A, Detraz I, Carcenac C, Savasta M, Brouillet E, Garin J, Elalouf JM. Discovering new bioactive neuropeptides in the striatum secretome using in vivo microdialysis and versatile proteomics. Mol Cell Proteomics 2009; 8:946-58. [PMID: 19164277 DOI: 10.1074/mcp.m800501-mcp200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The striatum, a major component of the brain basal nuclei, is central for planning and executing voluntary movements and undergoes lesions in neurodegenerative disorders such as Huntington disease. To perform highly integrated tasks, the striatum relies on a complex network of communication within and between brain regions with a key role devoted to secreted molecules. To characterize the rat striatum secretome, we combined in vivo microdialysis together with proteomics analysis of trypsin digests and peptidomics studies of native fragments. This versatile approach, carried out using different microdialysis probes and mass spectrometer devices, allowed evidencing with high confidence the expression of 88 proteins and 100 processed peptides. Their secretory pathways were predicted by in silico analysis. Whereas high molecular weight proteins were mainly secreted by the classical mode (94%), low molecular weight proteins equally used classical and non-classical modes (53 and 47%, respectively). In addition, our results suggested alternative secretion mechanisms not predicted by bioinformatics tools. Based on spectrum counting, we performed a relative quantification of secreted proteins and peptides in both basal and neuronal depolarization conditions. This allowed detecting a series of neuropeptide precursors and a 6-fold increase for neurosecretory protein VGF and proenkephalin (PENK) levels. A focused investigation and a long peptide experiment led to the identification of new secreted non-opioid PENK peptides, referred to as PENK 114-133, PENK 239-260, and PENK 143-185. Moreover we showed that injecting synthetic PENK 114-133 and PENK 239-260 into the striatum robustly increased glutamate release in this region. Thus, the combination of microdialysis and versatile proteomics methods shed new light on the secreted protein repertoire and evidenced novel neuropeptide transmitters.
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Affiliation(s)
- Benoît Bernay
- Laboratoire de PhysioGénomique, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM), Institut de Biologie et de Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique (CEA), F-91191 Gif-sur-Yvette, France.
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21
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Svetlov SI, Xiang Y, Oli MW, Foley DP, Huang G, Hayes RL, Ottens AK, Wang KKW. Identification and preliminary validation of novel biomarkers of acute hepatic ischaemia/reperfusion injury using dual-platform proteomic/degradomic approaches. Biomarkers 2008; 11:355-69. [PMID: 16908442 DOI: 10.1080/13547500600775110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hepatic ischaemia/reperfusion (I/R), a major cause of liver damage associated with multiple trauma, haemorrhagic and septic shock, and liver transplantation, contributes significantly to multiple organ failure. Development of novel sensitive biomarkers that detect early stages of liver damage is vital for effective management and treatment of ischaemic liver injury. By using high-throughput immunoblotting and cation-anion exchange chromatography/reversed-phase liquid chromatography-tandem mass-spectrometry, we identified several hepatic proteins, including argininosuccinate synthase (ASS) and estrogen sulfotransferase (EST-1), which were degraded in the liver and rapidly released into circulation during I/R injury. ASS accumulated in serum within 10 min, reached a steady state at 30 min, and persisted up until 3 h after reperfusion following 30 min of total hepatic ischaemia. EST-1 appeared rapidly in blood and attained maximum within 1 hour followed by a decline at 3 h of reperfusion. No ASS or EST-1 protein was detected in serum of control or sham operated rats. ASS and EST-1 exhibited greater sensitivity and specificity toward I/R liver injury as compared with alanine aminotransferase (ALT), an established marker of hepatocellular necrosis. In contrast, serum ASS and EST-1 were undetectable in rats with chronic alcoholic liver disease, while the levels of ALT protein were significantly increased. In addition, ASS, but not EST-1 or ALT accumulated in blood only 6 h after treatment with hepatotoxic combination of lipopolysaccharide and D-galactosamine. These data demonstrate the utility of ASS and EST-1 as novel sensitive and specific biomarkers of acute liver ischaemic injury for prospective clinical studies.
