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Yang J, Wang E, Chen W, Xu B, Chen C, Zhang G, Yao J. TMT-Based Proteomics Analysis of the Intervention Effect of Orlistat on Polycystic Ovary Syndrome Rats Induced by Letrozole Combined with a High-Fat Diet. ACS OMEGA 2023; 8:24831-24840. [DOI: https:/doi.org/10.1021/acsomega.3c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2024]
Affiliation(s)
- Jianmei Yang
- Department of Pediatric Endocrinology, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co. Ltd., Linyi 276006, Shandong, China
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong, China
| | - Enli Wang
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co. Ltd., Linyi 276006, Shandong, China
| | - Wenbin Chen
- Scientific Center, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Baihui Xu
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co. Ltd., Linyi 276006, Shandong, China
| | - Chen Chen
- Endocrinology, SBMS, Faculty of Medicine, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Guimin Zhang
- National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi 276006, Shandong, China
| | - Jingchun Yao
- State Key Laboratory of Integration and Innovation of Classic Formula and Modern Chinese Medicine, Lunan Pharmaceutical Group Co. Ltd., Linyi 276006, Shandong, China
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2
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Yang J, Wang E, Chen W, Xu B, Chen C, Zhang G, Yao J. TMT-Based Proteomics Analysis of the Intervention Effect of Orlistat on Polycystic Ovary Syndrome Rats Induced by Letrozole Combined with a High-Fat Diet. ACS OMEGA 2023; 8:24831-24840. [PMID: 37483206 PMCID: PMC10357523 DOI: 10.1021/acsomega.3c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023]
Abstract
Polycystic ovary syndrome (PCOS) is a complex gynecological endocrine and metabolic disease. Orlistat as a lipase inhibitor may improve the pathological characteristics of PCOS and is the sole antiobesity agent available in various countries. In this study, the PCOS rat models were established using letrozole and high-fat diet. Tandem Mass Tag labeling peptide coupled with liquid chromatography with tandem mass spectrometry (LC-MS/MS) approach was employed to investigate the differentially expressed ovarian proteins (DEPs) in the PCOS and control rats for the effect of PCOS, and in the PCOS and orlistat-treated PCOS rats for the effect of orlistat in PCOS. The orlistat attenuated the body weight gain; decreased the levels of testosterone, luteinizing hormone, a ratio of luteinizing/follicle-stimulating hormones; increased the level of estradiol; and recovered the estrous cycle in PCOS rats. In addition, 795 and 119 DEPs were found in PCOS and orlistat-treated PCOS groups, respectively. Based on the Gene Ontology and Kyoto Encyclopedia of Gene and Genomes pathway analysis of DEPs, orlistat restored the disturbed metabolism of linoleic acid, arachidonic acid, galactose, and glycerolipids, and then improved the chronic inflammation in PCOS rats. This study analyzed the ovarian proteome of orlistat-treated PCOS rats and identified targeted proteins, which explored the pathogenesis of PCOS and the potential effects of orlistat in PCOS rats.
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Affiliation(s)
- Jianmei Yang
- Department
of Pediatric Endocrinology, Shandong Provincial
Hospital affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
- State
Key Laboratory of Integration and Innovation of Classic Formula and
Modern Chinese Medicine, Lunan Pharmaceutical
Group Co. Ltd., Linyi 276006, Shandong, China
- Department
of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo
College of Medicine, Shandong University, Jinan 250021, Shandong, China
| | - Enli Wang
- State
Key Laboratory of Integration and Innovation of Classic Formula and
Modern Chinese Medicine, Lunan Pharmaceutical
Group Co. Ltd., Linyi 276006, Shandong, China
| | - Wenbin Chen
- Scientific
Center, Shandong Provincial Hospital affiliated
to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Baihui Xu
- State
Key Laboratory of Integration and Innovation of Classic Formula and
Modern Chinese Medicine, Lunan Pharmaceutical
Group Co. Ltd., Linyi 276006, Shandong, China
| | - Chen Chen
- Endocrinology,
SBMS, Faculty of Medicine, The University
of Queensland, St Lucia, QLD 4072, Australia
| | - Guimin Zhang
- National
Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi 276006, Shandong, China
| | - Jingchun Yao
- State
Key Laboratory of Integration and Innovation of Classic Formula and
Modern Chinese Medicine, Lunan Pharmaceutical
Group Co. Ltd., Linyi 276006, Shandong, China
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3
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Zhao A, Ma B, Xu L, Yao M, Zhang Y, Xue B, Ren J, Chang D, Liu J. Jiedu Tongluo Granules Ameliorates Post-stroke Depression Rat Model via Regulating NMDAR/BDNF Signaling Pathway. Front Pharmacol 2021; 12:662003. [PMID: 34093193 PMCID: PMC8173625 DOI: 10.3389/fphar.2021.662003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/28/2021] [Indexed: 01/26/2023] Open
Abstract
Post-stroke depression (PSD) is one of the most common stroke complications, which seriously affects stroke’s therapeutic effect and brings great pain for patients. The pathological mechanism of PSD has not been revealed. Jiedu Tongluo granules (JDTLG) is an effective traditional Chinese medicine for PSD treatment which is widely used in clinical treatment. JDTLG has a significant therapeutic effect against PSD, but the mechanism is still unclear. The PSD rat model was established by carotid artery embolization combined with chronic sleep deprivation followed by treating with JDTLG. Neurobehavioral and neurofunctional experiments were engaged in studying the neural function of rats. Histomorphology, proteomics, and western blotting researches were performed to investigate the potential molecular mechanisms related to JDTLG therapy. Oral treatment of JDTLG could significantly improve the symptoms of neurological deficit and depression symptoms of PSD rats. Proteomic analysis identified several processes that may involve the regulation of JDTLG on the PSD animal model, including energy metabolism, nervous system, and N-methyl-D-aspartate receptor (NMDAR)/brain-derived neurotrophic factor (BDNF) signal pathway. Our results showed that JDTLG could reduce glutamate (Glu) level and increase gamma-aminobutyric acid (GABA) level via regulating the NMDAR/BDNF pathway, which may play a vital role in the occurrence and development of PSD.
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Affiliation(s)
- Aimei Zhao
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Bo Ma
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Xu
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Mingjiang Yao
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Yehao Zhang
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Bingjie Xue
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Junguo Ren
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Dennis Chang
- NICM, Western Sydney University, Penrith, NSW, Australia
| | - Jianxun Liu
- Beijing Key Laboratory of Pharmacology of Chinese Materia Region, Institute of Basic Medical Sciences, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
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4
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Pumford AD, Arul AB, Ford KI, Robinson RAS. Automation of On-Resin Enrichment of S-Nitrosylated Proteins for Oxidized Cysteine-Selective cPILOT. VANDERBILT UNDERGRADUATE RESEARCH JOURNAL : VURJ 2021; 11:43-51. [PMID: 35615079 PMCID: PMC9129232 DOI: 10.15695/vurj.v11i1.5096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
S-Nitrosylation (SNO) is a cysteine post-translational modification that increases with normal aging and is present in Alzheimer's disease and other aging-related illnesses. Detection of SNO-modified proteins can be challenging; however, we previously developed a robust quantitative proteomics approach termed "Oxidized Cysteine-Selective combined precursor isobaric labeling and isobaric tagging (OxcyscPILOT)" that allows for detection of endogenous SNO-modified proteins. OxcyscPILOT involves enrichment of SNO-modified proteins using a thiol-based resin. This enrichment is performed manually, and wash steps with the resin require numerous stages and buffer reagents. The goal of this study is to transfer the manual protocol to an automated liquid handler system in order to reduce wash steps, increase sample throughput, and minimize experimental error. In order to accomplish this, we evaluated the Biomek i7 liquid handler automated workstation and a Positive Pressure ALP (PPA) apparatus to conduct automated on-resin enrichment. Our findings provide starting pressure conditions for the use of PPA in an automated OxcyscPILOT proteomics workflow that could be transferred to other robotic liquid handling systems.
