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Wadood AA, Zhang X. The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review. Curr Issues Mol Biol 2024; 46:6248-6266. [PMID: 38921044 PMCID: PMC11202932 DOI: 10.3390/cimb46060373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Omics approaches have significantly contributed to our understanding of several aspects of chicken reproduction. This review paper gives an overview of the use of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics to elucidate the mechanisms of chicken reproduction. Genomics has transformed the study of chicken reproduction by allowing the examination of the full genetic makeup of chickens, resulting in the discovery of genes associated with reproductive features and disorders. Transcriptomics has provided insights into the gene expression patterns and regulatory mechanisms involved in reproductive processes, allowing for a better knowledge of developmental stages and hormone regulation. Furthermore, proteomics has made it easier to identify and quantify the proteins involved in reproductive physiology to better understand the molecular mechanisms driving fertility, embryonic development, and egg quality. Metabolomics has emerged as a useful technique for understanding the metabolic pathways and biomarkers linked to reproductive performance, providing vital insights for enhancing breeding tactics and reproductive health. The integration of omics data has resulted in the identification of critical molecular pathways and biomarkers linked with chicken reproductive features, providing the opportunity for targeted genetic selection and improved reproductive management approaches. Furthermore, omics technologies have helped to create biomarkers for fertility and embryonic viability, providing the poultry sector with tools for effective breeding and reproductive health management. Finally, omics technologies have greatly improved our understanding of chicken reproduction by revealing the molecular complexities that underpin reproductive processes.
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Affiliation(s)
- Armughan Ahmed Wadood
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China;
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China;
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
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2
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Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics. Metabolites 2023; 13:metabo13020155. [PMID: 36837774 PMCID: PMC9964739 DOI: 10.3390/metabo13020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.
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3
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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4
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Meng Y, Qiu N, Guyonnet V, Mine Y. Unveiling and application of the chicken egg proteome: An overview on a two-decade achievement. Food Chem 2022; 393:133403. [PMID: 35689922 DOI: 10.1016/j.foodchem.2022.133403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 05/19/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022]
Abstract
Egg proteins are not only the most complete and ideal form of protein for human or embryo nutrition but also play the vital role in the food industry. Egg proteins are subjected to many potential changes under various conditions, which may further alter the nutritional value, physicochemical-properties, and bioactivities of proteins. Recent advances in our understanding of the proteome of raw egg matrix from different species and dynamic changes occurring during storage and incubation are developing rapidly. This review provides a comprehensive overview of the main characteristics of chicken egg proteome, covering all its components and applications under various conditions, such as markers detection, egg quality evaluation, genetic and biological unknown identification, and embryonic nutritional supplementation, which not only contributes to our in-depth understanding of each constituent functionality of proteome, but also provides information to increase the value to egg industry.
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Affiliation(s)
- Yaqi Meng
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ning Qiu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Vincent Guyonnet
- FFI Consulting Ltd, 2488 Lyn Road, Brockville, ON K6V 5T3, Canada
| | - Yoshinori Mine
- Department of Food Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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5
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Parastar H, Tauler R. Big (Bio)Chemical Data Mining Using Chemometric Methods: A Need for Chemists. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.201801134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hadi Parastar
- Department of Chemistry Sharif University of Technology Tehran Iran
| | - Roma Tauler
- Department of Environmental Chemistry IDAEA-CSIC 08034 Barcelona Spain
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6
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Yadav R, Chakraborty S, Ramakrishna W. Wheat grain proteomic and protein-metabolite interactions analyses provide insights into plant growth promoting bacteria-arbuscular mycorrhizal fungi-wheat interactions. PLANT CELL REPORTS 2022; 41:1417-1437. [PMID: 35396966 DOI: 10.1007/s00299-022-02866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Proteomic, protein-protein and protein-metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant's metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein-protein and protein-metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat-PGPB-AMF interactions leading to higher yield and biofortification.