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Affiliation(s)
- S I Svetlov
- Laboratory of Molecular and Cellular Mechanisims of Injury, University of Florida College of Medicine, Gainesville, FL 32610, USA.
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22
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Robinson DL, Hermans A, Seipel AT, Wightman RM. Monitoring rapid chemical communication in the brain. Chem Rev 2008; 108:2554-84. [PMID: 18576692 PMCID: PMC3110685 DOI: 10.1021/cr068081q] [Citation(s) in RCA: 454] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Donita L Robinson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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23
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Mihailova A, Karaszewski B, Faergestad EM, Hauser R, Nyka WM, Lundanes E, Greibrokk T. Two-dimensional LC-MS/MS in detection of peptides in hypothalamus of the rat subjected to hypoxic stress. J Sep Sci 2008; 31:468-79. [PMID: 18210376 DOI: 10.1002/jssc.200700269] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A capillary 2-D LC method coupled with IT MS has been used for separation and identification of peptides in rat hypothalamus. Animals of two different age groups (8 and 50 wk) were exposed to two different rates of CO(2 )in inhaled air to investigate the influence of different hypoxia/hypercapnia levels and their stress-related factor on the peptide excretion. Peptide compounds were fractionated (strong cation exchange chromatography), trapped, and separated (RP chromatography), and MS/MS mass spectra were used for identification. About 107 peptide compounds were identified and 88 of them were semiquantified. Among the characterized peptides, there were fragments from proteins such as proenkephalin A, proSAAS, prosomatostatin, prooxytocin, vasopressin, etc. Explorative principal component analysis (PCA) combined with hypothesis testing was applied to the obtained data to investigate the impact of age and hypoxic stress factors on the peptide pattern. Twenty-six peptides revealed significant differences in concentrations between the animal groups influenced by age and influx rate.
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24
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Saz JM, Marina ML. Application of micro- and nano-HPLC to the determination and characterization of bioactive and biomarker peptides. J Sep Sci 2008; 31:446-58. [PMID: 18266259 DOI: 10.1002/jssc.200700589] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews the works published since 2001 (included) on the micro/nano-HPLC analysis of bioactive and biomarker peptides. The main achievements related to the improvement of the detection sensitivity, quantitation repeatability and reproducibility, and separation selectivity are highlighted. A wide attention is paid to the application of micro/nano-HPLC to the analysis of bioactive peptides in biological matrices. The uses of micro/nano-HPLC in peptidomics to discover new endogenous bioactive peptides and to develop quantitation procedures to compare the levels of peptides of interest in two different biological samples are also considered. Finally, the application of micro/nano-HPLC to the analysis of biomarker peptides for various diseases is also included in this review.
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Affiliation(s)
- José María Saz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Alcalá, Alcalá de Henares, Madrid, Spain
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25
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Schmidt JJ, McIlwain S, Page D, Christie AE, Li L. Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons. J Proteome Res 2008; 7:887-96. [PMID: 18205299 DOI: 10.1021/pr070390p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing research efforts in large-scale mass spectral analyses of peptides and proteins have led to many advances in technology and method development for collecting data and improving the quality of data. However, the resultant large data sets often pose significant challenges in extracting useful information in a high-throughput manner. Here, we describe one such method where we analyzed a large mass spectral data set collected using decapod crustacean nervous tissue extracts separated via high-performance liquid chromatography (HPLC) coupled to high-resolution matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). Following their acquisition, the data collected from discrete LC fractions was compiled and analyzed using an in-house developed software package that deisotoped, compressed, calibrated, and matched peaks to a list of known crustacean neuropeptides. By processing these data via bioinformatics tools such as hierarchical clustering, more than 110 neuropeptides that belong to 14 peptide families were mapped in five crustacean species. Overall, we demonstrate the utility of MALDI-FTMS in combination with a bioinformatics software package for the elucidation and comparison of peptidomes of varying crustacean species. This study established an effective methodology and will provide the basis for future investigations into more comprehensive comparative peptidomics with larger collection of species and phyla in order to gain a deeper understanding of the evolution and diversification of peptide families.
