1
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Tashima AK, de Castro LM, Fricker LD. Quantitative Peptidomics Using Reductive Methylation of Amines. Methods Mol Biol 2024; 2758:109-124. [PMID: 38549011 DOI: 10.1007/978-1-0716-3646-6_6] [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
A number of different approaches have been used for quantitative peptidomics. In this protocol, we describe the method in which peptides are reacted with formaldehyde and sodium cyanoborohydride, which converts primary and secondary amines into tertiary amines. By using different combinations of regular reagents, deuterated reagents (2H), and reagents containing deuterium and 13C, it is possible to produce five isotopically distinct forms of the methylated peptides, which can be quantified by mass spectrometry. Peptides with free N-termini that are primary amines incorporate two methyl groups using this procedure, which differ by 2 Da for each of the five isotopic combinations. Peptides that contain unmodified lysine residues incorporate additional pairs of methyl groups, leading to larger mass differences between isotopic forms. The reagents are commercially available, relatively inexpensive, and chemically stable.
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Affiliation(s)
- Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Leandro M de Castro
- Biodiversity of Coastal Environments Postgraduate Program, Bioscience Institute, São Paulo State University, São Vicente, SP, Brazil
| | - Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
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2
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Profiling 26,000 Aplysia californica neurons by single cell mass spectrometry reveal neuronal populations with distinct neuropeptide profiles. J Biol Chem 2022; 298:102254. [PMID: 35835221 PMCID: PMC9396074 DOI: 10.1016/j.jbc.2022.102254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/03/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Neuropeptides are a chemically diverse class of cell-to-cell signaling molecules that are widely expressed throughout the central nervous system, often in a cell-specific manner. While cell-to-cell differences in neuropeptides is expected, it is often unclear how exactly neuropeptide expression varies among neurons. Here we created a microscopy-guided, high-throughput single cell matrix-assisted laser desorption/ionization mass spectrometry approach to investigate the neuropeptide heterogeneity of individual neurons in the central nervous system of the neurobiological model Aplysia californica, the California sea hare. In all, we analyzed more than 26,000 neurons from 18 animals and assigned 866 peptides from 66 prohormones by mass matching against an in silico peptide library generated from known Aplysia prohormones retrieved from the UniProt database. Louvain–Jaccard (LJ) clustering of mass spectra from individual neurons revealed 40 unique neuronal populations, or LJ clusters, each with a distinct neuropeptide profile. Prohormones and their related peptides were generally found in single cells from ganglia consistent with the prohormones’ previously known ganglion localizations. Several LJ clusters also revealed the cellular colocalization of behaviorally related prohormones, such as an LJ cluster exhibiting achatin and neuropeptide Y, which are involved in feeding, and another cluster characterized by urotensin II, small cardiac peptide, sensorin A, and FRFa, which have shown activity in the feeding network or are present in the feeding musculature. This mass spectrometry–based approach enables the robust categorization of large cell populations based on single cell neuropeptide content and is readily adaptable to the study of a range of animals and tissue types.
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3
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Peptidomic profiling of cerebrospinal fluid from patients with intracranial saccular aneurysms. J Proteomics 2021; 240:104188. [PMID: 33781962 DOI: 10.1016/j.jprot.2021.104188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023]
Abstract
Intracranial saccular aneurysms (ISA) represent 90%-95% of all intracranial aneurysm cases, characterizing abnormal pockets at arterial branch points. Ruptures lead to subarachnoid hemorrhages (SAH) and poor prognoses. We applied mass spectrometry-based peptidomics to investigate the peptidome of twelve cerebrospinal fluid (CSF) samples collected from eleven patients diagnosed with ISA. For peptide profile analyses, participants were classified into: 1) ruptured intracranial saccular aneurysms (RIA), 2) unruptured intracranial saccular aneurysms (UIA), and late-ruptured intracranial saccular aneurysms (LRIA). Altogether, a total of 2199 peptides were detected by both Mascot and Peaks software, from which 484 (22.0%) were unique peptides. All unique peptides presented conserved chains, domains, regions of protein modulation and/or post-translational modification sites related to human diseases. Gene Ontology (GO) analyses of peptide precursor proteins showed that 42% are involved in binding, 56% in cellular anatomical entities, and 39% in intercellular signaling molecules. Unique peptides identified in patients diagnosed with RIA have a larger molecular weight and a distinctive developmental process compared to UIA and LRIA (P ≤ 0.05). Continued investigations will allow the characterization of the biological and clinical significance of the peptides identified in the present study, as well as identify prototypes for peptide-based pharmacological therapies to treat ISA. SIGNIFICANCE.