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Affiliation(s)
- Radheshyam Yadav
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Sudip Chakraborty
- Department of Computational Sciences, Central University of Punjab, VPO Ghudda, Punjab, India
| | - Wusirika Ramakrishna
- Department of Biochemistry, Central University of Punjab, VPO Ghudda, Punjab, India.
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7
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Forgrave LM, Wang M, Yang D, DeMarco ML. Proteoforms and their expanding role in laboratory medicine. Pract Lab Med 2022; 28:e00260. [PMID: 34950758 PMCID: PMC8672040 DOI: 10.1016/j.plabm.2021.e00260] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/31/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
The term “proteoforms” describes the range of different structures of a protein product of a single gene, including variations in amino acid sequence and post-translational modifications. This diversity in protein structure contributes to the biological complexity observed in living organisms. As the concentration of a particular proteoform may increase or decrease in abnormal physiological states, proteoforms have long been used in medicine as biomarkers of health and disease. Notably, the analytical approaches used to analyze proteoforms have evolved considerably over the years. While ligand binding methods continue to play a large role in proteoform measurement in the clinical laboratory, unanticipated or unknown post-translational modifications and sequence variants can upend even extensively tested and vetted assays that have successfully made it through the medical regulatory process. As an alternate approach, mass spectrometry—with its high molecular selectivity—has become an essential tool in detection, characterization, and quantification of proteoforms in biological fluids and tissues. This review explores the analytical techniques used for proteoform detection and quantification, with an emphasis on mass spectrometry and its various applications in clinical research and patient care including, revealing new biomarker targets, helping improve the design of contemporary ligand binding in vitro diagnostics, and as mass spectrometric laboratory developed tests used in routine patient care.
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Affiliation(s)
- Lauren M. Forgrave
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Meng Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - David Yang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, Providence Health Care, 1081 Burrard St, Vancouver, V6Z 1Y6, Canada
- Corresponding author. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
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8
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res 2021; 20:4203-4211. [PMID: 34236868 PMCID: PMC8349881 DOI: 10.1021/acs.jproteome.1c00446] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample cleanup to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.
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Affiliation(s)
- Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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10
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Liao WT, Hung CH, Liang SS, Yu S, Lu JH, Lee CH, Chai CY, Yu HS. Anti-Inflammatory Effects Induced by Near-Infrared Light Irradiation through M2 Macrophage Polarization. J Invest Dermatol 2021; 141:2056-2066.e10. [PMID: 33676947 DOI: 10.1016/j.jid.2020.11.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 11/18/2022]
Abstract
Near-infrared (NIR) can penetrate the dermis. NIR is able to regulate cutaneous component cells and immune cells and shows significant anti-inflammatory therapeutic effects. However, the mechanisms of these effects are largely unknown. The purpose of this study is to elucidate NIR-induced molecular mechanisms on macrophages because macrophages play initial roles in directing immune responses by their M1 or M2 polarizations. Proteomic analysis revealed that NIR radiation enhanced the expression of mitochondrial respiratory gene citrate synthase. This increased citrate synthase expression was triggered by NIR-induced H3K4 hypermethylation on the citrate synthase gene promoter but not by heat, which led to macrophage M2 polarization and finally resulted in TGFβ1 release from CD4+ cells. These cellular effects were validated in human primary macrophages and abdominal NIR-irradiated mouse experiments. In a phorbol 12-myristate 13-acetate‒induced inflammatory model on mouse ear, we confirmed that NIR irradiation induced significant anti-inflammatory effects through decreased M1 counts, reduced TNF-α, and increased CCL22 and/or TGFβ1 levels.
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Affiliation(s)
- Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hsing Hung
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pediatrics, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pediatrics, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Shin Liang
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Sebastian Yu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Dermatology, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jian-He Lu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hung Lee
- Department of Dermatology, Kaohsiung Chang Gung Memorial Hospital of the C.G.M.F., Kaohsiung, Taiwan
| | - Chee-Yin Chai
- Department of Pathology, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Su Yu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Dermatology, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Taiwan.