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5
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Artiukhov AV, Grabarska A, Gumbarewicz E, Aleshin VA, Kähne T, Obata T, Kazantsev AV, Lukashev NV, Stepulak A, Fernie AR, Bunik VI. Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. Sci Rep 2020; 10:1886. [PMID: 32024885 PMCID: PMC7002488 DOI: 10.1038/s41598-020-58701-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
The biological significance of the DHTKD1-encoded 2-oxoadipate dehydrogenase (OADH) remains obscure due to its catalytic redundancy with the ubiquitous OGDH-encoded 2-oxoglutarate dehydrogenase (OGDH). In this work, metabolic contributions of OADH and OGDH are discriminated by exposure of cells/tissues with different DHTKD1 expression to the synthesized phosphonate analogues of homologous 2-oxodicarboxylates. The saccharopine pathway intermediates and phosphorylated sugars are abundant when cellular expressions of DHTKD1 and OGDH are comparable, while nicotinate and non-phosphorylated sugars are when DHTKD1 expression is order(s) of magnitude lower than that of OGDH. Using succinyl, glutaryl and adipoyl phosphonates on the enzyme preparations from tissues with varied DHTKD1 expression reveals the contributions of OADH and OGDH to oxidation of 2-oxoadipate and 2-oxoglutarate in vitro. In the phosphonates-treated cells with the high and low DHTKD1 expression, adipate or glutarate, correspondingly, are the most affected metabolites. The marker of fatty acid β-oxidation, adipate, is mostly decreased by the shorter, OGDH-preferring, phosphonate, in agreement with the known OGDH dependence of β-oxidation. The longest, OADH-preferring, phosphonate mostly affects the glutarate level. Coupled decreases in sugars and nicotinate upon the OADH inhibition link the perturbation in glucose homeostasis, known in OADH mutants, to the nicotinate-dependent NAD metabolism.
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Affiliation(s)
- Artem V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aneta Grabarska
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Ewelina Gumbarewicz
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Vasily A Aleshin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Biochemistry, George W. Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, USA
| | | | | | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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6
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Harper MM, Rudd D, Meyer KJ, Kanthasamy AG, Anantharam V, Pieper AA, Vázquez-Rosa E, Shin MK, Chaubey K, Koh Y, Evans LP, Bassuk AG, Anderson MG, Dutca L, Kudva IT, John M. Identification of chronic brain protein changes and protein targets of serum auto-antibodies after blast-mediated traumatic brain injury. Heliyon 2020; 6:e03374. [PMID: 32099918 PMCID: PMC7029173 DOI: 10.1016/j.heliyon.2020.e03374] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 02/03/2020] [Indexed: 12/13/2022] Open
Abstract
In addition to needing acute emergency management, blast-mediated traumatic brain injury (TBI) is also a chronic disorder with delayed-onset symptoms that manifest and progress over time. While the immediate consequences of acute blast injuries are readily apparent, chronic sequelae are harder to recognize. Indeed, the identification of individuals with mild-TBI or TBI-induced symptoms is greatly impaired in large part due to the lack of objective and robust biomarkers. The purpose of this study was to address these need by identifying candidates for serum-based biomarkers of blast TBI, and also to identify unique or differentially regulated protein expression in the thalamus in C57BL/6J mice exposed to blast using high throughput qualitative screens of protein expression. To identify thalamic proteins differentially or uniquely associated with blast exposure, we utilized an antibody-based affinity-capture strategy (referred to as "proteomics-based analysis of depletomes"; PAD) to deplete thalamic lysates from blast-treated mice of endogenous thalamic proteins also found in control mice. Analysis of this "depletome" detected 75 unique proteins, many with associations to the myelin sheath. To identify blast-associated proteins eliciting production of circulating autoantibodies, serum antibodies of blast-treated mice were immobilized, and their immunogens subsequently identified by proteomic analysis of proteins specifically captured following incubation with thalamic lysates (a variant of a strategy referred to as "proteomics-based expression library screening"; PELS). This analysis identified 46 blast-associated immunogenic proteins, including 6 shared in common with the PAD analysis (ALDOA, PHKB, HBA-A1, DPYSL2, SYN1, and CKB). These proteins and their autoantibodies are appropriate for further consideration as biomarkers of blast-mediated TBI.
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Affiliation(s)
- Matthew M. Harper
- The Iowa City Department of Veterans Affairs Medical Center, Center for the Prevention and Treatment of Visual Loss, Iowa City, IA, USA
- The University of Iowa Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Danielle Rudd
- The Iowa City Department of Veterans Affairs Medical Center, Center for the Prevention and Treatment of Visual Loss, Iowa City, IA, USA
| | - Kacie J. Meyer
- The University of Iowa Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | | | | | - Andrew A. Pieper
- Harrington Discovery Institute, University Hospitals of Cleveland, Department of Psychiatry Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes VA Medical Center, Cleveland, OH 44106, USA
| | - Edwin Vázquez-Rosa
- Harrington Discovery Institute, University Hospitals of Cleveland, Department of Psychiatry Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes VA Medical Center, Cleveland, OH 44106, USA
| | - Min-Kyoo Shin
- Harrington Discovery Institute, University Hospitals of Cleveland, Department of Psychiatry Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes VA Medical Center, Cleveland, OH 44106, USA
| | - Kalyani Chaubey
- Harrington Discovery Institute, University Hospitals of Cleveland, Department of Psychiatry Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes VA Medical Center, Cleveland, OH 44106, USA
| | - Yeojung Koh
- Harrington Discovery Institute, University Hospitals of Cleveland, Department of Psychiatry Case Western Reserve University, Geriatric Research Education and Clinical Centers, Louis Stokes VA Medical Center, Cleveland, OH 44106, USA
| | - Lucy P. Evans
- The University of Iowa Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- The University of Iowa Department of Neurology, University of Iowa, Iowa City, IA, USA
- The University of Iowa Department of Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Alexander G. Bassuk
- The University of Iowa Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- The University of Iowa Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Michael G. Anderson
- The Iowa City Department of Veterans Affairs Medical Center, Center for the Prevention and Treatment of Visual Loss, Iowa City, IA, USA
- The University of Iowa Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
- The University of Iowa Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Laura Dutca
- The Iowa City Department of Veterans Affairs Medical Center, Center for the Prevention and Treatment of Visual Loss, Iowa City, IA, USA
| | - Indira T. Kudva
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, IA, USA
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7
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Ugras S, Daniels MJ, Fazelinia H, Gould NS, Yocum AK, Luk KC, Luna E, Ding H, McKennan C, Seeholzer S, Martinez D, Evans P, Brown D, Duda JE, Ischiropoulos H. Induction of the Immunoproteasome Subunit Lmp7 Links Proteostasis and Immunity in α-Synuclein Aggregation Disorders. EBioMedicine 2018; 31:307-319. [PMID: 29759483 PMCID: PMC6014061 DOI: 10.1016/j.ebiom.2018.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/03/2018] [Accepted: 05/03/2018] [Indexed: 01/22/2023] Open
Abstract
Accumulation of aggregated α-synuclein into Lewy bodies is thought to contribute to the onset and progression of dopaminergic neuron degeneration in Parkinson's disease (PD) and related disorders. Although protein aggregation is associated with perturbation of proteostasis, how α-synuclein aggregation affects the brain proteome and signaling remains uncertain. In a mouse model of α-synuclein aggregation, 6% of 6215 proteins and 1.6% of 8183 phosphopeptides changed in abundance, indicating conservation of proteostasis and phosphorylation signaling. The proteomic analysis confirmed changes in abundance of proteins that regulate dopamine synthesis and transport, synaptic activity and integrity, and unearthed changes in mRNA binding, processing and protein translation. Phosphorylation signaling changes centered on axonal and synaptic cytoskeletal organization and structural integrity. Proteostatic responses included a significant increase in the levels of Lmp7, a component of the immunoproteasome. Increased Lmp7 levels and activity were also quantified in postmortem human brains with PD and dementia with Lewy bodies. Functionally, the immunoproteasome degrades α-synuclein aggregates and generates potentially antigenic peptides. Expression and activity of the immunoproteasome may represent testable targets to induce adaptive responses that maintain proteome integrity and modulate immune responses in protein aggregation disorders.
