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Oliver N, Choi MJ, Arul AB, Whitaker MD, Robinson RAS. Establishing Quality Control Metrics for Large-Scale Plasma Proteomic Sample Preparation. ACS MEASUREMENT SCIENCE AU 2024; 4:442-451. [PMID: 39184360 PMCID: PMC11342454 DOI: 10.1021/acsmeasuresciau.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 08/27/2024]
Abstract
Large-scale plasma proteomics studies have been transformed due to the multiplexing and automation of sample preparation workflows. However, these workflows can suffer from reproducibility issues, a lack of standardized quality control (QC) metrics, and the assessment of variation before liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The incorporation of robust QC metrics in sample preparation workflows ensures better reproducibility, lower assay variation, and better-informed decisions for troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of patient samples (N = 808) using tandem mass tag (TMT) 16-plex batches (N = 58). The proteomic workflow consisted of protein depletion, protein digestion, TMT labeling, and fractionation. Five QC sample types (QCstd, QCdig, QCpool, QCTMT, and QCBSA) were created to measure the performance of sample preparation prior to the final LC-MS/MS analysis. We measured <10% CV for individual sample preparation steps in the proteomic workflow based on data from various QC sample steps. The establishment of robust measures for QC of sample preparation steps allowed for greater confidence in prepared samples for subsequent LC-MS/MS analysis. This study also provides recommendations for standardized QC metrics that can assist with future large-scale cohort sample preparation workflows.
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Affiliation(s)
- Nekesa
C. Oliver
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Min Ji Choi
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Albert B. Arul
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marsalas D. Whitaker
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Memory and Alzheimer’s Center, Vanderbilt
University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37232, United States
- Vanderbilt
Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Neurology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
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Xing C, Hang Z, Guo W, Li Y, Shah R, Zhao Y, Zeng Z, Du H. Stem cells from human exfoliated deciduous teeth rejuvenate the liver in naturally aged mice by improving ribosomal and mitochondrial proteins. Cytotherapy 2023; 25:1285-1292. [PMID: 37815776 DOI: 10.1016/j.jcyt.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND AIMS Aging is accompanied by a decline in cellular proteome homeostasis, mitochondrial, and metabolic function. Mesenchymal stromal cell (MSC) therapies have been reported to extend lifespan and delay some age-related pathologies, yet the anti-aging rate and mechanisms remain unclear. Here, we investigated the effects and mechanism by transplantation of stem cells from human exfoliated deciduous teeth (SHED) into the naturally aged mice model. METHODS SHED were cultured in vitro and injected into mice by caudal vein. The in vivo imaging uncovered that SHED labeled by DiR dye mainly migrated to the liver, spleen, and lung organs of wild-type mice. As the main metabolic organ and SHED homing place, the liver was selected for proteomics and aging clock algorithm (LiverClock) analysis, which was constructed to estimate the proteomic pattern related to liver age state. RESULTS After 6 months of continuous SHED injections, the liver proteomic pattern was reversed from senescent (∼30 months) to a youthful state (∼3 months), accompanied with upregulation of hepatocytes marker genes, anti-aging protein Klotho, a global improvement of liver functional pathways proteins, and a dramatic regulation of ribosomal and mitochondrial proteins, including upregulation of translation elongation and ribosome-sparing proteins Rpsa and Rplp0; elongation factors Eif4a1, Eef1b2, Eif5a; protein-folding chaperones Hsp90aa and Hspe1; ATP synthesis proteins Atp5b, Atp5o, Atp5j; and downregulation of most ribosomal proteins, suggesting that the proteome homeostasis destruction and mitochondria dysfunction in the aged mice liver might be relieved after SHED treatment. CONCLUSIONS SHED treatment could dramatically relieve the senescent state of the aged liver, affect ribosome component proteins and upregulate the ribosomal biogenesis proteins in the aged mice liver. These results may help understand the improvements and mechanisms of SHED treatment in anti-aging.
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Affiliation(s)
- Cencan Xing
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
| | - Zhongci Hang
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
| | - Wenhuan Guo
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China; Reproductive Center, Peking University Third Hospital, Beijing, China
| | - Yingxian Li
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Roshan Shah
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
| | - Yihan Zhao
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China
| | - Zehua Zeng
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China.
| | - Hongwu Du
- Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing (USTB), Beijing, China.