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Affiliation(s)
- Joshua J Schmidt
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, USA
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26
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Li L, Sweedler JV. Peptides in the brain: mass spectrometry-based measurement approaches and challenges. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:451-483. [PMID: 20636086 DOI: 10.1146/annurev.anchem.1.031207.113053] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The function and activity of almost every circuit in the human brain are modified by the signaling peptides (SPs) surrounding the neurons. As the complement of peptides can vary even in adjacent neurons and their physiological actions can occur over a broad range of concentrations, the required figures of merit for techniques to characterize SPs are surprisingly stringent. In this review, we describe the formation and catabolism of SPs and highlight a range of mass spectrometric techniques used to characterize SPs. Approaches that supply high chemical information content, direct tissue profiling, spatially resolved data, and temporal information on peptide release are also described. Because of advances in measurement technologies, our knowledge of SPs has greatly increased over the last decade, and SP discoveries will continue as the capabilities of modern measurement approaches improve.
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Affiliation(s)
- Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, 53705-2222, USA.
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27
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Hernández E, Benavente F, Sanz-Nebot V, Barbosa J. Analysis of opioid peptides by on-line SPE-CE-ESI-MS. Electrophoresis 2007; 28:3957-65. [DOI: 10.1002/elps.200700845] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Drabik A, Bierczynska-Krzysik A, Bodzon-Kulakowska A, Suder P, Kotlinska J, Silberring J. Proteomics in neurosciences. MASS SPECTROMETRY REVIEWS 2007; 26:432-50. [PMID: 17405153 DOI: 10.1002/mas.20131] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This review provides an outline of the most important proteomic applications in the study of neurodegenerative disorders including Alzheimer's (AD), Parkinson's (PD), Huntington's (HD), and prion diseases, and also discusses advances in cancer and addiction. One of the scopes is to illustrate the potential of proteomics in the biomarkers discovery of these diseases. Finally, this article comments the advantages and drawbacks of the most commonly used techniques and methods for samples preparation.
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Affiliation(s)
- Anna Drabik
- Faculty of Chemistry and Regional Laboratory, Jagiellonian University, Krakow, Poland
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29
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Parkin MC, Wei H, O'Callaghan JP, Kennedy RT. Sample-dependent effects on the neuropeptidome detected in rat brain tissue preparations by capillary liquid chromatography with tandem mass spectrometry. Anal Chem 2007; 77:6331-8. [PMID: 16194096 DOI: 10.1021/ac050712d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of sample extraction and preparation on neuropeptidomic analysis of brain tissue by capillary liquid chromatography with tandem mass spectrometry was investigated. In agreement with previous reports, analysis of peptide extracts of brain tissue from animals sacrificed by microwave irradiation, which fixes tissue, allows identification of neuronally derived peptides whereas similar analysis of tissue from animals sacrificed without fixation does not. A comparison of a physical method for cell lysis (sonication) to physical combined with chemical cell lysis (sonication with detergent treatment) revealed that the latter method increased the number of neuronally derived peptides positively identified by approximately 3-fold, from 16 to 44, for analysis of microwave-fixed rat striatum. Use of synaptosome preparations also allowed detection of neuronally derived peptides (23 positively identified) without a requirement of microwave fixation, suggesting that this method may be a useful alternative for sample preparation. Although numerous peptides were identified in these experiments, several known neuropeptides were not detected including neuropeptide Y and neurotensin. Chemical properties such as hydrophobicity and atypical gas-phase fragmentation were found to account for the inability to detect these peptides. These results suggest that further improvement in sample preparation and automated spectral interpretation are needed to provide better coverage of neuropeptides in mammalian tissues. A total of 39 novel neuronally derived peptides, including some originating from proenkephalin and phosphatidylethanolamine binding protein, were identified in striatum and synaptosome.