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Affiliation(s)
- Scott Ugras
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Malcolm J Daniels
- Pharmacology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Neal S Gould
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | | | - Kelvin C Luk
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esteban Luna
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hua Ding
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Chris McKennan
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Statistics, University of Chicago, 60637, USA
| | - Steven Seeholzer
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Dan Martinez
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Perry Evans
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel Brown
- Parkinson's Disease Research, Education and Clinical Center, Michael J. Crescenz VA Medical Center, USA; Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, USA
| | - John E Duda
- Parkinson's Disease Research, Education and Clinical Center, Michael J. Crescenz VA Medical Center, USA; Neurology, Perelman School of Medicine, University of Pennsylvania, USA
| | - Harry Ischiropoulos
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia Research Institute and Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Ding X, Kong X, Chen Y, Zhang C, Hua Y, Li X. Selective Extraction and Antioxidant Properties of Thiol-Containing Peptides in Soy Glycinine Hydrolysates. Molecules 2018; 23:E1909. [PMID: 30065200 PMCID: PMC6222310 DOI: 10.3390/molecules23081909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 11/17/2022] Open
Abstract
A highly selective procedure to extract thiol-containing peptides (TCPs) from complicated soy glycinin hydrolysates (SGHs) was described. This procedure included the reduction of disulfide bonds by 1,4-dithiothreitol (DTT) and enrichment of TCPs through Thiopropyl-Sephrose 6B covalent chromatography. TCPs were confirmed using a strategy based on mass shift after differential alkylation of sulfhydryl groups with iodoacetamide and N-ethylmaleimide by matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF-MS). The antioxidant activities of TCPs were evaluated using chemical assays. DTT reduction increased the concentration of sulfhydryl groups from 1.8 μmol/g to 113.8 μmol/g. The efficiency of the extraction was improved by optimizing the loading of sample, extraction and desorption time and the content of desorption reagent. Both of the adsorption and desorption process were found to fit a pseudo-second order model. MALDI-TOF-MS showed that 36 of the 45 extracted peptides were TCPs. The EC50 of TCPs for DPPH, hydroxyl radical, and superoxide anion radical was 0.1, 1.49 and 0.084 mg/mL, respectively. The reducing power of TCPs (0.2 mg/mL) was of 0.375. These results suggest that the combination of DTT reduction and Thiopropyl-Sepharose 6B covalent chromatograph was a successful pathway to extract TCPs from SGHs and the TCPs could be used as potential antioxidants.
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Affiliation(s)
- Xiuzhen Ding
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, Grain Process Engineering and Technology Center In Shandong Province, School of Food Science and Engineering, Shandong Agricultural University, 61 Daizong Avenue, Taian 271018, China.
| | - Xiangzhen Kong
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Yeming Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Caimeng Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Yufei Hua
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Xiangyang Li
- Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, Grain Process Engineering and Technology Center In Shandong Province, School of Food Science and Engineering, Shandong Agricultural University, 61 Daizong Avenue, Taian 271018, China.
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9
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Vacano GN, Gibson DS, Turjoman AA, Gawryluk JW, Geiger JD, Duncan M, Patterson D. Proteomic analysis of six- and twelve-month hippocampus and cerebellum in a murine Down syndrome model. Neurobiol Aging 2017; 63:96-109. [PMID: 29245059 DOI: 10.1016/j.neurobiolaging.2017.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/09/2017] [Accepted: 11/17/2017] [Indexed: 02/07/2023]
Abstract
This study was designed to investigate the brain proteome of the Ts65Dn mouse model of Down syndrome. We profiled the cerebellum and hippocampus proteomes of 6- and 12-month-old trisomic and disomic mice by difference gel electrophoresis. We quantified levels of 2082 protein spots and identified 272 (170 unique UniProt accessions) by mass spectrometry. Four identified proteins are encoded by genes trisomic in the Ts65Dn mouse. Three of these (CRYZL11, EZR, and SOD1) were elevated with p-value <0.05, and 2 proteins encoded by disomic genes (MAPRE3 and PHB) were reduced. Intergel comparisons based on age (6 vs. 12 months) and brain region (cerebellum vs. hippocampus) revealed numerous differences. Specifically, 132 identified proteins were different between age groups, and 141 identified proteins were different between the 2 brain regions. Our results suggest that compensatory mechanisms exist, which ameliorate the effect of trisomy in the Ts65Dn mice. Differences observed during aging may play a role in the accelerated deterioration of learning and memory seen in Ts65Dn mice.
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Affiliation(s)
- Guido N Vacano
- Knoebel Institute for Healthy Aging, Eleanor Roosevelt Institute, and Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - David S Gibson
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Denver School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Abdullah Arif Turjoman
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Denver School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Jeremy W Gawryluk
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Jonathan D Geiger
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Mark Duncan
- Division of Endocrinology, Metabolism and Diabetes, University of Colorado Denver School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - David Patterson
- Knoebel Institute for Healthy Aging, Eleanor Roosevelt Institute, and Department of Biological Sciences, University of Denver, Denver, CO, USA.
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10
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Evolution of complexity in the zebrafish synapse proteome. Nat Commun 2017; 8:14613. [PMID: 28252024 PMCID: PMC5337974 DOI: 10.1038/ncomms14613] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/15/2017] [Indexed: 11/09/2022] Open
Abstract
The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characterization of the proteomes and ultrastructure of central synapses in zebrafish and analyse the importance of the TSGD. While the TSGD increases overall synapse proteome complexity, the postsynaptic density (PSD) proteome of zebrafish has lower complexity than mammals. A highly conserved set of ∼1,000 proteins is shared across vertebrates. PSD ultrastructural features are also conserved. Lineage-specific proteome differences indicate that vertebrate species evolved distinct synapse types and functions. The data sets are a resource for a wide range of studies and have important implications for the use of zebrafish in modelling human synaptic diseases. Systematic analysis of the zebrafish synapse proteome has been lacking. Here the authors characterize the ultrastructure of zebrafish synapse and compare the proteomes of postsynaptic density in zebrafish and mice, offering a resource for future studies using zebrafish to model diseases.
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11
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Law HCH, Szeto SSW, Quan Q, Zhao Y, Zhang Z, Krakovska O, Lui LT, Zheng C, Lee SMY, Siu KWM, Wang Y, Chu IK. Characterization of the Molecular Mechanisms Underlying the Chronic Phase of Stroke in a Cynomolgus Monkey Model of Induced Cerebral Ischemia. J Proteome Res 2017; 16:1150-1166. [PMID: 28102082 DOI: 10.1021/acs.jproteome.6b00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stroke is one of the main causes of mortality and long-term disability worldwide. The pathophysiological mechanisms underlying this disease are not well understood, particularly in the chronic phase after the initial ischemic episode. In this study, a Macaca fascicularis stroke model consisting of two sample groups, as determined by MRI-quantified infarct volumes as a measure of the stroke severity 28 days after the ischemic episode, was evaluated using qualitative and quantitative proteomics analyses. By using multiple online multidimensional liquid chromatography platforms, 8790 nonredundant proteins were identified that condensed to 5223 protein groups at 1% global false discovery rate (FDR). After the application of a conservative criterion (5% local FDR), 4906 protein groups were identified from the analysis of cerebral cortex. Of the 2068 quantified proteins, differential proteomic analyses revealed that 31 and 23 were dysregulated in the elevated- and low-infarct-volume groups, respectively. Neurogenesis, synaptogenesis, and inflammation featured prominently as the cellular processes associated with these dysregulated proteins. Protein interaction network analysis revealed that the dysregulated proteins for inflammation and neurogenesis were highly connected, suggesting potential cross-talk between these processes in modulating the cytoskeletal structure and dynamics in the chronic phase poststroke. Elucidating the long-term consequences of brain tissue injuries from a cellular prospective, as well as the molecular mechanisms that are involved, would provide a basis for the development of new potentially neurorestorative therapies.
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Affiliation(s)
- Henry C H Law
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Samuel S W Szeto
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Quan Quan
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Yun Zhao
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Zaijun Zhang
- Institute of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University , Guangzhou 510632, China
| | - Olga Krakovska
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , Toronto, Ontario M3J 1P3, Canada
| | - Leong Ting Lui
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
| | - Chengyou Zheng
- Institute of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University , Guangzhou 510632, China
| | - Simon M-Y Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau , Avenue Padre Tomás Pereira S.J., Taipa, Macau 999078, China
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University , Toronto, Ontario M3J 1P3, Canada.,Department of Chemistry and Biochemistry, University of Windsor , Windsor, Ontario N9B 3P4, Canada
| | - Yuqiang Wang
- Institute of New Drug Research and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine, College of Pharmacy, Jinan University , Guangzhou 510632, China
| | - Ivan K Chu
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
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12
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Protein Fractionation and Enrichment Prior to Proteomics Sample Preparation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:23-41. [DOI: 10.1007/978-3-319-41448-5_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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13
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Proteomic Profiling for Identification of Novel Biomarkers Differentially Expressed in Human Ovaries from Polycystic Ovary Syndrome Patients. PLoS One 2016; 11:e0164538. [PMID: 27846214 PMCID: PMC5112797 DOI: 10.1371/journal.pone.0164538] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 09/27/2016] [Indexed: 12/17/2022] Open
Abstract
Objectives To identify differential protein expression pattern associated with polycystic ovary syndrome (PCOS). Methods Twenty women were recruited for the study, ten with PCOS as a test group and ten without PCOS as a control group. Differential in-gel electrophoresis (DIGE) analysis and mass spectroscopy were employed to identify proteins that were differentially expressed between the PCOS and normal ovaries. The differentially expressed proteins were further validated by western blot (WB) and immunohistochemistry (IHC). Results DIGE analysis revealed eighteen differentially expressed proteins in the PCOS ovaries of which thirteen were upregulated, and five downregulated. WB and IHC confirmed the differential expression of membrane-associated progesterone receptor component 1 (PGRMC1), retinol-binding protein 1 (RBP1), heat shock protein 90B1, calmodulin 1, annexin A6, and tropomyosin 2. Also, WB analysis revealed significantly (P<0.05) higher expression of PGRMC1 and RBP1 in PCOS ovaries as compared to the normal ovaries. The differential expression of the proteins was also validated by IHC. Conclusions The present study identified novel differentially expressed proteins in the ovarian tissues of women with PCOS that can serve as potential biomarkers for the diagnosis and development of novel therapeutics for the treatment of PCOS using molecular interventions.