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Tang CM, Zhang Z, Sun Y, Ding WJ, Yang XC, Song YP, Ling MY, Li XH, Yan R, Zheng YJ, Yu N, Zhang WH, Wang Y, Wang SP, Gao HQ, Zhao CL, Xing YQ. Multi-omics reveals aging-related pathway in natural aging mouse liver. Heliyon 2023; 9:e21011. [PMID: 37920504 PMCID: PMC10618800 DOI: 10.1016/j.heliyon.2023.e21011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/01/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Aging is associated with gradual changes in liver structure, altered metabolites and other physiological/pathological functions in hepatic cells. However, its characterized phenotypes based on altered metabolites and the underlying biological mechanism are unclear. Advancements in high-throughput omics technology provide new opportunities to understand the pathological process of aging. Here, in our present study, both metabolomics and phosphoproteomics were applied to identify the altered metabolites and phosphorylated proteins in liver of young (the WTY group) and naturally aged (the WTA group) mice, to find novel biomarkers and pathways, and uncover the biological mechanism. Analysis showed that the body weights, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) increased in the WTA group. The grips decreased with age, while the triglyceride (TG) and cholesterol (TC) did not change significantly. The increase of fibrosis, accumulation of inflammatory cells, hepatocytes degeneration, the deposition of lipid droplets and glycogen, the damaged mitochondria, and deduction of endoplasmic reticulum were observed in the aging liver under optical and electron microscopes. In addition, a network of metabolites and phosphorylated proteomes of the aging liver was established. Metabolomics detected 970 metabolites in the positive ion mode and 778 metabolites in the negative ion mode. A total of 150 pathways were pooled. Phosphoproteomics identified 2618 proteins which contained 16621 phosphosites. A total of 164 pathways were detected. 65 common pathways were detected in two omics. Phosphorylated protein heat shock protein HSP 90-alpha (HSP90A) and v-raf murine viral oncogene homolog B1(BRAF), related to cancer pathway, were significantly upregulated in aged mice liver. Western blot verified that protein expression of MEK and ERK, downstream of BRAF pathway were elevated in the liver of aging mice. However, the protein expression of BRAF was not a significant difference. Overall, these findings revealed a close link between aging and cancer and contributed to our understanding of the multi-omics changes in natural aging.
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Affiliation(s)
- Cong-min Tang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Institute of Basic Medical Sciences, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
- Department of Ultrasound, Shandong Provincial Third Hospital, Jinan 250031, Shandong Province, China
| | - Zhen Zhang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yan Sun
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Wen-jing Ding
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Institute of Basic Medical Sciences, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Xue-chun Yang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Institute of Basic Medical Sciences, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Yi-ping Song
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Ming-ying Ling
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Institute of Basic Medical Sciences, Qilu Hospital, Shandong University, Jinan 250012, Shandong Province, China
| | - Xue-hui Li
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Rong Yan
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yu-jing Zheng
- Shandong Precision Medicine Engineering Laboratory of Bacterial Anti-tumor Drugs, Jinan 250101, Shandong Province, China
| | - Na Yu
- Shandong Precision Medicine Engineering Laboratory of Bacterial Anti-tumor Drugs, Jinan 250101, Shandong Province, China
| | - Wen-hua Zhang
- Shandong Precision Medicine Engineering Laboratory of Bacterial Anti-tumor Drugs, Jinan 250101, Shandong Province, China
| | - Yong Wang
- Shandong Precision Medicine Engineering Laboratory of Bacterial Anti-tumor Drugs, Jinan 250101, Shandong Province, China
| | - Shao-peng Wang
- Shandong Precision Medicine Engineering Laboratory of Bacterial Anti-tumor Drugs, Jinan 250101, Shandong Province, China
| | - Hai-qing Gao
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Chuan-li Zhao
- Dept of Hematology, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
| | - Yan-qiu Xing
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
- Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan 250012, Shandong Province, China
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Bowser BL, Robinson RAS. Enhanced Multiplexing Technology for Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:379-400. [PMID: 36854207 DOI: 10.1146/annurev-anchem-091622-092353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification of thousands of proteins and their relative levels of expression has furthered understanding of biological processes and disease and stimulated new systems biology hypotheses. Quantitative proteomics workflows that rely on analytical assays such as mass spectrometry have facilitated high-throughput measurements of proteins partially due to multiplexing. Multiplexing allows proteome differences across multiple samples to be measured simultaneously, resulting in more accurate quantitation, increased statistical robustness, reduced analysis times, and lower experimental costs. The number of samples that can be multiplexed has evolved from as few as two to more than 50, with studies involving more than 10 samples being denoted as enhanced multiplexing or hyperplexing. In this review, we give an update on emerging multiplexing proteomics techniques and highlight advantages and limitations for enhanced multiplexing strategies.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