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4
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Thimet Oligopeptidase Biochemical and Biological Significances: Past, Present, and Future Directions. Biomolecules 2020; 10:biom10091229. [PMID: 32847123 PMCID: PMC7565970 DOI: 10.3390/biom10091229] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/15/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15, THOP1) is a metallopeptidase ubiquitously distributed in mammalian tissues. Beyond its previously well characterized role in major histocompatibility class I (MHC-I) antigen presentation, the recent characterization of the THOP1 C57BL6/N null mice (THOP1−/−) phenotype suggests new key functions for THOP1 in hyperlipidic diet-induced obesity, insulin resistance and non-alcoholic liver steatosis. Distinctive levels of specific intracellular peptides (InPeps), genes and microRNAs were observed when comparing wild type C57BL6/N to THOP1−/− fed either standard or hyperlipidic diets. A possible novel mechanism of action was suggested for InPeps processed by THOP1, which could be modulating protein-protein interactions and microRNA processing, thus affecting the phenotype. Together, research into the biochemical and biomedical significance of THOP1 suggests that degradation by the proteasome is a step in the processing of various proteins, not merely for ending their existence. This allows many functional peptides to be generated by proteasomal degradation in order to, for example, control mRNA translation and the formation of protein complexes.
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5
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Lefevre E, Gooch H, Josh P, Alexander S, Eyles DW, Burne TH. Functional and molecular changes in the nucleus accumbens of MK-801-sensitized rats. Behav Pharmacol 2019; 30:383-395. [DOI: 10.1097/fbp.0000000000000447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Dowd S, Mustroph ML, Romanova EV, Southey BR, Pinardo H, Rhodes JS, Sweedler JV. Exploring Exercise- and Context-Induced Peptide Changes in Mice by Quantitative Mass Spectrometry. ACS OMEGA 2018; 3:13817-13827. [PMID: 30411050 PMCID: PMC6210063 DOI: 10.1021/acsomega.8b01713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
Recent research suggests that exercise may help facilitate abstinence from cocaine addiction, though the mechanisms are not well understood. In mice, wheel running accelerates the extinction of conditioned place preference (CPP) for cocaine, providing an animal model for evaluating potential neurological mechanisms. The objective of this study was to quantify dynamic changes in endogenous peptides in the amygdala and dentate gyrus of the hippocampus in mice exposed to a context paired with the effects of cocaine, and in response to exercise. Male C57BL/6J mice conditioned to cocaine were housed with or without running wheels for 30 days. Following a CPP test and final exposure to either a cocaine- or saline-associated context, peptides were measured in brain tissue extracts using label-free matrix-assisted laser desorption/ionization mass spectrometry (MS) and stable isotopic labeling with liquid chromatography and electrospray ionization MS. CPP in mice was significantly reduced with running, which correlated to decreased myelin basic protein derivatives in the dentate gyrus extracts, possibly reflecting increased unmyelinated granule neuron density. Exposure to a cocaine-paired context increased hemoglobin-derived peptides in runners and decreased an actin-derived peptide in sedentary animals. These results allowed us to characterize a novel set of biomarkers that are responsive to exercise in the hippocampus and in a cocaine-paired context in the amygdala.