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Affiliation(s)
- Mark C Parkin
- Department of Chemistry University of Michigan, Ann Arbor, Michigan 48109, USA
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30
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Mihailova A, Karaszewski B, Hauser R, Lundanes E, Greibrokk T. Identification of neuropeptides in rat brain rhinencephalon. J Sep Sci 2007; 30:249-56. [PMID: 17390620 DOI: 10.1002/jssc.200600317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A capillary two-dimensional liquid chromatography method coupled with ion trap mass spectrometry has been used for separation and identification of neuropeptides in rat rhinencephalon. Animals of three different age groups were exposed to slow and quick CO2 influx. The neuropeptides were extracted by solid phase extraction and the purified extracts were analysed by 2-D HPLC. The compounds were fractionated (strong cation exchange column), trapped and separated, and MS/MS fragment mass spectra were used for identification. About thirty peptide compounds were identified. A significant difference between concentration levels of "stressed" (quick CO2 influx) and "non-stressed" (slow CO2 influx) rats was found for 25 of the identified peptides.
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31
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Myasein KT, Pulido JS, Hatfield RM, McCannel CA, Dundervill RF, Shippy SA. Sub-microlitre dialysis system to enable trace level peptide detection from volume-limited biological samples using MALDI-TOF-MS. Analyst 2007; 132:1046-52. [PMID: 17893809 DOI: 10.1039/b707783a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detection of peptides with mass spectrometry from volume-limited biological samples is a challenging task due to low sample volume, a broad range of peptide concentrations down to trace levels, endogenous high proteins and salt levels. Previously, a microspotting method was presented for trace-level peptide detection with MALDI-MS from sub-microlitre samples with biological salt levels. However, in the presence of proteins, peptide signals are significantly reduced. This paper presents a novel dialysis device for removal of proteins from sub-microlitre samples using a semipermeable hollow fiber membrane to enhance peptide detection. A dialysis device was constructed to perform sub-microlitre dialysis to remove proteins from complex samples. Angiotensin I was used as a model peptide in the presence of 350 mg L(-1) BSA prepared in physiological saline to mimic biological samples. In the absence of BSA, clear angiotensin I peaks were seen at 250 pM, yet in the presence of the BSA, 10 nM angiotensin I was barely detected. After dialysis, peak detection was improved to a 500 pM level. Protein removal and peptide recovery (approximately 66%) were determined using CE-LIF. Clinical vitreous samples as low as 200 nL were successfully dialyzed in 30 min and a 3-fold increase in peptide peaks were detected with greatly improved signals. This method is simple and can be a useful technique for trace level peptide detection from volume-limited biological samples.
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Affiliation(s)
- Kyaw ThetMaw Myasein
- Department of Chemistry (M/C 111), University of Illinois at Chicago (UIC), 845 W Taylor ST, Chicago, Illinois 60607, USA
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32
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Sanz-Nebot V, Benavente F, Hernández E, Barbosa J. Evaluation of the electrophoretic behaviour of opioid peptides. Anal Chim Acta 2006; 577:68-76. [PMID: 17723655 DOI: 10.1016/j.aca.2006.06.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 06/12/2006] [Accepted: 06/13/2006] [Indexed: 11/26/2022]
Abstract
A general equation established in a previous study was used to model the electrophoretic mobility of a series of opioid peptides as a function of pH of the separation electrolyte. The concordance between the predicted and the experimental electrophoretic mobilities was excellent and the optimum pH for the separation of the modelled compounds could be predicted from a limited amount of experimental data. The equations were also useful for the accurate determination of the ionization constants of the polyprotic analytes. It was also demonstrated that if ionization constant values are known, the CE separations of the studied peptides can easily be predicted taking into account the classical semiempirical relationships between electrophoretic mobility and charge-to-mass ratio (m(e) versus q/M(alpha)). The separations simulated considering the accurate charge-to-mass ratios of each peptide at a certain pH value were in good agreement with the experimental results. Once an optimum separation pH value and a running buffer compatible with electrospray mass spectrometry (ESI) detection were selected, a method for the separation and characterization of this series of analytes by capillary electrophoresis-electrospray ionization mass spectrometry (CE-ESI-MS) was established using a commercial sheath-flow interface. Method validation was performed in order to prove the suitability of the proposed method for quantitative analysis. Thus, quality parameters, such as repeatability, reproducibility, limits of detection and linearity were determined.
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Affiliation(s)
- Victoria Sanz-Nebot
- Department of Analytical Chemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Spain.