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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Khan T, Dasgupta S, Ghosh N, Chaudhury K. Proteomics in idiopathic pulmonary fibrosis: the quest for biomarkers. Mol Omics 2021; 17:43-58. [PMID: 33073811 DOI: 10.1039/d0mo00108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a debilitating chronic progressive and fibrosing lung disease that culminates in the destruction of alveolar integrity and dismal prognosis. Its etiology is unknown and pathophysiology remains unclear. While great advances have been made in elucidating the pathogenesis mechanism, considerable gaps related to information on pathogenetic pathways and key protein targets involved in the clinical course of the disease exist. These issues need to be addressed for better clinical management of this highly challenging disease. Omics approach has revolutionized the entire area of disease understanding and holds promise in its translation to clinical biomarker discovery. This review outlines the contribution of proteomics towards identification of important biomarkers in IPF in terms of their clinical utility, i.e. prognosis, differential diagnosis, disease progression and treatment monitoring. The major dysregulated pathways associated with IPF are also discussed. Based on numerous proteomics studies on human and animal models, it is proposed that IPF pathogenesis involves complex interactions of several pathways such as oxidative stress, endoplasmic reticulum stress, unfolded protein response, coagulation system, inflammation, abnormal wounding, fibroblast proliferation, fibrogenesis and deposition of extracellular matrix. These pathways and their key path-changing mediators need further validation in large well-planned multi-centric trials at various geographical locations for successful development of clinical biomarkers of this confounding disease.
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Affiliation(s)
- Tila Khan
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
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Ruhaak L, Cobbaert C. Quantifying apolipoprotein(a) in the era of proteoforms and precision medicine. Clin Chim Acta 2020; 511:260-268. [DOI: 10.1016/j.cca.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/19/2022]
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14
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Identification and Detection of Bioactive Peptides in Milk and Dairy Products: Remarks about Agro-Foods. Molecules 2020; 25:molecules25153328. [PMID: 32707993 PMCID: PMC7435915 DOI: 10.3390/molecules25153328] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023] Open
Abstract
Food-based components represent major sources of functional bioactive compounds. Milk is a rich source of multiple bioactive peptides that not only help to fulfill consumers 'nutritional requirements but also play a significant role in preventing several health disorders. Understanding the chemical composition of milk and its products is critical for producing consistent and high-quality dairy products and functional dairy ingredients. Over the last two decades, peptides have gained significant attention by scientific evidence for its beneficial health impacts besides their established nutrient value. Increasing awareness of essential milk proteins has facilitated the development of novel milk protein products that are progressively required for nutritional benefits. The need to better understand the beneficial effects of milk-protein derived peptides has, therefore, led to the development of analytical approaches for the isolation, separation and identification of bioactive peptides in complex dairy products. Continuous emphasis is on the biological function and nutritional characteristics of milk constituents using several powerful techniques, namely omics, model cell lines, gut microbiome analysis and imaging techniques. This review briefly describes the state-of-the-art approach of peptidomics and lipidomics profiling approaches for the identification and detection of milk-derived bioactive peptides while taking into account recent progress in their analysis and emphasizing the difficulty of analysis of these functional and endogenous peptides.
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Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry. Molecules 2020; 25:molecules25133028. [PMID: 32630776 PMCID: PMC7411631 DOI: 10.3390/molecules25133028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.
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Achour B, Al-Majdoub ZM, Rostami-Hodjegan A, Barber J. Mass Spectrometry of Human Transporters. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:223-247. [PMID: 32084322 DOI: 10.1146/annurev-anchem-091719-024553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transporters are key to understanding how an individual will respond to a particular dose of a drug. Two patients with similar systemic concentrations may have quite different local concentrations of a drug at the required site. The transporter profile of any individual depends upon a variety of genetic and environmental factors, including genotype, age, and diet status. Robust models (virtual patients) are therefore required and these models are data hungry. Necessary data include quantitative transporter profiles at the relevant organ. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is currently the most powerful method available for obtaining this information. Challenges include sourcing the tissue, isolating the hydrophobic membrane-embedded transporter proteins, preparing the samples for MS (including proteolytic digestion), choosing appropriate quantification methodology, and optimizing the LC-MS/MS conditions. Great progress has been made with all of these, especially within the last few years, and is discussed here.