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Affiliation(s)
- Sarah
E. Dowd
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
| | - Martina L. Mustroph
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
| | - Elena V. Romanova
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
| | - Bruce R. Southey
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
| | - Heinrich Pinardo
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
| | - Justin S. Rhodes
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department
of Chemistry, Neuroscience Program, Beckman Institute, Department of Animal Sciences, and Department of
Psychology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, 63-5, Urbana, Illinois 61801, United States
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7
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Yang N, Anapindi KDB, Rubakhin SS, Wei P, Yu Q, Li L, Kenny PJ, Sweedler JV. Neuropeptidomics of the Rat Habenular Nuclei. J Proteome Res 2018. [PMID: 29518334 DOI: 10.1021/acs.jproteome.7b00811] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Conserved across vertebrates, the habenular nuclei are a pair of small symmetrical structures in the epithalamus. The nuclei functionally link the forebrain and midbrain by receiving input from and projecting to several brain regions. Each habenular nucleus comprises two major asymmetrical subnuclei, the medial and lateral habenula. These subnuclei are associated with different physiological processes and disorders, such as depression, nicotine addiction, and encoding aversive stimuli or omitting expected rewarding stimuli. Elucidating the functions of the habenular nuclei at the molecular level requires knowledge of their neuropeptide complement. In this work, three mass spectrometry (MS) techniques-liquid chromatography (LC) coupled to Orbitrap tandem MS (MS/MS), LC coupled to Fourier transform (FT)-ion cyclotron resonance (ICR) MS/MS, and matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS-were used to uncover the neuropeptide profiles of the rodent medial and lateral habenula. With the assistance of tissue stabilization and bioinformatics, a total of 262 and 177 neuropeptides produced from 27 and 20 prohormones were detected and identified from the medial and lateral habenula regions, respectively. Among these neuropeptides, 136 were exclusively found in the medial habenula, and 51 were exclusively expressed in the lateral habenula. Additionally, novel sites of sulfation, a rare post-translational modification, on the secretogranin I prohormone are identified. The results demonstrate that these two small brain nuclei have a rich and differentiated peptide repertoire, with this information enabling a range of follow-up studies.
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Affiliation(s)
- Ning Yang
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Pingli Wei
- Chemistry Department , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Qing Yu
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Lingjun Li
- Chemistry Department , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Paul J Kenny
- Department of Pharmacology & Systems Therapeutics , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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8
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Dasgupta S, Castro LM, Tashima AK, Fricker L. Quantitative Peptidomics Using Reductive Methylation of Amines. Methods Mol Biol 2018; 1719:161-174. [PMID: 29476510 DOI: 10.1007/978-1-4939-7537-2_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A number of different approaches have been used for quantitative peptidomics. In this protocol we describe the method in which peptides are reacted with formaldehyde and sodium cyanoborohydride, which converts primary and secondary amines into tertiary amines. By using different combinations of regular reagents, deuterated reagents (2H), and reagents containing deuterium and 13C, it is possible to produce five isotopically distinct forms of the methylated peptides which can be quantified by mass spectrometry. Peptides with free N-termini that are primary amines incorporate two methyl groups using this procedure, which differ by 2 Da for each of the five isotopic combinations. Peptides that contain unmodified lysine residues incorporate additional pairs of methyl groups, leading to larger mass differences between isotopic forms. The reagents are commercially available, relatively inexpensive, and chemically stable.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Leandro M Castro
- Bioscience Institute, São Paulo State University, São Vicente, SP, Brazil
| | - Alexandre K Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Lloyd Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Lee JE. Neuropeptidomics: Mass Spectrometry-Based Identification and Quantitation of Neuropeptides. Genomics Inform 2016; 14:12-9. [PMID: 27103886 PMCID: PMC4838524 DOI: 10.5808/gi.2016.14.1.12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/23/2022] Open
Abstract
Neuropeptides produced from prohormones by selective action of endopeptidases are vital signaling molecules, playing a critical role in a variety of physiological processes, such as addiction, depression, pain, and circadian rhythms. Neuropeptides bind to post-synaptic receptors and elicit cellular effects like classical neurotransmitters. While each neuropeptide could have its own biological function, mass spectrometry (MS) allows for the identification of the precise molecular forms of each peptide without a priori knowledge of the peptide identity and for the quantitation of neuropeptides in different conditions of the samples. MS-based neuropeptidomics approaches have been applied to various animal models and conditions to characterize and quantify novel neuropeptides, as well as known neuropeptides, advancing our understanding of nervous system function over the past decade. Here, we will present an overview of neuropeptides and MS-based neuropeptidomic strategies for the identification and quantitation of neuropeptides.