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Donnarumma F, Murray KK. Laser ablation sample transfer for localized LC-MS/MS proteomic analysis of tissue. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:261-8. [PMID: 27041656 DOI: 10.1002/jms.3744] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 05/25/2023]
Abstract
We have developed a mid-infrared laser ablation sampling technique for nano-flow liquid chromatography coupled with tandem mass spectrometry proteomic profiling of discrete regions from biological samples. Laser ablation performed in transmission geometry was used to transfer material from 50-µm thick tissue sections mounted on a glass microscope slide to a capturing solvent. Captured samples were processed using filter-aided sample preparation and enzymatically digested to produce tryptic peptides for data-dependent analysis with an ion trap mass spectrometer. Comparison with ultraviolet laser capture microdissection from neighboring regions on the same tissue section revealed that infrared laser ablation transfer has higher reproducibility between samples from different consecutive sections. Both techniques allowed for proteomics investigation of different organelles without the addition of surfactants.
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Affiliation(s)
- Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
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15
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Quantitative map of multiple auditory cortical regions with a stereotaxic fine-scale atlas of the mouse brain. Sci Rep 2016; 6:22315. [PMID: 26924462 PMCID: PMC4770424 DOI: 10.1038/srep22315] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/12/2016] [Indexed: 11/08/2022] Open
Abstract
Optical imaging studies have recently revealed the presence of multiple auditory cortical regions in the mouse brain. We have previously demonstrated, using flavoprotein fluorescence imaging, at least six regions in the mouse auditory cortex, including the anterior auditory field (AAF), primary auditory cortex (AI), the secondary auditory field (AII), dorsoanterior field (DA), dorsomedial field (DM), and dorsoposterior field (DP). While multiple regions in the visual cortex and somatosensory cortex have been annotated and consolidated in recent brain atlases, the multiple auditory cortical regions have not yet been presented from a coronal view. In the current study, we obtained regional coordinates of the six auditory cortical regions of the C57BL/6 mouse brain and illustrated these regions on template coronal brain slices. These results should reinforce the existing mouse brain atlases and support future studies in the auditory cortex.
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16
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Wang Y, Javed I, Liu Y, Lu S, Peng G, Zhang Y, Qing H, Deng Y. Effect of Prolonged Simulated Microgravity on Metabolic Proteins in Rat Hippocampus: Steps toward Safe Space Travel. J Proteome Res 2015; 15:29-37. [PMID: 26523826 DOI: 10.1021/acs.jproteome.5b00777] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mitochondria are not only the main source of energy in cells but also produce reactive oxygen species (ROS), which result in oxidative stress when in space. This oxidative stress is responsible for energy imbalances and cellular damage. In this study, a rat tail suspension model was used in individual experiments for 7 and 21 days to explore the effect of simulated microgravity (SM) on metabolic proteins in the hippocampus, a vital brain region involved in learning, memory, and navigation. A comparative (18)O-labeled quantitative proteomic strategy was used to observe the differential expression of metabolic proteins. Forty-two and sixty-seven mitochondrial metabolic proteins were differentially expressed after 21 and 7 days of SM, respectively. Mitochondrial Complex I, III, and IV, isocitrate dehydrogenase and malate dehydrogenase were down-regulated. Moreover, DJ-1 and peroxiredoxin 6, which defend against oxidative damage, were up-regulated in the hippocampus. Western blot analysis of proteins DJ-1 and COX 5A confirmed the mass spectrometry results. Despite these changes in mitochondrial protein expression, no obvious cell apoptosis was observed after 21 days of SM. The results of this study indicate that the oxidative stress induced by SM has profound effects on metabolic proteins.
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Affiliation(s)
- Yun Wang
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Iqbal Javed
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Yahui Liu
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Song Lu
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Guang Peng
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Yongqian Zhang
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Hong Qing
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Yulin Deng
- School of Life Sciences, Beijing Institute of Technology , No. 5 Zhongguancun South Street, Beijing 100081, P.R. China
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17
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Wang Y, Iqbal J, Liu Y, Su R, Lu S, Peng G, Zhang Y, Qing H, Deng Y. Effects of simulated microgravity on the expression of presynaptic proteins distorting the GABA/glutamate equilibrium - A proteomics approach. Proteomics 2015; 15:3883-91. [DOI: 10.1002/pmic.201500302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/28/2015] [Accepted: 09/07/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Yun Wang
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Javed Iqbal
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Yahui Liu
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Rui Su
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Song Lu
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Guang Peng
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Yongqian Zhang
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Hong Qing
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
| | - Yulin Deng
- School of Life Sciences; Beijing Institute of Technology; Beijing P.R. China
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18
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Sundberg M, Bergquist J, Ramström M. High-abundant protein depletion strategies applied on dog cerebrospinal fluid and evaluated by high-resolution mass spectrometry. Biochem Biophys Rep 2015; 3:68-75. [PMID: 30338299 PMCID: PMC6189695 DOI: 10.1016/j.bbrep.2015.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/18/2015] [Accepted: 07/22/2015] [Indexed: 12/27/2022] Open
Abstract
As the number of fully sequenced animal genomes and the performance of advanced mass spectrometry-based proteomics techniques are continuously improving, there is now a great opportunity to increase the knowledge of various animal proteomes. This research area is further stimulated by a growing interest from veterinary medicine and the pharmaceutical industry. Cerebrospinal fluid (CSF) is a good source for better understanding of diseases related to the central nervous system, both in humans and other animals. In this study, four high-abundant protein depletion columns, developed for human or rat serum, were evaluated for dog CSF. For the analysis, a shotgun proteomics approach, based on nanoLC-LTQ Orbitrap MS/MS, was applied. All the selected approaches were shown to deplete dog CSF with different success. It was demonstrated that the columns significantly improved the coverage of the detected dog CSF proteome. An antibody-based column showed the best performance, in terms of efficiency, repeatability and the number of proteins detected in the sample. In total 983 proteins were detected. Of those, 801 proteins were stated as uncharacterized in the UniProt database. To the best of our knowledge, this is the so far largest number of proteins reported for dog CSF in one single study. We evaluated four high-abundant protein depletion kits on dog CSF. High abundant depletion kit developed for humans/rats can be used for dog CSF. Protein depletion of dog CSF gives extended coverage of the CSF proteome. In total, 983 dog proteins were identified in this study.
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Affiliation(s)
- Mårten Sundberg
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Margareta Ramström
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
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19
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Raju K, Doulias PT, Evans P, Krizman EN, Jackson JG, Horyn O, Daikhin Y, Nissim I, Yudkoff M, Nissim I, Sharp KA, Robinson MB, Ischiropoulos H. Regulation of brain glutamate metabolism by nitric oxide and S-nitrosylation. Sci Signal 2015; 8:ra68. [PMID: 26152695 DOI: 10.1126/scisignal.aaa4312] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nitric oxide (NO) is a signaling intermediate during glutamatergic neurotransmission in the central nervous system (CNS). NO signaling is in part accomplished through cysteine S-nitrosylation, a posttranslational modification by which NO regulates protein function and signaling. In our investigation of the protein targets and functional impact of S-nitrosylation in the CNS under physiological conditions, we identified 269 S-nitrosocysteine residues in 136 proteins in the wild-type mouse brain. The number of sites was significantly reduced in the brains of mice lacking endothelial nitric oxide synthase (eNOS(-/-)) or neuronal nitric oxide synthase (nNOS(-/-)). In particular, nNOS(-/-) animals showed decreased S-nitrosylation of proteins that participate in the glutamate/glutamine cycle, a metabolic process by which synaptic glutamate is recycled or oxidized to provide energy. (15)N-glutamine-based metabolomic profiling and enzymatic activity assays indicated that brain extracts from nNOS(-/-) mice converted less glutamate to glutamine and oxidized more glutamate than those from mice of the other genotypes. GLT1 [also known as EAAT2 (excitatory amino acid transporter 2)], a glutamate transporter in astrocytes, was S-nitrosylated at Cys(373) and Cys(561) in wild-type and eNOS(-/-) mice, but not in nNOS(-/-) mice. A form of rat GLT1 that could not be S-nitrosylated at the equivalent sites had increased glutamate uptake compared to wild-type GLT1 in cells exposed to an S-nitrosylating agent. Thus, NO modulates glutamatergic neurotransmission through the selective, nNOS-dependent S-nitrosylation of proteins that govern glutamate transport and metabolism.