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33
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Southey BR, Amare A, Zimmerman TA, Rodriguez-Zas SL, Sweedler JV. NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides. Nucleic Acids Res 2006; 34:W267-72. [PMID: 16845008 PMCID: PMC1538825 DOI: 10.1093/nar/gkl161] [Citation(s) in RCA: 175] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
NeuroPred is a web application designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. The user can study one amino acid sequence or multiple sequences simultaneously, selecting from several prediction models and optional, user-defined functions. Logistic regression models are trained on experimentally verified or published cleavage data from mollusks, mammals and insects, and amino acid motifs reported to be associated with cleavage. Confidence interval limits of the probabilities of cleavage indicate the precision of the predictions; these predictions are transformed into cleavage or non-cleavage events according to user-defined thresholds. In addition to the precursor sequence, NeuroPred accepts user-specified cleavage information, providing model accuracy statistics based on observed and predicted cleavages. Neuropred also computes the mass of the predicted peptides, including user-selectable post-translational modifications. The resulting mass list aids the discovery and confirmation of new neuropeptides using mass spectrometry techniques. The NeuroPred application, manual, reference manuscripts and training sequences are available at .
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Affiliation(s)
- Bruce R. Southey
- Department of Animal Sciences, University of IllinoisUrbana, IL, USA
- Department of Chemistry, University of IllinoisUrbana, IL, USA
| | - Andinet Amare
- Department of Chemistry, University of IllinoisUrbana, IL, USA
| | | | | | - Jonathan V. Sweedler
- Department of Chemistry, University of IllinoisUrbana, IL, USA
- To whom correspondence should be addressed. Tel: +1 217 244 7359; Fax: +1 217 244 8068;
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34
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Amare A, Hummon AB, Southey B, Zimmerman TA, Rodriguez-Zas SL, Sweedler JV. Bridging neuropeptidomics and genomics with bioinformatics: Prediction of mammalian neuropeptide prohormone processing. J Proteome Res 2006; 5:1162-7. [PMID: 16674105 PMCID: PMC2548284 DOI: 10.1021/pr0504541] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neuropeptides are an important class of cell to cell signaling molecules that are difficult to predict from genetic information because of their large number of post-translational modifications. The transition from prohormone genetic sequence information to the determination of the biologically active neuropeptides requires the identification of the cleaved basic sites, among the many possible cleavage sites, that exist in the prohormone. We report a binary logistic regression model trained on mammalian prohormones that is more sensitive than existing methods in predicting these processing sites, and demonstrate the application of this method to mammalian neuropeptidomic studies. By comparing the predictive abilities of a binary logistic model trained on molluscan prohormone cleavages with the reported model, we establish the need for phyla-specific models.
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Affiliation(s)
- Andinet Amare
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Amanda B. Hummon
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Bruce Southey
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Tyler A. Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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35
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Bergström SK, Goiny M, Danielsson R, Ungerstedt U, Andersson M, Markides KE. Screening of microdialysates taken before and after induced liver damage; on-line solid phase extraction-electrospray ionization-mass spectrometry. J Chromatogr A 2006; 1120:21-6. [PMID: 16480729 DOI: 10.1016/j.chroma.2006.01.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 01/20/2006] [Accepted: 01/26/2006] [Indexed: 02/08/2023]
Abstract
A novel method is described to follow known and unknown compounds in biological processes using microdialysis sampling and mass spectrometric detection. By implementation of internal standard, desalting/enrichment for the sample work-up, and multivariate data analysis, this methodology is a basis for future applications in early diagnosis of diseases and organ damage, as a complement to the routinely used clinical methods for biological samples. The present study includes screening without specific target analytes, of samples collected by microdialysis from liver of anaesthetized rats before and after local damage to this organ. Sample series were classified by principal component analysis, and the stimulation was identified in the chemical patterns produced by the presented analytical tool.
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Affiliation(s)
- Sara K Bergström
- Department of Chemistry, Analytical Chemistry, Uppsala University, Box 599, SE-751 24 Uppsala, Sweden.