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Affiliation(s)
- Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
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10
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Ong TH, Romanova EV, Roberts-Galbraith RH, Yang N, Zimmerman TA, Collins JJ, Lee JE, Kelleher NL, Newmark PA, Sweedler JV. Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea. J Biol Chem 2016; 291:8109-20. [PMID: 26884331 PMCID: PMC4825013 DOI: 10.1074/jbc.m115.709196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Tissue regeneration is a complex process that involves a mosaic of molecules that vary spatially and temporally. Insights into the chemical signaling underlying this process can be achieved with a multiplex and untargeted chemical imaging method such as mass spectrometry imaging (MSI), which can enablede novostudies of nervous system regeneration. A combination of MSI and multivariate statistics was used to differentiate peptide dynamics in the freshwater planarian flatwormSchmidtea mediterraneaat different time points during cephalic ganglia regeneration. A protocol was developed to makeS. mediterraneatissues amenable for MSI. MS ion images of planarian tissue sections allow changes in peptides and unknown compounds to be followed as a function of cephalic ganglia regeneration. In conjunction with fluorescence imaging, our results suggest that even though the cephalic ganglia structure is visible after 6 days of regeneration, the original chemical composition of these regenerated structures is regained only after 12 days. Differences were observed in many peptides, such as those derived from secreted peptide 4 and EYE53-1. Peptidomic analysis further identified multiple peptides from various known prohormones, histone proteins, and DNA- and RNA-binding proteins as being associated with the regeneration process. Mass spectrometry data also facilitated the identification of a new prohormone, which we have named secreted peptide prohormone 20 (SPP-20), and is up-regulated during regeneration in planarians.
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Affiliation(s)
- Ta-Hsuan Ong
- From the Department of Chemistry, and the Beckman Institute
| | | | - Rachel H Roberts-Galbraith
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | - Ning Yang
- From the Department of Chemistry, and the Beckman Institute
| | | | - James J Collins
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | - Ji Eun Lee
- From the Department of Chemistry, and the Beckman Institute
| | - Neil L Kelleher
- the Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60611
| | - Phillip A Newmark
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
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11
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Tillmaand EG, Yang N, Kindt CAC, Romanova EV, Rubakhin SS, Sweedler JV. Peptidomics and Secretomics of the Mammalian Peripheral Sensory-Motor System. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2051-2061. [PMID: 26392278 PMCID: PMC4655166 DOI: 10.1007/s13361-015-1256-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 06/01/2023]
Abstract
The dorsal root ganglion (DRG) and its anatomically and functionally associated spinal nerve and ventral and dorsal roots are important components of the peripheral sensory-motor system in mammals. The cells within these structures use a number of peptides as intercellular signaling molecules. We performed a variety of mass spectrometry (MS)-based characterizations of peptides contained within and secreted from these structures, and from isolated and cultured DRG cells. Liquid chromatography-Fourier transform MS was utilized in DRG and nerve peptidome analysis. In total, 2724 peptides from 296 proteins were identified in tissue extracts. Neuropeptides are among those detected, including calcitonin gene-related peptide I, little SAAS, and known hemoglobin-derived peptides. Solid phase extraction combined with direct matrix-assisted laser desorption/ionization time-of-flight MS was employed to investigate the secretome of these structures. A number of peptides were detected in the releasate from semi-intact preparations of DRGs and associated nerves, including neurofilament- and myelin basic protein-related peptides. A smaller set of analytes was observed in releasates from cultured DRG neurons. The peptide signals observed in the releasates have been mass-matched to those characterized and identified in homogenates of entire DRGs and associated nerves. This data aids our understanding of the chemical composition of the mammalian peripheral sensory-motor system, which is involved in key physiological functions such as nociception, thermoreception, itch sensation, and proprioception.
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Affiliation(s)
- Emily G Tillmaand
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ning Yang
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Callie A C Kindt
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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12
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Ye H, Wang J, Zhang Z, Jia C, Schmerberg C, Catherman AD, Thomas PM, Kelleher NL, Li L. Defining the Neuropeptidome of the Spiny Lobster Panulirus interruptus Brain Using a Multidimensional Mass Spectrometry-Based Platform. J Proteome Res 2015; 14:4776-91. [PMID: 26390183 DOI: 10.1021/acs.jproteome.5b00627] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decapod crustaceans are important animal models for neurobiologists due to their relatively simple nervous systems with well-defined neural circuits and extensive neuromodulation by a diverse set of signaling peptides. However, biochemical characterization of these endogenous neuropeptides is often challenging due to limited sequence information about these neuropeptide genes and the encoded preprohormones. By taking advantage of sequence homology in neuropeptides observed in related species using a home-built crustacean neuropeptide database, we developed a semi-automated sequencing strategy to characterize the neuropeptidome of Panulirus interruptus, an important aquaculture species, with few known neuropeptide preprohormone sequences. Our streamlined process searched the high mass accuracy and high-resolution data acquired on a LTQ-Orbitrap with a flexible algorithm in ProSight that allows for sequence discrepancy from reported sequences in our database, resulting in the detection of 32 neuropeptides, including 19 novel ones. We further improved the overall coverage to 51 neuropeptides with our multidimensional platform that employed multiple analytical techniques including dimethylation-assisted fragmentation, de novo sequencing using nanoliquid chromatography-electrospray ionization-quadrupole-time-of-flight (nanoLC-ESI-Q-TOF), direct tissue analysis, and mass spectrometry imaging on matrix-assisted laser desorption/ionization (MALDI)-TOF/TOF. The high discovery rate from this unsequenced model organism demonstrated the utility of our neuropeptide discovery pipeline and highlighted the advantage of utilizing multiple sequencing strategies. Collectively, our study expands the catalog of crustacean neuropeptides and more importantly presents an approach that can be adapted to exploring neuropeptidome from species that possess limited sequence information.