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Affiliation(s)
- Brahim Achour
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
- Certara, Princeton, New Jersey 08540, USA
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
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Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
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18
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Min CW, Gupta R, Agrawal GK, Rakwal R, Kim ST. Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach. Expert Rev Proteomics 2019; 16:795-804. [PMID: 31398080 DOI: 10.1080/14789450.2019.1654860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022]
Abstract
Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life forms. Nevertheless, the analysis of plant proteomes, especially those of samples that contain high-abundance proteins (HAPs), such as soybean seeds, remains challenging. Areas covered: Here, we review recent progress in soybean seed proteomics and highlight advances in HAPs depletion methods and peptide pre-fractionation, identification, and quantification methods. We also suggest a pipeline for future proteomic analysis, in order to increase the dynamic coverage of the soybean seed proteome. Expert opinion: Because HAPs limit the dynamic resolution of the soybean seed proteome, the depletion of HAPs is a prerequisite of high-throughput proteome analysis, and owing to the use of two-dimensional gel electrophoresis-based proteomic approaches, few soybean seed proteins have been identified or characterized. Recent advances in proteomic technologies, which have significantly increased the proteome coverage of other plants, could be used to overcome the current complexity and limitation of soybean seed proteomics.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba , Tsukuba , Ibaraki , Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
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19
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Capelli-Peixoto J, Mule SN, Tano FT, Palmisano G, Stolf BS. Proteomics and Leishmaniasis: Potential Clinical Applications. Proteomics Clin Appl 2019; 13:e1800136. [PMID: 31347770 DOI: 10.1002/prca.201800136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/02/2019] [Indexed: 02/06/2023]
Abstract
Leishmaniases are diseases caused by protozoan parasites of the genus Leishmania. They are endemic in 98 countries, affect around 12 million people worldwide and may present several distinct clinical forms. Unfortunately, there are only a few drugs available for treatment of leishmaniasis, which are toxic and not always effective. Different parasite species and different clinical forms require optimization of the treatment or more specific therapies, which are not available. The emergence of resistance is also a matter of concern. Besides, diagnosis can sometimes be complicated due to atypical manifestations and associations with other pathologies. In this review, proteomic data are presented and discussed in terms of their application in important issues in leishmaniasis such as parasite resistance to chemotherapy, diagnosis of active disease in patients and dogs, markers for different clinical forms, identification of virulence factors, and their potential use in vaccination. It is shown that proteomics has contributed to the discovery of potential biomarkers for prognosis, diagnosis, therapeutics, monitoring of disease progression, treatment follow-up and identification of vaccine candidates for specific diseases. However, the authors believe its capabilities have not yet been fully explored for routine clinical analysis for several reasons, which will be presented in this review.
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Affiliation(s)
- Janaína Capelli-Peixoto
- Leishmaniasis laboratory, Institute of Biomedical Sciences, Department of Parasitology, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- GlycoProteomics laboratory, Institute of Biomedical Sciences, Department of Parasitology, University of São Paulo, São Paulo, Brazil
| | - Fabia Tomie Tano
- Leishmaniasis laboratory, Institute of Biomedical Sciences, Department of Parasitology, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics laboratory, Institute of Biomedical Sciences, Department of Parasitology, University of São Paulo, São Paulo, Brazil
| | - Beatriz Simonsen Stolf
- Leishmaniasis laboratory, Institute of Biomedical Sciences, Department of Parasitology, University of São Paulo, São Paulo, Brazil
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Cunsolo V, Foti S, Ner‐Kluza J, Drabik A, Silberring J, Muccilli V, Saletti R, Pawlak K, Harwood E, Yu F, Ciborowski P, Anczkiewicz R, Altweg K, Spoto G, Pawlaczyk A, Szynkowska MI, Smoluch M, Kwiatkowska D. Mass Spectrometry Applications. Mass Spectrom (Tokyo) 2019. [DOI: 10.1002/9781119377368.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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21