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Poinsot V, Lacroix M, Maury D, Chataigne G, Feurer B, Couderc F. Recent advances in amino acid analysis by capillary electrophoresis. Electrophoresis 2006; 27:176-94. [PMID: 16421950 DOI: 10.1002/elps.200500512] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper describes a number of articles that have been published on amino acid analysis using CE during the period from June 2003 to May 2005. This review article follows the previous ones of Smith (Electrophoresis 1999, 20, 3078-3083), Prata et al. (Electrophoresis 2001, 22, 4129-4138), and Poinsot et al. (Electrophoresis 2003, 24, 4047-4062). Several new developments in amino acid analysis with CE are reported concerning UV detection, LIF, MS, and NMR. In addition, we describe articles concerning clinical and pharmaceutical studies, neuroclinical applications, and agricultural and food analysis.
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Affiliation(s)
- Véréna Poinsot
- Université Paul Sabatier, IMRCP, UMR 5623, Toulouse, France
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Chapter 3.4 In vivo peptidomics: discovery and monitoring of neuropeptides using microdialysis and liquid chromatography with mass spectrometry. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1569-7339(06)16016-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Chapter 3.1 Liquid chromatographic methods used for microdialysis: an overview. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1569-7339(06)16013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Fu Q, Li L. De Novo Sequencing of Neuropeptides Using Reductive Isotopic Methylation and Investigation of ESI QTOF MS/MS Fragmentation Pattern of Neuropeptides with N-Terminal Dimethylation. Anal Chem 2005; 77:7783-95. [PMID: 16316189 DOI: 10.1021/ac051324e] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A stable-isotope dimethyl labeling strategy was previously shown to be a useful tool for quantitative proteomics. More recently, N-terminal dimethyl labeling was also reported for peptide sequencing in combination with database searching. Here, we extend these previous studies by incorporating N-terminal isotopic dimethylation for de novo sequencing of neuropeptides directly from tissue extract without any genomic information. We demonstrated several new sequencing applications of this method in addition to the identification of the N-terminal residue using the enhanced a(1) ion. The isotopic labeling also provides easier and more confident de novo sequencing of peptides by comparing similar MS/MS fragmentation patterns of the isotopically labeled peptide pairs. The current study on neuropeptides shows several distinct fragmentation patterns after N-terminal dimethylation which have not been reported previously. The y((n-1)) ion is enhanced in multiply charged peptides and is weak or missing in singly charged peptides. The MS/MS spectra of singly charged peptides are simplified due to the enhanced N-terminal fragments and suppressed internal fragments. The neutral loss of dimethylamine is also observed. The mechanisms for the above fragmentations are proposed. Finally, the structures of the immonium ion and related ions of N(alpha), N(epsilon)-tetramethylated lysine and N(epsilon)-dimethylated lysine are explored.
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Affiliation(s)
- Qiang Fu
- School of Pharmacy and Department of Chemistry, University of Wisconsin at Madison, 53705-2222, USA
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Abstract
Microdialysis has been used in many tissues, including skin, brain, adipose tissue, muscle, kidney, and gastrointestinal tract, to recover low-molecular mass endogenous mediators, metabolites, and xenobiotics from the interstitial space. Recently, molecules of larger molecular mass, such as plasma proteins, cytokines, growth factors, and neuropeptides, have also been recovered successfully using larger-pore membranes. Microdialysis recovery of large molecules offers the opportunity to identify patterns of protein expression in a variety of tissue spaces and to evaluate clinically useful biomarkers of disease. From this may develop a better understanding of the disease process and its diagnosis and more targeted approaches to therapy.
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Affiliation(s)
- Geraldine F Clough
- Infection, Inflammation and Repair Research Division, School of Medicine, University of Southampton, UK.