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Affiliation(s)
- Hui Ye
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University , Nanjing 210009, China.,School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | | | - Zichuan Zhang
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Claire Schmerberg
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Adam D Catherman
- Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence and Chemistry of Life Processes Institute, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,School of Life Sciences, Tianjin University , No. 92 Weijin Road, Nankai District, Tianjin 300072, China
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13
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Romanova EV, Rubakhin SS, Ossyra JR, Zombeck JA, Nosek MR, Sweedler JV, Rhodes JS. Differential peptidomics assessment of strain and age differences in mice in response to acute cocaine administration. J Neurochem 2015. [PMID: 26223348 DOI: 10.1111/jnc.13265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurochemical differences in the hypothalamic-pituitary axis between individuals and between ages may contribute to differential susceptibility to cocaine abuse. This study measured peptide levels in the pituitary gland (Pit) and lateral hypothalamus (LH) in adolescent (age 30 days) and adult (age 65 days) mice from four standard inbred strains, FVB/NJ, DBA/2J, C57BL/6J, and BALB/cByJ, which have previously been characterized for acute locomotor responses to cocaine. Individual peptide profiles were analyzed using mass spectrometric profiling and principal component analysis. Sequences of assigned peptides were verified by tandem mass spectrometry. Principal component analysis classified all strains according to their distinct peptide profiles in Pit samples from adolescent mice, but not adults. Select pro-opiomelanocortin-derived peptides were significantly higher in adolescent BALB/cByJ and DBA/2J mice than in FVB/NJ or C57BL/6J mice. A subset of peptides in the LH, but not in the Pit, was altered by cocaine in adolescents. A 15 mg/kg dose of cocaine induced greater peptide alterations than a 30 mg/kg dose, particularly in FVB/NJ animals, with larger differences in adolescents than adults. Neuropeptides in the LH affected by acute cocaine administration included pro-opiomelanocortin-, myelin basic protein-, and glutamate transporter-derived peptides. The observed peptide differences could contribute to differential behavioral sensitivity to cocaine among strains and ages. Peptides were measured using mass spectrometry (MALDI-TOF) in individual lateral hypothalamus and pituitary samples from four strains and two ages of inbred mice in response to acute cocaine administration. Principal component analyses (PCA) classified the strains according to their peptide profiles from adolescent mice, and a subset of peptides in the lateral hypothalamus was altered by cocaine in adolescents.
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Affiliation(s)
- Elena V Romanova
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Stanislav S Rubakhin
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John R Ossyra
- Department of Psychology, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan A Zombeck
- Department of Psychology, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Michael R Nosek
- Department of Psychology, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Justin S Rhodes
- Department of Psychology, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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14
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Romanova EV, Sweedler JV. Peptidomics for the discovery and characterization of neuropeptides and hormones. Trends Pharmacol Sci 2015; 36:579-86. [PMID: 26143240 DOI: 10.1016/j.tips.2015.05.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/31/2022]
Abstract
The discovery of neuropeptides as signaling molecules with paracrine or hormonal regulatory functions has led to trailblazing advances in physiology and fostered the characterization of numerous neuropeptide-binding G protein-coupled receptors (GPCRs) as potential drug targets. The impact on human health has been tremendous: approximately 30% of commercial drugs act via the GPCR pathway. However, about 25% of the GPCRs encoded by the mammalian genome still lack their pharmacological identity. Searching for the orphan GPCR endogenous ligands that are likely to be neuropeptides has proved to be a formidable task. Here we describe the mass spectrometry (MS)-based technologies and experimental strategies that have been successful in achieving high-throughput characterization of endogenous peptides in nervous and endocrine systems.