- Department of Neurology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Memory and Alzheimer's Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Brain Institute, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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5
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Zhakiyanova MS, Seilgazina SM, Ygiyeva A, Dzhamanova GI, Derbyshev KY. Age changes in extramural digestive glands of sheep and rabbits in the postembryonic period. Open Vet J 2023; 13:123-130. [PMID: 36777441 PMCID: PMC9897495 DOI: 10.5455/ovj.2023.v13.i1.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 12/27/2022] [Indexed: 02/05/2023] Open
Abstract
Background The study of the peculiarities of the anatomy of sheep and rabbits' digestive systems is an important way to improve the efficiency of these animals' breeding. Aim The aim of the presented research was to study structural changes of such digestive glands as the liver and the pancreas which occur in the process of ontogenesis in sheep and rabbits. Methods Sheep of the "Kazakh fat-tailed semi-coarse-wooled" breed (n = 8) raised in the "Sayan" private peasant agriculture and rabbits of the "Grey Giant" breed (n = 8), raised on the mini rabbit farm of the Agriculture Faculty of Shakarim University were used in the research.Two experimental animal groups were formed (of sheep, "Kazakh fat-tailed semi-coarse-wooled" breed, n = 8; rabbits, "Grey Giant" breed, n = 8). The liver and pancreas' ontogenesis development has been studied in these animals. Results The study presents a holistic view of the macro-microscopic structure of the liver and the pancreas of animals in crucial age periods, stages, and phases of postembryonic ontogenesis (by the example of sheep and rabbits). The authors have traced age stages of adaptive change and structural-functional change of stromal-parenchymatous structures of the liver in sheep and rabbits taking into account stages and crucial phases of development. Conclusion Development of the liver and the pancreas are characterized by discontinuous growth in the process of postnatal ontogenesis. A crucially important period is the first months after birth, during which the weight and functionality of these organs grow rapidly.
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Affiliation(s)
- Meiramgul S Zhakiyanova
- Agrarian Faculty, University Named after Shakarim of Semey City, Semey, Republic of Kazakhstan
| | - Saule M Seilgazina
- Agrarian Faculty, University Named after Shakarim of Semey City, Semey, Republic of Kazakhstan
| | - Akerke Ygiyeva
- Agrarian Faculty, University Named after Shakarim of Semey City, Semey, Republic of Kazakhstan
| | - Gulnara I Dzhamanova
- Agrarian Faculty, University Named after Shakarim of Semey City, Semey, Republic of Kazakhstan
| | - Kamil Y Derbyshev
- Agrarian Faculty, University Named after Shakarim of Semey City, Semey, Republic of Kazakhstan
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6
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Quantitative proteomics to study aging in rabbit spleen tissues. Exp Gerontol 2022; 167:111908. [PMID: 35932934 DOI: 10.1016/j.exger.2022.111908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
Abstract
Aging is a process that occurs in tissues and across species, leading to the degradation of many biological processes. We previously demonstrated that rabbits are a feasible model for studying aging due to their genetic homology and relatively short lifespan in comparison to humans. We utilized a cPILOT multiplexing strategy to identify proteomic changes in spleen tissues of young, middle, and old aged rabbits. We identified 63 proteins that change significantly (p < 0.05) with age and notably these proteins relate to nucleotide and RNA binding, DNA repair, actin regulation, and immune system pathways. Here, we explore the implications of aging in the spleen and demonstrate the utility of a rabbit model to understand aging processes.
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7
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Akbari B, Baghaei-Yazdi N, Bahmaie M, Mahdavi Abhari F. The role of plant-derived natural antioxidants in reduction of oxidative stress. Biofactors 2022; 48:611-633. [PMID: 35229925 DOI: 10.1002/biof.1831] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/31/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022]
Abstract
Free radicals are a group of damaging molecules produced during the normal metabolism of cells in the human body. Exposure to ultraviolet radiation, cigarette smoking, and other environmental pollutants enhances free radicals in the human body. The destructive effects of free radicals may also cause harm to membranes, enzymes, and DNA, leading to several human diseases such as cancer, atherosclerosis, malaria, coronavirus disease (COVID-19), rheumatoid arthritis, and neurodegenerative illnesses. This process occurs when there is an imbalance between free radicals and antioxidant defenses. Since antioxidants scavenge free radicals and repair damaged cells, increasing the consumption of fruits and vegetables containing high antioxidant values is recommended to slow down oxidative stress in the body. Additionally, natural products demonstrated a wide range of biological impacts such as anti-inflammatory, anti-aging, anti-atherosclerosis, and anti-cancer properties. Hence, in this review article, our goal is to explore the role of natural therapeutic antioxidant effects to reduce oxidative stress in the diseases.