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Liu CC, Huang JS, Tyrrell DLJ, Dovichi NJ. Capillary electrophoresis-electrospray-mass spectrometry of nucleosides and nucleotides: application to phosphorylation studies of anti-human immunodeficiency virus nucleosides in a human hepatoma cell line. Electrophoresis 2005; 26:1424-31. [PMID: 15761917 DOI: 10.1002/elps.200410423] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report the use of capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) for the determination of antiretroviral dideoxynucleosides (ddNs), their nucleotides, and a set of ribonucleosides and ribonucleotides. A CE system for separation of most commonly used antiretroviral ddNs has been developed based on a basic buffer with a volatile electrolyte suitable for ESI-MS detection in an untreated capillary column. Positive and negative ionization modes are investigated and compared for sensitive and stable electrospray performance. A 14-compound mixture of nucleosides and nucleotides is profiled in a single capillary zone electrophoresis separation with a distinct elution order: electroosmotic flow, ddNs, mononucleotides, dinucleotides, and trinucleotides in less than 18 min. The fragmentation pathways of the nucleosides and nucleotides in ESI-MS have been interpreted. Concentration limits of detection are 100 to 200 nM with an injection volume of approximately 10 nL. This technique has been used to detect naturally occurring nucleotides and to study the metabolism of lamivudine (3TC) in the human hepatoma cell line Hep G2. 3TC and its metabolites 3TC-monophosphate, 3TC-diphosphate, and 3TC-triphosphate were detected after 10 h of incubation of 3TC with the cells.
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Jakubowski JA, Hatcher NG, Sweedler JV. Online microdialysis-dynamic nanoelectrospray ionization-mass spectrometry for monitoring neuropeptide secretion. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:924-31. [PMID: 15934039 DOI: 10.1002/jms.869] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Although mass spectrometric approaches offer a sensitive method for identifying cell-cell signaling peptides, the high salt-containing environment of extracellular solutions often complicates characterization of these microscale samples. Accordingly, we have developed a miniature hollow-fiber microdialysis device optimized for desalting small-volume neuronal samples online, with the device directly connected to a modified dynamic nanoelectrospray ionization assembly interfaced with an ion trap mass spectrometer. Improvements over existing designs include placement of a capillary insert within the microdialysis fiber to minimize volume, as well as the use of a microinjector that enables 1 microl sample injections. We present detailed evaluation of peptide recoveries within the microdialysis fiber by liquid chromatography-electrospray ionization-ion trap-mass spectrometry analysis of tissue homogenate in artificial seawater with and without microdialysis. Analyte recoveries after microdialysis ranged from 6 to 78% with higher recoveries of more hydrophilic peptides, while little correlation between mass and percentage recovery was observed in the range studied (2000 to 6000 Da). Recoveries of peptides were the lowest for the analytes with the highest initial mass spectrometry signal intensity. Finally, we illustrate the utility of this microdialysis device for desalting neuropeptides secreted from preparations of the peptidergic bag cell neurons of the marine mollusk, Aplysia californica. Without microdialysis, the high concentration of salts ( approximately 0.5 M) prevented detection of peptides, whereas following online microdialysis-dynamic nanoelectrospray mass spectrometry of stimulated releasate, three peptides (acidic peptide, acidic peptide 1-24 and delta-bag cell peptide) were detected.
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Affiliation(s)
- Jennifer A Jakubowski
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA
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Plock N, Kloft C. Microdialysis—theoretical background and recent implementation in applied life-sciences. Eur J Pharm Sci 2005; 25:1-24. [PMID: 15854796 DOI: 10.1016/j.ejps.2005.01.017] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Revised: 01/20/2005] [Accepted: 01/21/2005] [Indexed: 11/26/2022]
Abstract
In the past decade microdialysis has become a method of choice in the study of unbound tissue concentrations of both endogenous and exogenous substances. Microdialysis has been shown to offer information about substances directly at the site of action while being well tolerable and safe. The large variety of its field of application has been demonstrated. However, a few challenges have to be met to make this method generally applicable in routine applications. This review will provide an overview over theoretical aspects that have to be considered during the implementation of microdialysis. Moreover, a comparison between microdialysis and other tissue sampling techniques will demonstrate advantages and limitations of the methods mentioned. Subsequently, it will present a critical synopsis of a variety of scientific/biomedical applications of this method with emphasis on the most recent literature, focussing on target tissues while giving examples of substances examined. It is concluded that microdialysis will be of great value in future investigations of pharmacokinetics, pharmacodynamics and in monitoring of disease status and progression.
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Affiliation(s)
- Nele Plock
- Department of Clinical Pharmacy, Institute of Pharmacy, Freie Universitaet Berlin, Kelchstr. 31, D-12169 Berlin, Germany
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