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Affiliation(s)
- Elena V Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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15
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dela Peña I, de la Peña JB, Kim BN, Han DH, Noh M, Cheong JH. Gene expression profiling in the striatum of amphetamine-treated spontaneously hypertensive rats which showed amphetamine conditioned place preference and self-administration. Arch Pharm Res 2014; 38:865-75. [PMID: 25163681 DOI: 10.1007/s12272-014-0470-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/19/2014] [Indexed: 12/11/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD), the most commonly diagnosed neurobehavioral disorder of childhood, is usually treated with psychostimulants (e.g., amphetamine). Little is known about the neuronal and behavioral consequences of chronic amphetamine use or abuse in individuals with ADHD. Of all ADHD animal models, the spontaneously hypertensive rat (SHR) is the most validated and widely used. Here, we analyzed striatal transcriptomes in amphetamine-pretreated SHRs (5 mg/kg, i.p. for 7 days [twice daily]), which showed a conditioned place preference to and self-administration of amphetamine. Microarray analyses revealed increased mRNA expression of 55 genes (>1.65-fold increase), while 17 genes were downregulated (<0.6-fold) in the striatum of SHRs. The main functional categories overrepresented among the differentially expressed genes in the striatum include those involved in transcription (e.g., Cebpb, Per2), genes associated with angiogenesis (e.g., Kdr, Klf5), cell adhesion (e.g., Col11a1, Ctgf), apoptosis (e.g., Nfkbia, Perp) and neuronal development (e.g., Egr2, Nr4a3). In conclusion, we dissected the striatal transcriptional responses to the reinforcing effects of repeated amphetamine treatment in the SHR model of ADHD. Future studies should determine the influence of these altered transcripts on amphetamine reinforcement in amphetamine-treated SHRs, and the clinical relevance of the present findings with regard to amphetamine use/abuse in ADHD individuals.
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Affiliation(s)
- Ike dela Peña
- Uimyung Research Institute for Neuroscience, Sahmyook University, 26-21 Kongreung-2-dong, Hwarangro-815, Nowon-gu, Seoul, 139-742, Korea
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16
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Zhang X, Petruzziello F, Rainer G. Extending the scope of neuropeptidomics in the mammalian brain. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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17
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Modulation of behavioral networks by selective interneuronal inactivation. Mol Psychiatry 2014; 19:580-7. [PMID: 24322205 PMCID: PMC4179403 DOI: 10.1038/mp.2013.167] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/04/2013] [Accepted: 10/17/2013] [Indexed: 12/15/2022]
Abstract
Gamma-aminobutyric acid (GABA)-ergic disturbances are hallmark features of schizophrenia and other neuropsychiatric disorders and encompass multiple interneuronal cell types. Using bacterial artificial chromosome-driven, miRNA silencing technology we generated transgenic mouse lines that suppress glutamic acid decarboxylase 1 (GAD1) in either cholecystokinin (CCK)- or neuropeptide Y (NPY)-expressing interneurons. In situ lipidomic and proteomic analyses on brain tissue sections revealed distinct, brain region-specific profiles in each transgenic line. Behavioral analyses revealed that suppression of GAD1 in CCK+ interneurons resulted in locomotor and olfactory sensory changes, whereas suppression in NPY+ interneurons affected anxiety-related behaviors and social interaction. Both transgenic mouse lines had altered sensitivity to amphetamine albeit in opposite directions. Together, these data argue that reduced GAD1 expression leads to altered molecular and behavioral profiles in a cell type-dependent manner, and that these subpopulations of interneurons are strong and opposing modulators of dopamine system function. Furthermore, our findings also support the hypothesis that neuronal networks are differentially controlled by diverse inhibitory subnetworks.
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18
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Gorini G, Adron Harris R, Dayne Mayfield R. Proteomic approaches and identification of novel therapeutic targets for alcoholism. Neuropsychopharmacology 2014; 39:104-30. [PMID: 23900301 PMCID: PMC3857647 DOI: 10.1038/npp.2013.182] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 01/01/2023]
Abstract
Recent studies have shown that gene regulation is far more complex than previously believed and does not completely explain changes at the protein level. Therefore, the direct study of the proteome, considerably different in both complexity and dynamicity to the genome/transcriptome, has provided unique insights to an increasing number of researchers. During the past decade, extraordinary advances in proteomic techniques have changed the way we can analyze the composition, regulation, and function of protein complexes and pathways underlying altered neurobiological conditions. When combined with complementary approaches, these advances provide the contextual information for decoding large data sets into meaningful biologically adaptive processes. Neuroproteomics offers potential breakthroughs in the field of alcohol research by leading to a deeper understanding of how alcohol globally affects protein structure, function, interactions, and networks. The wealth of information gained from these advances can help pinpoint relevant biomarkers for early diagnosis and improved prognosis of alcoholism and identify future pharmacological targets for the treatment of this addiction.