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Affiliation(s)
- Karthik Raju
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paschalis-Thomas Doulias
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Perry Evans
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Elizabeth N Krizman
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Joshua G Jackson
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Oksana Horyn
- Division of Genetic and Metabolic Disease, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Yevgeny Daikhin
- Division of Genetic and Metabolic Disease, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Ilana Nissim
- Division of Genetic and Metabolic Disease, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Marc Yudkoff
- Division of Genetic and Metabolic Disease, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Itzhak Nissim
- Division of Genetic and Metabolic Disease, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA. Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kim A Sharp
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael B Robinson
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA. Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA. Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Harry Ischiropoulos
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA. Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA. Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Protein expression profiles characterize distinct features of mouse cerebral cortices at different developmental stages. PLoS One 2015; 10:e0125608. [PMID: 25915664 PMCID: PMC4411115 DOI: 10.1371/journal.pone.0125608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 03/25/2015] [Indexed: 01/18/2023] Open
Abstract
The proper development of the mammalian cerebral cortex requires precise protein synthesis and accurate regulation of protein expression levels. To reveal signatures of protein expression in developing mouse cortices, we here generate proteomic profiles of cortices at embryonic and postnatal stages using tandem mass spectrometry (MS/MS). We found that protein expression profiles are mostly consistent with biological features of the developing cortex. Gene Ontology (GO) and KEGG pathway analyses demonstrate conserved molecules that maintain cortical development such as proteins involved in metabolism. GO and KEGG pathway analyses further identify differentially expressed proteins that function at specific stages, for example proteins regulating the cell cycle in the embryonic cortex, and proteins controlling axon guidance in the postnatal cortex, suggesting that distinct protein expression profiles determine biological events in the developing cortex. Furthermore, the STRING network analysis has revealed that many proteins control a single biological event, such as the cell cycle regulation, through cohesive interactions, indicating a complex network regulation in the cortex. Our study has identified protein networks that control the cortical development and has provided a protein reference for further investigation of protein interactions in the cortex.
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21
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Ding X, Hua Y, Chen Y, Zhang C, Kong X. Heavy metal complexation of thiol-containing peptides from soy glycinin hydrolysates. Int J Mol Sci 2015; 16:8040-58. [PMID: 25867477 PMCID: PMC4425066 DOI: 10.3390/ijms16048040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/03/2015] [Accepted: 04/07/2015] [Indexed: 11/24/2022] Open
Abstract
Many thiol-containing molecules show heavy metal complexation ability and are used as antidotes. In this study, the potential function associated with thiol-containing peptides (TCPs) from soy protein hydrolysates as natural detoxicants for heavy metals is reported. TCPs enriched by Thiopropyl-Sepharose 6B covalent chromatography had different molecular weight distributions as well as different numbers of proton dissociable groups, depending on the proteases and degree of hydrolysis. The major contribution of sulfhydryl groups was confirmed by the largest pH decrease between 8.0 and 8.5 of the pH titration curves. The complexation of TCPs with heavy metalswas evaluated by stability constants (βn) of TCP-metal complexes whose stoichiometry was found to be 1:1 (ML) and 1:2 (ML2). TCPs from degree of hydrolysis of 25% hydrolysates gave high affinities towards Hg2+, Cd2+, and Pb2+ (giving similar or even bigger lgβ values than that of glutathione). A significantly positive correlation was found between the logarithm of stability constants for ML2 (lgβ2) and the sulfhydryl group content. Molecular weight distribution of TCPs affected the complexation with Pb2+ notably more than Hg2+ and Cd2+. These results suggest that soy TCPs have the potential to be used in the formulation of functional foods to counteract heavy metal accumulation in humans.
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Affiliation(s)
- Xiuzhen Ding
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yufei Hua
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yeming Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Caimeng Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Xiangzhen Kong
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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22
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Gu L, Evans AR, Robinson RAS. Sample multiplexing with cysteine-selective approaches: cysDML and cPILOT. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:615-630. [PMID: 25588721 DOI: 10.1007/s13361-014-1059-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/22/2014] [Accepted: 11/22/2014] [Indexed: 06/04/2023]
Abstract
Cysteine-selective proteomics approaches simplify complex protein mixtures and improve the chance of detecting low abundant proteins. It is possible that cysteinyl-peptide/protein enrichment methods could be coupled to isotopic labeling and isobaric tagging methods for quantitative proteomics analyses in as few as two or up to 10 samples, respectively. Here we present two novel cysteine-selective proteomics approaches: cysteine-selective dimethyl labeling (cysDML) and cysteine-selective combined precursor isotopic labeling and isobaric tagging (cPILOT). CysDML is a duplex precursor quantification technique that couples cysteinyl-peptide enrichment with on-resin stable-isotope dimethyl labeling. Cysteine-selective cPILOT is a novel 12-plex workflow based on cysteinyl-peptide enrichment, on-resin stable-isotope dimethyl labeling, and iodoTMT tagging on cysteine residues. To demonstrate the broad applicability of the approaches, we applied cysDML and cPILOT methods to liver tissues from an Alzheimer's disease (AD) mouse model and wild-type (WT) controls. From the cysDML experiments, an average of 850 proteins were identified and 594 were quantified, whereas from the cPILOT experiment, 330 and 151 proteins were identified and quantified, respectively. Overall, 2259 unique total proteins were detected from both cysDML and cPILOT experiments. There is tremendous overlap in the proteins identified and quantified between both experiments, and many proteins have AD/WT fold-change values that are within ~20% error. A total of 65 statistically significant proteins are differentially expressed in the liver proteome of AD mice relative to WT. The performance of cysDML and cPILOT are demonstrated and advantages and limitations of using multiple duplex experiments versus a single 12-plex experiment are highlighted.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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23
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Barth J, Volknandt W. Proteomic investigations of the synaptic vesicle interactome. Expert Rev Proteomics 2014; 8:211-20. [DOI: 10.1586/epr.11.7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Samways DSK. Applications for mass spectrometry in the study of ion channel structure and function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:237-61. [PMID: 24952185 DOI: 10.1007/978-3-319-06068-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Ion channels are intrinsic membrane proteins that form gated ion-permeable pores across biological membranes. Depending on the type, ion channels exhibit sensitivities to a diverse range of stimuli including changes in membrane potential, binding by diffusible ligands, changes in temperature and direct mechanical force. The purpose of these proteins is to facilitate the passive diffusion of ions down their respective electrochemical gradients into and out of the cell, and between intracellular compartments. In doing so, ion channels can affect transmembrane potentials and regulate the intracellular homeostasis of the important second messenger, Ca(2+). The ion channels of the plasma membrane are of particular clinical interest due to their regulation of cell excitability and cytosolic Ca(2+) levels, and the fact that they are most amenable to manipulation by exogenously applied drugs and toxins. A critical step in improving the pharmacopeia of chemicals available that influence the activity of ion channels is understanding how their three-dimensional structure imparts function. Here, progress has been slow relative to that for soluble protein structures in large part due to the limitations of applying conventional structure determination methods, such as X-ray crystallography, nuclear magnetic resonance imaging, and mass spectrometry, to membrane proteins. Although still an underutilized technique in the assessment of membrane protein structure, recent advances have pushed mass spectrometry to the fore as an important complementary approach to studying the structure and function of ion channels. In addition to revealing the subtle conformational changes in ion channel structure that accompany gating and permeation, mass spectrometry is already being used effectively for identifying tissue-specific posttranslational modifications and mRNA splice variants. Furthermore, the use of mass spectrometry for high-throughput proteomics analysis, which has proven so successful for soluble proteins, is already providing valuable insight into the functional interactions of ion channels within the context of the macromolecular-signaling complexes that they inhabit in vivo. In this chapter, the potential for mass spectrometry as a complementary approach to the study of ion channel structure and function will be reviewed with examples of its application.