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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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22
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Nguyen TPH, Patrick CJ, Parry LJ, Familari M. Using proteomics to advance the search for potential biomarkers for preeclampsia: A systematic review and meta-analysis. PLoS One 2019; 14:e0214671. [PMID: 30951540 PMCID: PMC6450632 DOI: 10.1371/journal.pone.0214671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Preeclampsia (PE) is a leading cause of maternal and perinatal morbidity and mortality worldwide. Although predictive multiparametric screening is being developed, it is not applicable to nulliparous women, and is not applied to low-risk women. As PE is considered a heterogenous disorder, it is unlikely that any single multiparametric screening protocol containing a small group of biomarkers could have the required accuracy to predict all PE subgroups. Given the etiology of PE is complex and not fully understood, it begs the question, whether the search for biomarkers based on the predominant view of impaired placentation involving factors predominately implicated in angiogenesis and inflammation, has been too limiting. Here we highlight the enormous potential of state-of-the-art, high-throughput proteomics, to provide a comprehensive and unbiased approach to biomarker identification. METHODS AND FINDINGS Our literature search identified 1336 articles; after review, 45 studies with proteomic data from PE women that were eligible for inclusion. From 710 proteins with altered abundance, we identified 13 common circulating proteins, some of which had not been previously considered as prospective biomarkers of PE. An additional search of the literature for original publications testing any of the 13 common proteins using non-proteomic techniques was also undertaken. Strikingly, 9 of these common proteins had been independently evaluated in PE studies as potential biomarkers. CONCLUSION This study highlights the potential of using high-throughput data sets, which are comprehensive and without bias, to identify a profile of proteins that may improve predictions of PE and understanding of its etiology. We bring to the attention of the medical and research communities that the strengths and advantages of using data from high-throughput studies for biomarker discovery would be increased dramatically, if first and second trimester samples were collected for proteomics, and if standardized guidelines for patient reporting and data collection were implemented.
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Affiliation(s)
| | | | - Laura Jean Parry
- School of BioSciences, University of Melbourne, Parkville, Australia
| | - Mary Familari
- School of BioSciences, University of Melbourne, Parkville, Australia
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23
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Ribeiro DG, de Almeida RF, Fontes W, de Souza Castro M, de Sousa MV, Ricart CAO, da Cunha RNV, Lopes R, Scherwinski-Pereira JE, Mehta A. Stress and cell cycle regulation during somatic embryogenesis plays a key role in oil palm callus development. J Proteomics 2018; 192:137-146. [PMID: 30194057 DOI: 10.1016/j.jprot.2018.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 11/19/2022]
Abstract
Oil palm is an oleaginous plant of relevant economic importance since its fruits are rich in vegetable oil. These plants have a single apical meristem and the main method for vegetative propagation is somatic embryogenesis. The aim of this study was to identify differentially abundant proteins from oil palm genotypes contrasting in the capacity of embryogenic competence acquisition, using shotgun proteomics. Oil palm leaves were subjected to callus induction and the material was collected in biological triplicates at 14 and 90 days of callus induction. LC-MS/MS analysis was performed and revealed a total of 4695 proteins. Responsive and non-responsive genotypes were compared at 14 and 90 days of callus induction and 221 differentially abundant proteins were obtained. The data analysis revealed several proteins mainly related to energy metabolism, stress response and regulation of cell cycle, further analyzed by qRT-PCR, which seem important for embryogenic development. We suggest some of these proteins as key factors for the success of callus formation in oil palm including antioxidant and cell division proteins as well as proteins involved in the ubiquitination pathway. These proteins may also be potential biomarkers for the acquisition of embryogenic competence. SIGNIFICANCE: Antioxidant and cell division proteins as well as proteins involved in the ubiquitination pathway are key factors for the success of callus formation in oil palm. The proteins identified in this study may be potential biomarkers for embryogenic competence acquisition.