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Affiliation(s)
- Behnaz Akbari
- School of Medicine, Department of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Namdar Baghaei-Yazdi
- College of Liberal Arts & Sciences, School of Life Sciences, University of Westminster, London, UK
| | - Manochehr Bahmaie
- Department of Chemistry, Islamic Azad University, North Tehran Branch, Tehran, Iran
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Moaddel R, Ubaida‐Mohien C, Tanaka T, Lyashkov A, Basisty N, Schilling B, Semba RD, Franceschi C, Gorospe M, Ferrucci L. Proteomics in aging research: A roadmap to clinical, translational research. Aging Cell 2021; 20:e13325. [PMID: 33730416 PMCID: PMC8045948 DOI: 10.1111/acel.13325] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023] Open
Abstract
The identification of plasma proteins that systematically change with age and, independent of chronological age, predict accelerated decline of health is an expanding area of research. Circulating proteins are ideal translational "omics" since they are final effectors of physiological pathways and because physicians are accustomed to use information of plasma proteins as biomarkers for diagnosis, prognosis, and tracking the effectiveness of treatments. Recent technological advancements, including mass spectrometry (MS)-based proteomics, multiplexed proteomic assay using modified aptamers (SOMAscan), and Proximity Extension Assay (PEA, O-Link), have allowed for the assessment of thousands of proteins in plasma or other biological matrices, which are potentially translatable into new clinical biomarkers and provide new clues about the mechanisms by which aging is associated with health deterioration and functional decline. We carried out a detailed literature search for proteomic studies performed in different matrices (plasma, serum, urine, saliva, tissues) and species using multiple platforms. Herein, we identified 232 proteins that were age-associated across studies. Enrichment analysis of the 232 age-associated proteins revealed metabolic pathways previously connected with biological aging both in animal models and in humans, most remarkably insulin-like growth factor (IGF) signaling, mitogen-activated protein kinases (MAPK), hypoxia-inducible factor 1 (HIF1), cytokine signaling, Forkhead Box O (FOXO) metabolic pathways, folate metabolism, advance glycation end products (AGE), and receptor AGE (RAGE) metabolic pathway. Information on these age-relevant proteins, likely expanded and validated in longitudinal studies and examined in mechanistic studies, will be essential for patient stratification and the development of new treatments aimed at improving health expectancy.
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Affiliation(s)
- Ruin Moaddel
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | | | - Toshiko Tanaka
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | - Alexey Lyashkov
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | | | | | - Richard D Semba
- Wilmer Eye Institute Johns Hopkins University School of Medicine Baltimore MD USA
| | - Claudio Franceschi
- University of Bologna and IRCCS Institute of Neurological Sciences Bologna Italy
| | - Myriam Gorospe
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | - Luigi Ferrucci
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
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Amin B, Robinson RAS. Dataset of quantitative proteomic analysis to understand aging processes in rabbit liver. Data Brief 2020; 31:105701. [PMID: 32490075 PMCID: PMC7262418 DOI: 10.1016/j.dib.2020.105701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 11/27/2022] Open
Abstract
Here, we present a proteomics dataset of liver proteins to understand aging in rabbits, which complements the publication “Quantitative proteomics to study aging in rabbit liver” [1]. This dataset was generated to understand the molecular basis and metabolic changes of aging processes in liver, which is the main organ involved in metabolism, detoxification, transport, and signaling. Proteins from young, middle, and old age rabbits were extracted and digested. Generated peptides were labeled with light or heavy dimethyl groups at their N-termini, while lysine amines were labeled with TMT10-plex using a cPILOT workflow [2]. Labeled peptides were fractionated by basic pH reverse phase chromatography and analyzed with online reverse phase LC coupled with tandem mass spectrometry (MS/MS and MS3). The RAW files were generated using a Fusion Lumos Orbitrap mass spectrometer (Thermo Scientific) and processed with Proteome Discoverer (PD) version 2.2 to generate a list of identified and quantified proteins. Data was searched against the Rabbit UniProtKB redundant database. A total of 3,867 proteins were identified corresponding to 2,586 protein groups and 22,229 peptides. Dynamic levels of age-related proteins associated with fat metabolism, mitochondrial dysfunction, and protein degradation were detected. The mass spectrometry proteomics data (RAW files) and processed Proteome Discoverer 2.2 files (MSF files) have been deposited to the Proteomics Identification Database (PRIDE) ProteomeXchange Consortium and can be accessed with the dataset identifier PDX013220 (http://www.ebi.ac.uk/pride/archive/projects/PXD013220).
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Affiliation(s)
- Bushra Amin
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235.,Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232.,Vanderbilt Memory & Alzheimer's Center, Nashville, TN 37212.,Vanderbilt Institute of Chemical Biology, Nashville, TN 37232.,Vanderbilt Brain Institute, Nashville, TN 37232
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