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Affiliation(s)
- Damien S K Samways
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA,
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Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
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26
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SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping. J Proteomics 2013; 91:164-71. [PMID: 23851314 DOI: 10.1016/j.jprot.2013.06.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/25/2013] [Accepted: 06/29/2013] [Indexed: 11/20/2022]
Abstract
UNLABELLED Multidimensional peptide fractionation is widely used in proteomics to reduce the complexity of peptide mixtures prior to mass spectrometric analysis. Here, we describe the sequential use of strong cation exchange and reversed phase liquid chromatography in both basic and acidic pH buffers for separating tryptic peptides from complex mixtures of proteins. Strong cation exchange exclusively separates peptide by their charge state into neutral, singly and multi-charged species. To further reduce complexity, each peptide group was separated by reversed phase liquid chromatography at basic pH and the resultant fractions were analyzed by LC-MS/MS. This workflow was applied to a soluble protein lysate from mouse embryonic fibroblast cells, and more than 5000 proteins from 29,843 peptides were identified. The high selectivity displayed during the SCX step (93% to 100%) and the overlaps between proteins identified from the SCX-separated peptide groups, are interesting assets of the procedure. BIOLOGICAL SIGNIFICANCE The present work shows how complex mixture of peptides can be selectively separated by SCX based essentially on the net charge of peptides. The proposed workflow results in three well-defined subset of peptides of specific amino acid composition, which are representative of the constituent proteins. The very high selectivity obtained (93% to 99%) on the peptide side, underscores for the first time the possibility of SCX chromatography to aid in validating identified peptides.
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27
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Guingab-Cagmat JD, Cagmat EB, Hayes RL, Anagli J. Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery. Front Neurol 2013; 4:61. [PMID: 23750150 PMCID: PMC3668328 DOI: 10.3389/fneur.2013.00061] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 05/12/2013] [Indexed: 01/18/2023] Open
Abstract
Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed.
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Paulech J, Solis N, Edwards AV, Puckeridge M, White MY, Cordwell SJ. Large-Scale Capture of Peptides Containing Reversibly Oxidized Cysteines by Thiol-Disulfide Exchange Applied to the Myocardial Redox Proteome. Anal Chem 2013; 85:3774-80. [DOI: 10.1021/ac400166e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jana Paulech
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Nestor Solis
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Alistair V.G. Edwards
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Max Puckeridge
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Melanie Y. White
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Stuart J. Cordwell
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
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29
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Liddy KA, White MY, Cordwell SJ. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome Med 2013; 5:20. [PMID: 23445784 PMCID: PMC3706772 DOI: 10.1186/gm424] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The more than 300 currently identified post-translational modifications (PTMs) provides great scope for subtle or dramatic alteration of protein structure and function. Furthermore, the rapid and transient nature of many PTMs allows efficient signal transmission in response to internal and environmental stimuli. PTMs are predominantly added by enzymes, and the enzymes responsible (such as kinases) are thus attractive targets for therapeutic interventions. Modifications can be grouped according to their stability or transience (reversible versus irreversible): irreversible types (such as irreversible redox modifications or protein deamidation) are often associated with aging or tissue injury, whereas transient modifications are associated with signal propagation and regulation. This is particularly important in the setting of heart disease, which comprises a diverse range of acute (such as ischemia/reperfusion), chronic (such as heart failure, dilated cardiomyopathy) and genetic (such as hypertrophic cardiomyopathy) disease states, all of which have been associated with protein PTM. Recently the interplay between diverse PTMs has been suggested to also influence cellular function, with cooperation or competition for sites of modification possible. Here we discuss the utility of proteomics for examining PTMs in the context of the molecular mechanisms of heart disease.
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Affiliation(s)
- Kiersten A Liddy
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia
| | - Melanie Y White
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia ; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006 Sydney, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia ; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006 Sydney, Australia
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30
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Saxena S, Dupont S, Meghah V, Lakshmi MGM, Singh SK, Swamy CVB, Idris MM. Proteome map of the neural complex of the tunicate Ciona intestinalis, the closest living relative to vertebrates. Proteomics 2013; 13:860-5. [PMID: 23300126 DOI: 10.1002/pmic.201200148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 11/13/2012] [Accepted: 11/28/2012] [Indexed: 11/07/2022]
Abstract
Ciona intestinalis (the common sea squirt) is the closest living chordate relative to vertebrates with cosmopolitan presence worldwide. It has a relatively simple nervous system and development, making it a widely studied alternative model system in neuroscience and developmental biology. The use of Ciona as a model organism has increased significantly after the draft genome was published. In this study, we describe the first proteome map of the neural complex of C. intestinalis. A total of 544 proteins were identified based on 1DE and 2DE FTMS/ITMSMS analyses. Proteins were annotated against the Ciona database and analyzed to predict their molecular functions, roles in biological processes, and position in constructed network pathways. The identified Ciona neural complex proteome was found to map onto vertebrate nervous system pathways, including cytoskeleton remodeling neurofilaments, cell adhesion through the histamine receptor signaling pathway, γ-aminobutyric acid-A receptor life cycle neurophysiological process, glycolysis, and amino acid metabolism. The proteome map of the Ciona neural complex is the first step toward a better understanding of several important processes, including the evolution and regeneration capacity of the Ciona nervous system.
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Affiliation(s)
- Sandeep Saxena
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Andhra Pradesh, India
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31
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Siegel D. Applications of reversible covalent chemistry in analytical sample preparation. Analyst 2012; 137:5457-82. [PMID: 23013801 DOI: 10.1039/c2an35697j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.
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Affiliation(s)
- David Siegel
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str 11, 12489 Berlin, Germany.
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32
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Protein pre-fractionation with a mixed-bed ion exchange column in 3D LC–MS/MS proteome analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 905:96-104. [DOI: 10.1016/j.jchromb.2012.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 08/05/2012] [Accepted: 08/06/2012] [Indexed: 11/19/2022]
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33
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Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C. PaxDb, a database of protein abundance averages across all three domains of life. Mol Cell Proteomics 2012; 11:492-500. [PMID: 22535208 PMCID: PMC3412977 DOI: 10.1074/mcp.o111.014704] [Citation(s) in RCA: 354] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 03/26/2012] [Indexed: 02/04/2023] Open
Abstract
Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels. These extend from a few molecules per cell for signaling proteins, to millions of molecules for structural proteins. When addressing fundamental questions related to protein evolution, translation and folding, but also in routine laboratory work, a simple rough estimate of the average wild type abundance of each detectable protein in an organism is often desirable. Here, we introduce a meta-resource dedicated to integrating information on absolute protein abundance levels; we place particular emphasis on deep coverage, consistent post-processing and comparability across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. By aggregating and averaging over the various samples, conditions and cell-types, the resulting integrated data set achieves increased coverage and a high dynamic range. We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually. The current PaxDb-release 2.1 (at http://pax-db.org/) presents whole-organism data as well as tissue-resolved data, and covers 85,000 proteins in 12 model organisms. All values can be seamlessly compared across organisms via pre-computed orthology relationships.
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Affiliation(s)
- M. Wang
- From the ‡Institute of Molecular Life Sciences, and
- §Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - M. Weiss
- From the ‡Institute of Molecular Life Sciences, and
- §Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - M. Simonovic
- From the ‡Institute of Molecular Life Sciences, and
- §Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - G. Haertinger
- From the ‡Institute of Molecular Life Sciences, and
- §Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | | | - C. von Mering
- From the ‡Institute of Molecular Life Sciences, and
- §Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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34
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Slebos RJC, Jehmlich N, Brown B, Yin Z, Chung CH, Yarbrough WG, Liebler DC. Proteomic analysis of oropharyngeal carcinomas reveals novel HPV-associated biological pathways. Int J Cancer 2012; 132:568-79. [PMID: 22733545 DOI: 10.1002/ijc.27699] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 06/08/2012] [Indexed: 01/06/2023]
Abstract
Oropharyngeal carcinoma (OPC) can be classified into two equally prevalent subtypes depending on the presence of human papillomavirus (HPV). Patients with HPV-positive (HPV+) OPC represent a unique cohort with a distinct tumor biology and clinical behavior compared to HPV-negative (HPV-) OPC. Genetic studies have demonstrated chromosomal and gene expression changes associated with distinct subclasses of OPC; however, the proteomic consequences of HPV infection are not known. We analyzed sets of ten HPV+ and ten HPV- OPCs and ten normal adult oral epithelia using a standardized global proteomic analysis platform. This analysis yielded a total of 2,653 confidently identified proteins from which we chose 31 proteins on the basis of expression differences between HPV+, HPV- and normal epithelium for targeted protein quantitation. Analysis of differentially expressed proteins by HPV status revealed enrichment of proteins involved in epithelial cell development, keratinization and extracellular matrix organization in HPV- OPC, whereas enrichment of proteins in DNA initiation and replication and cell cycle control was found for HPV+ OPC. Enrichment analysis for transcription factor targets identified transcription factors E2F1 and E2F4 to be highly expressed in HPV+ OPC. We also found high expression of argininosuccinate synthase 1 in HPV+ OPC, suggesting that HPV+ OPC is more dependent on conditionally essential amino acid, arginine, and this was confirmed on a OPC-specific tissue microarray. These identified proteomic changes reveal novel driving molecular pathways for HPV+ and HPV- OPCs that may be pertinent in therapeutic strategies and outcomes of OPC.