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Affiliation(s)
- Daiane Gonzaga Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, DF, Brazil; Programa de Pós-graduação em Botânica, University of Brasília, Brasilia, DF, Brazil
| | - Raphael Ferreira de Almeida
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, DF, Brazil; Programa de Pós-graduação em Botânica, University of Brasília, Brasilia, DF, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasilia, DF, Brazil
| | - Mariana de Souza Castro
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasilia, DF, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasilia, DF, Brazil
| | - Carlos André Ornelas Ricart
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasília, Brasilia, DF, Brazil
| | | | | | - Jonny Everson Scherwinski-Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, DF, Brazil; Programa de Pós-graduação em Botânica, University of Brasília, Brasilia, DF, Brazil.
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, DF, Brazil.
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24
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Andjelković U, Josić D. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Tauler R, Parastar H. Big (Bio)Chemical Data Mining Using Chemometric Methods: A Need for Chemists. Angew Chem Int Ed Engl 2018; 61:e201801134. [DOI: 10.1002/anie.201801134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Roma Tauler
- IDAEA-CSIC Environmental Chemistry Jordi Girona 18-26 08034 Barcelona SPAIN
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26
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Ibort P, Imai H, Uemura M, Aroca R. Proteomic analysis reveals that tomato interaction with plant growth promoting bacteria is highly determined by ethylene perception. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:43-59. [PMID: 29145071 DOI: 10.1016/j.jplph.2017.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Feeding an increasing global population as well as reducing environmental impact of crops is the challenge for the sustainable intensification of agriculture. Plant-growth-promoting bacteria (PGPB) management could represent a suitable method but elucidation of their action mechanisms is essential for a proper and effective utilization. Furthermore, ethylene is involved in growth and response to environmental stimuli but little is known about the implication of ethylene perception in PGPB activity. The ethylene-insensitive tomato never ripe and its isogenic wild-type cv. Pearson lines inoculated with Bacillus megaterium or Enterobacter sp. C7 strains were grown until mature stage to analyze growth promotion, and bacterial inoculation effects on root proteomic profiles. Enterobacter C7 promoted growth in both plant genotypes, meanwhile Bacillus megaterium PGPB activity was only noticed in wt plants. Moreover, PGPB inoculation affected proteomic profile in a strain- and genotype-dependent manner modifying levels of stress-related and interaction proteins, and showing bacterial inoculation effects on antioxidant content and phosphorus acquisition capacity. Ethylene perception is essential for properly recognition of Bacillus megaterium and growth promotion mediated in part by increased levels of reduced glutathione. In contrast, Enterobacter C7 inoculation improves phosphorus nutrition keeping plants on growth independently of ethylene sensitivity.
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Affiliation(s)
- Pablo Ibort
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain.
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain.
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27
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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28
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Capriotti AL, Cavaliere C, Cavazzini A, Gasparrini F, Pierri G, Piovesana S, Laganà A. A multidimensional liquid chromatography–tandem mass spectrometry platform to improve protein identification in high-throughput shotgun proteomics. J Chromatogr A 2017; 1498:176-182. [DOI: 10.1016/j.chroma.2017.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/20/2017] [Accepted: 03/17/2017] [Indexed: 01/13/2023]
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29
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Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S. Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:387-99. [DOI: 10.1089/omi.2016.0065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Debasish Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
| | - Santosh Noronha
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P. Wangikar
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Proteomics Laboratory, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology, Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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30
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Aroso M, Ferreira R, Freitas A, Vitorino R, Gomez-Lazaro M. New insights on the mitochondrial proteome plasticity in Parkinson's disease. Proteomics Clin Appl 2016; 10:416-29. [PMID: 26749507 DOI: 10.1002/prca.201500092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 12/09/2015] [Accepted: 01/04/2016] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative diseases whose relentless progression results in severe disability. Although PD aetiology is unknown, growing evidences point to the mitochondrial involvement in the pathobiology of this disorder. So, it seems imperative to understand the means by which the molecular pathways harboured in this organelle are regulated. With the advances in MS-based proteomics, there is a substantial expectation in the increased knowledge of mitochondrial protein dynamics. Still, few studies have been performed on mitochondrial protein profiling in the context of PD. In order to integrate data from these studies, network analyses were performed taking into consideration variables such as model of PD, cell line, or tissue origin. Overall, data retrieved from these analyses highlighted the modulation of the biological processes related with "generation of energy," "cellular metabolism," and "mitochondrial transport" in PD. However, it was noted that the impact of sample type and/or PD model on the biological processes was modulated by the disease. Moreover, technical considerations related to protein characterization using gel-based or gel-free MS approaches should be considered in data comparison among different studies. Data from the present review will help to envisage future studies targeting these mechanisms.