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Affiliation(s)
- Giorgio Gorini
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
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19
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Salisbury JP, Boggio KJ, Hsu YWA, Quijada J, Sivachenko A, Gloeckner G, Kowalski PJ, Easterling ML, Rosbash M, Agar JN. A rapid MALDI-TOF mass spectrometry workflow for Drosophila melanogaster differential neuropeptidomics. Mol Brain 2013; 6:60. [PMID: 24373546 PMCID: PMC4022047 DOI: 10.1186/1756-6606-6-60] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/20/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Neuropeptides are a diverse category of signaling molecules in the nervous system regulating a variety of processes including food intake, social behavior, circadian rhythms, learning, and memory. Both the identification and functional characterization of specific neuropeptides are ongoing fields of research. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of nervous tissues from a variety of organisms allows direct detection and identification of neuropeptides. Here, we demonstrate an analysis workflow that allows for the detection of differences in specific neuropeptides amongst a variety of neuropeptides being simultaneously measured. For sample preparation, we describe a straight-forward and rapid (minutes) method where individual adult Drosophila melanogaster brains are analyzed. Using a MATLAB-based data analysis workflow, also compatible with MALDI-TOF mass spectra obtained from other sample preparations and instrumentation, we demonstrate how changes in neuropeptides levels can be detected with this method. RESULTS Over fifty isotopically resolved ion signals in the peptide mass range are reproducibly observed across experiments. MALDI-TOF MS profile spectra were used to statistically identify distinct relative differences in organ-wide endogenous levels of detected neuropeptides between biological conditions. In particular, three distinct levels of a particular neuropeptide, pigment dispersing factor, were detected by comparing groups of preprocessed spectra obtained from individual brains across three different D. melanogaster strains, each of which express different amounts of this neuropeptide. Using the same sample preparation, MALDI-TOF/TOF tandem mass spectrometry confirmed that at least 14 ion signals observed across experiments are indeed neuropeptides. Among the identified neuropeptides were three products of the neuropeptide-like precursor 1 gene previously not identified in the literature. CONCLUSIONS Using MALDI-TOF MS and preprocessing/statistical analysis, changes in relative levels of a particular neuropeptide in D. melanogaster tissue can be statistically detected amongst a variety of neuropeptides. While the data analysis methods should be compatible with other sample preparations, the presented sample preparation method was sufficient to identify previously unconfirmed D. melanogaster neuropeptides.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jeffrey N Agar
- Depts of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, MA 02115, USA.
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Romanova EV, Dowd SE, Sweedler JV. Quantitation of endogenous peptides using mass spectrometry based methods. Curr Opin Chem Biol 2013; 17:801-8. [PMID: 23790312 DOI: 10.1016/j.cbpa.2013.05.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/24/2013] [Indexed: 10/26/2022]
Abstract
The mass spectrometry-based 'omics' sub-discipline that focuses on comprehensive, often exploratory, analyses of endogenous peptides involved in cell-to-cell communication is oftentimes referred to as peptidomics. Although the progress in bioanalytical technology development for peptide discovery has been tremendous, perhaps the largest advances have involved robust quantitative mass spectrometric approaches and data mining algorithms. These efforts have accelerated the discovery and validation of biomarkers, functionally important posttranslational modifications, and unexpected molecular interactions, information that aids drug development. In this article we outline the current approaches used in quantitative peptidomics and the technical challenges that stimulate new advances in the field, while also reviewing the newest literature on functional characterizations of endogenous peptides using quantitative mass spectrometry.
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Affiliation(s)
- Elena V Romanova
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013; 61:186-218. [PMID: 23623823 PMCID: PMC3891841 DOI: 10.1016/j.ymeth.2013.04.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 03/29/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.
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Affiliation(s)
- George E Craft
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Anshu Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT, 06508
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Qian K, Liu F, Yang J, Huang X, Gu W, Jambhrunkar S, Yuan P, Yu C. Pore size-optimized periodic mesoporous organosilicas for the enrichment of peptides and polymers. RSC Adv 2013. [DOI: 10.1039/c3ra41332b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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