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Affiliation(s)
- Robbert J C Slebos
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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35
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Wagner SA, Beli P, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C. Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues. Mol Cell Proteomics 2012; 11:1578-85. [PMID: 22790023 PMCID: PMC3518112 DOI: 10.1074/mcp.m112.017905] [Citation(s) in RCA: 229] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Posttranslational modifications of proteins increase the complexity of the cellular proteome and enable rapid regulation of protein functions in response to environmental changes. Protein ubiquitylation is a central regulatory posttranslational modification that controls numerous biological processes including proteasomal degradation of proteins, DNA damage repair and innate immune responses. Here we combine high-resolution mass spectrometry with single-step immunoenrichment of di-glycine modified peptides for mapping of endogenous putative ubiquitylation sites in murine tissues. We identify more than 20,000 unique ubiquitylation sites on proteins involved in diverse biological processes. Our data reveals that ubiquitylation regulates core signaling pathways common for each of the studied tissues. In addition, we discover that ubiquitylation regulates tissue-specific signaling networks. Many tissue-specific ubiquitylation sites were obtained from brain highlighting the complexity and unique physiology of this organ. We further demonstrate that different di-glycine-lysine-specific monoclonal antibodies exhibit sequence preferences, and that their complementary use increases the depth of ubiquitylation site analysis, thereby providing a more unbiased view of protein ubiquitylation.
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Affiliation(s)
- Sebastian A Wagner
- Department of Proteomics, The NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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36
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Kikuchi T, Hassanein M, Amann JM, Liu Q, Slebos RJC, Rahman SMJ, Kaufman JM, Zhang X, Hoeksema MD, Harris BK, Li M, Shyr Y, Gonzalez AL, Zimmerman LJ, Liebler DC, Massion PP, Carbone DP. In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers. Mol Cell Proteomics 2012; 11:916-32. [PMID: 22761400 DOI: 10.1074/mcp.m111.015370] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Advances in proteomic analysis of human samples are driving critical aspects of biomarker discovery and the identification of molecular pathways involved in disease etiology. Toward that end, in this report we are the first to use a standardized shotgun proteomic analysis method for in-depth tissue protein profiling of the two major subtypes of nonsmall cell lung cancer and normal lung tissues. We identified 3621 proteins from the analysis of pooled human samples of squamous cell carcinoma, adenocarcinoma, and control specimens. In addition to proteins previously shown to be implicated in lung cancer, we have identified new pathways and multiple new differentially expressed proteins of potential interest as therapeutic targets or diagnostic biomarkers, including some that were not identified by transcriptome profiling. Up-regulation of these proteins was confirmed by multiple reaction monitoring mass spectrometry. A subset of these proteins was found to be detectable and differentially present in the peripheral blood of cases and matched controls. Label-free shotgun proteomic analysis allows definition of lung tumor proteomes, identification of biomarker candidates, and potential targets for therapy.
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Affiliation(s)
- Takefumi Kikuchi
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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37
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He Q, Man L, Ji Y, Zhang S, Jiang M, Ding F, Gu X. Comparative Proteomic Analysis of Differentially Expressed Proteins between Peripheral Sensory and Motor Nerves. J Proteome Res 2012; 11:3077-89. [DOI: 10.1021/pr300186t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qianru He
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
| | - Lili Man
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
| | - Yuhua Ji
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
| | - Shuqiang Zhang
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
| | - Maorong Jiang
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
| | - Fei Ding
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
| | - Xiaosong Gu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, Jiangsu Province 226001,
P. R. China
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38
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Shevchenko G, Musunuri S, Wetterhall M, Bergquist J. Comparison of Extraction Methods for the Comprehensive Analysis of Mouse Brain Proteome using Shotgun-based Mass Spectrometry. J Proteome Res 2012; 11:2441-51. [DOI: 10.1021/pr201169q] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ganna Shevchenko
- Department of Physical
and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Sravani Musunuri
- Department of Physical
and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Magnus Wetterhall
- Department of Physical
and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Physical
and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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39
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Alkhas A, Hood BL, Oliver K, Teng PN, Oliver J, Mitchell D, Hamilton CA, Maxwell GL, Conrads TP. Standardization of a Sample Preparation and Analytical Workflow for Proteomics of Archival Endometrial Cancer Tissue. J Proteome Res 2011; 10:5264-71. [DOI: 10.1021/pr2007736] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Addie Alkhas
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, Maryland, United States
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Brian L. Hood
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Kate Oliver
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, Maryland, United States
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Pang-ning Teng
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Julie Oliver
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - David Mitchell
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Chad A. Hamilton
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, Maryland, United States
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - G. Larry Maxwell
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
- Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Fairfax, Virgina, United States
| | - Thomas P. Conrads
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
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40
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Betancourt LH, Sánchez A, Pérez Y, Fernandez de Cossio J, Gil J, Toledo P, Iguchi S, Aimoto S, González LJ, Padrón G, Takao T, Besada V. Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: Evaluation in proteomic studies using peptide-centric database searches. J Proteomics 2011; 74:2210-3. [DOI: 10.1016/j.jprot.2011.04.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/26/2011] [Accepted: 04/29/2011] [Indexed: 10/18/2022]
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41
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Analysis of membrane and hydrophilic proteins simultaneously derived from the mouse brain using cloud-point extraction. Anal Bioanal Chem 2011; 400:2827-36. [DOI: 10.1007/s00216-011-5037-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 04/15/2011] [Accepted: 04/16/2011] [Indexed: 12/30/2022]
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42
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Giron P, Dayon L, Sanchez JC. Cysteine tagging for MS-based proteomics. MASS SPECTROMETRY REVIEWS 2011; 30:366-395. [PMID: 21500242 DOI: 10.1002/mas.20285] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 11/13/2009] [Accepted: 11/13/2009] [Indexed: 05/30/2023]
Abstract
Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.
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Affiliation(s)
- Priscille Giron
- Biomedical Proteomics Research Group, Structural Biology and Bioinformatics Department, University of Geneva, Geneva, Switzerland
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43
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Wang Y, Yang F, Gritsenko MA, Wang Y, Clauss T, Liu T, Shen Y, Monroe ME, Lopez-Ferrer D, Reno T, Moore RJ, Klemke RL, Camp DG, Smith RD. Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics 2011; 11:2019-26. [PMID: 21500348 PMCID: PMC3120047 DOI: 10.1002/pmic.201000722] [Citation(s) in RCA: 441] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/12/2011] [Accepted: 02/10/2011] [Indexed: 12/17/2022]
Abstract
In this study, we evaluated a concatenated low pH (pH 3) and high pH (pH 10) reversed-phase liquid chromatography strategy as a first dimension for two-dimensional liquid chromatography tandem mass spectrometry ("shotgun") proteomic analysis of trypsin-digested human MCF10A cell sample. Compared with the more traditional strong cation exchange method, the use of concatenated high pH reversed-phase liquid chromatography as a first-dimension fractionation strategy resulted in 1.8- and 1.6-fold increases in the number of peptide and protein identifications (with two or more unique peptides), respectively. In addition to broader identifications, advantages of the concatenated high pH fractionation approach include improved protein sequence coverage, simplified sample processing, and reduced sample losses. The results demonstrate that the concatenated high pH reversed-phased strategy is an attractive alternative to strong cation exchange for two-dimensional shotgun proteomic analysis.
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Affiliation(s)
- Yuexi Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yingchun Wang
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of sciences, Beijing, P. R. China
| | - Therese Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yufeng Shen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel Lopez-Ferrer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Theresa Reno
- Department of Pathology and UC San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard L. Klemke
- Department of Pathology and UC San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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44
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Bayés A, van de Lagemaat LN, Collins MO, Croning MDR, Whittle IR, Choudhary JS, Grant SGN. Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nat Neurosci 2011; 14:19-21. [PMID: 21170055 PMCID: PMC3040565 DOI: 10.1038/nn.2719] [Citation(s) in RCA: 335] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 11/12/2010] [Indexed: 02/06/2023]
Abstract
We isolated the postsynaptic density from human neocortex (hPSD) and identified 1,461 proteins. hPSD mutations cause 133 neurological and psychiatric diseases and were enriched in cognitive, affective and motor phenotypes underpinned by sets of genes. Strong protein sequence conservation in mammalian lineages, particularly in hub proteins, indicates conserved function and organization in primate and rodent models. The hPSD is an important structure for nervous system disease and behavior.
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Affiliation(s)
- Alex Bayés
- Genes to Cognition Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire, UK
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45
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Gilany K, Lakpour N, Vafakhah M, Sadeghi MR. The Profile of Human Sperm Proteome; A Mini-review. J Reprod Infertil 2011; 12:193-9. [PMID: 23926502 PMCID: PMC3719287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Accepted: 06/29/2011] [Indexed: 11/12/2022] Open
Abstract
New advances in mass spectrometry-based proteomics technology are having a major impact on our understanding of how human spermatozoa acquire their capacity for fertilization. A complete analysis of the proteins found in the human spermatozoa is essential for understanding the events leading up to, and including, fertilization and early embryo development. In this short review, we have collected the human sperm proteome from the literature and analyzed it by the Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Bioinformatics analysis demonstrated that the collected 1,300 proteins were involved in various metabolic pathways including catabolic processes. Additionally, the majority of the collected human sperm proteome belonged to cytoplasm. Application of the multi-dimensional protein identification technology (MudPIT) for obtaining a better coverage of the hydrophobic and basic proteins of the human sperm proteome is recommended.
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Affiliation(s)
- Kambiz Gilany
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran,Corresponding Author: Kambiz Gilany, Department of Embryology, Reproductive Biotechnology Research Center, Avicenna Research Institute, Shahid Beheshti University, Tehran, Iran. E-mail:
| | - Niknam Lakpour
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mohtaram Vafakhah
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mohammad Reza Sadeghi
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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46
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Cerda O, Baek JH, Trimmer JS. Mining recent brain proteomic databases for ion channel phosphosite nuggets. ACTA ACUST UNITED AC 2010; 137:3-16. [PMID: 21149544 PMCID: PMC3010060 DOI: 10.1085/jgp.201010555] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Voltage-gated ion channels underlie electrical activity of neurons and are dynamically regulated by diverse cell signaling pathways that alter their phosphorylation state. Recent global mass spectrometric–based analyses of the mouse brain phosphoproteome have yielded a treasure trove of new data as to the extent and nature of phosphorylation of numerous ion channel principal or α subunits in mammalian brain. Here we compile and review data on 347 phosphorylation sites (261 unique) on 42 different voltage-gated ion channel α subunits that were identified in these recent studies. Researchers in the ion channel field can now begin to explore the role of these novel in vivo phosphorylation sites in the dynamic regulation of the localization, activity, and expression of brain ion channels through multisite phosphorylation of their principal subunits.
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Affiliation(s)
- Oscar Cerda
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, Davis, CA 95616, USA
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47
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Guo X, Zhang P, Qi Y, Chen W, Chen X, Zhou Z, Sha J. Proteomic analysis of male 4C germ cell proteins involved in mouse meiosis. Proteomics 2010; 11:298-308. [PMID: 21204256 DOI: 10.1002/pmic.200900726] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 09/30/2010] [Accepted: 10/20/2010] [Indexed: 11/07/2022]
Abstract
Male meiosis is a specialized type of cell division that gives rise to sperm. Errors in this process can result in the generation of aneuploid gametes, which are associated with birth defects and infertility in humans. Until now, there has been a lack of a large-scale identification of proteins involved in male meiosis in mammals. In this study, we report the high-confidence identification of 3625 proteins in mouse male germ cells with 4C DNA content undergoing meiosis I. Of these, 397 were found to be testis specific. Bioinformatics analysis of the proteome led to the identification of 28 proteins known to be essential for male meiosis in mice. We also found 172 proteins that had yeast orthologs known to be essential for meiosis. Chromosome distribution analysis of the proteome showed underrepresentation of the identified proteins on the X chromosome, which may be due to meiotic sex chromosome inactivation. Characterization of the proteome of 4C germ cells from mouse testis provides an inventory of proteins, which is useful for understanding meiosis and the mechanisms of male infertility.
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Affiliation(s)
- Xuejiang Guo
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, P R China
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48
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Tu C, Rudnick PA, Martinez MY, Cheek KL, Stein SE, Slebos RJC, Liebler DC. Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res 2010; 9:4982-91. [PMID: 20677825 DOI: 10.1021/pr100646w] [Citation(s) in RCA: 266] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Immunoaffinity depletion with antibodies to the top 7 or top 14 high-abundance plasma proteins is used to enhance detection of lower abundance proteins in both shotgun and targeted proteomic analyses. We evaluated the effects of top 7/top 14 immunodepletion on the shotgun proteomic analysis of human plasma. Our goal was to evaluate the impact of immunodepletion on detection of proteins across detectable ranges of abundance. The depletion columns afforded highly repeatable and efficient plasma protein fractionation. Relatively few nontargeted proteins were captured by the depletion columns. Analyses of unfractionated and immunodepleted plasma by peptide isoelectric focusing (IEF), followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), demonstrated enrichment of nontargeted plasma proteins by an average of 4-fold, as assessed by MS/MS spectral counting. Either top 7 or top 14 immunodepletion resulted in a 25% increase in identified proteins compared to unfractionated plasma. Although 23 low-abundance (<10 ng mL(-1)) plasma proteins were detected, they accounted for only 5-6% of total protein identifications in immunodepleted plasma. In both unfractionated and immunodepleted plasma, the 50 most abundant plasma proteins accounted for 90% of cumulative spectral counts and precursor ion intensities, leaving little capacity to sample lower abundance proteins. Untargeted proteomic analyses using current LC-MS/MS platforms-even with immunodepletion-cannot be expected to efficiently discover low-abundance, disease-specific biomarkers in plasma.
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Affiliation(s)
- Chengjian Tu
- The Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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Lin D, Li J, Slebos RJC, Liebler DC. Cysteinyl peptide capture for shotgun proteomics: global assessment of chemoselective fractionation. J Proteome Res 2010; 9:5461-72. [PMID: 20731415 PMCID: PMC2948434 DOI: 10.1021/pr1007015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The complexity of cell and tissue proteomes presents one of the most significant technical challenges in proteomic biomarker discovery. Multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based shotgun proteomics can be coupled with selective enrichment of cysteinyl peptides (Cys-peptides) to reduce sample complexity and increase proteome coverage. Here we evaluated the impact of Cys-peptide enrichment on global proteomic inventories. We employed a new cleavable thiol-reactive biotinylating probe, N-(2-(2-(2-(2-(3-(1-hydroxy-2-oxo-2-phenylethyl)phenoxy)acetamido)ethoxy)-ethoxy)ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide (IBB), to capture Cys-peptides after digestion. Treatment of tryptic digests with the IBB reagent followed by streptavidin capture and mild alkaline hydrolysis releases a highly purified population of Cys-peptides with a residual S-carboxymethyl tag. Isoelectric focusing (IEF) followed by LC-MS/MS of Cys-peptides significantly expanded proteome coverage in Saccharomyces cerevisiae (yeast) and in human colon carcinoma RKO cells. IBB-based fractionation enhanced detection of Cys-proteins in direct proportion to their cysteine content. The degree of enrichment typically was 2-8-fold but ranged up to almost 20-fold for a few proteins. Published copy number annotation for the yeast proteome enabled benchmarking of MS/MS spectral count data to yeast protein abundance and revealed selective enrichment of cysteine-rich, lower abundance proteins. Spectral count data further established this relationship in RKO cells. Enhanced detection of low abundance proteins was due to the chemoselectivity of Cys-peptide capture, rather than simplification of the peptide mixture through fractionation.
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Affiliation(s)
- De Lin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8575, USA
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50
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Baek JH, Cerda O, Trimmer JS. Mass spectrometry-based phosphoproteomics reveals multisite phosphorylation on mammalian brain voltage-gated sodium and potassium channels. Semin Cell Dev Biol 2010; 22:153-9. [PMID: 20932926 DOI: 10.1016/j.semcdb.2010.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 09/23/2010] [Accepted: 09/28/2010] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium and potassium channels underlie electrical activity of neurons, and are dynamically regulated by diverse cell signaling pathways that ultimately exert their effects by altering the phosphorylation state of channel subunits. Recent mass spectrometric-based studies have led to a new appreciation of the extent and nature of phosphorylation of these ion channels in mammalian brain. This has allowed for new insights into how neurons dynamically regulate the localization, activity and expression through multisite ion channel phosphorylation.
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Affiliation(s)
- Je-Hyun Baek
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95616-8519, United States
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