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Affiliation(s)
- Miguel Aroso
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- Department of Chemistry, QOPNA, Mass Spectrometry Center, University of Aveiro, Aveiro, Portugal
| | - Ana Freitas
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, University of Porto, Porto, Portugal.,Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Chemistry, QOPNA, Mass Spectrometry Center, University of Aveiro, Aveiro, Portugal.,Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Maria Gomez-Lazaro
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, University of Porto, Porto, Portugal
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31
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Recent trends in the analysis of bioactive peptides in milk and dairy products. Anal Bioanal Chem 2016; 408:2677-85. [PMID: 26800979 DOI: 10.1007/s00216-016-9303-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 02/07/2023]
Abstract
Food-derived constituents represent important sources of several classes of bioactive compounds. Among them peptides have gained great attention in the last two decades thanks to the scientific evidence of their beneficial effects on health in addition to their established nutritional value. Several functionalities for bioactive peptides have been described, including antioxidative, antihypertensive, anti-inflammatory, immunomodulatory, and antimicrobial activity. They are now considered as novel and potential dietary ingredients to promote human health, though in some cases they may also have detrimental effects on health. Bioactive peptides can be naturally occurring, produced in vitro by enzymatic hydrolysis, and formed in vivo during gastrointestinal digestion of proteins. Thus, the need to gain a better understanding of the positive health effects of food peptides has prompted the development of analytical strategies for their isolation, separation, and identification in complex food matrices. Dairy products and milk are potential sources of bioactive peptides: several of them possess extra-nutritional physiological functions that qualify them to be classified under the functional food label. In this trends article we briefly describe the state-of-the-art of peptidomics methods for the identification and discovery of bioactive peptides, also considering recent progress in their analysis and highlighting the difficulty in the analysis of short amino acid sequences and endogenous peptides.
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32
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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Porous silica enhanced proteolysis during Off-Gel separation for efficient protein identification. Talanta 2015; 144:1182-8. [PMID: 26452945 DOI: 10.1016/j.talanta.2015.07.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/30/2015] [Indexed: 11/22/2022]
Abstract
An advanced approach is developed in this work for simultaneous on-line separation and digestion of proteins by combining the Off-Gel isoelectric focusing (IEF) and enzymatic nanoreactor enhanced proteolysis. The nanoreactor was prepared by preloading trypsin in amino-functionalized macroporous silica, and then directly added into Off-Gel wells. With the nanoreactor loaded Off-Gel device, effective digestion of proteins happened during IEF electrophoresis to generate directly fractionated tryptic peptides, which not only accelerated the experimental flow but also avoided sample loss, leading to a more comprehensive protein identification from complex biological samples. A successful identification of 3592 proteins was achieved from Hela cell line by using the approach followed with LC-MS/MS analysis, while only 1877 proteins were identified from the same sample when using standard in-solution proteolysis followed with Off-Gel electrophoresis and then LC-MS/MS analysis. Therefore, we have demonstrated that the approach can greatly simplify high-throughput proteomics and significantly improve protein identification.
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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35
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Yakovleva ME, Welinder C, Sugihara Y, Pawłowski K, Rezeli M, Wieslander E, Malm J, Marko-Varga G. Workflow for large-scale analysis of melanoma tissue samples. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Hedrick VE, LaLand MN, Nakayasu ES, Paul LN. Digestion, Purification, and Enrichment of Protein Samples for Mass Spectrometry. ACTA ACUST UNITED AC 2015; 7:201-222. [PMID: 26331527 DOI: 10.1002/9780470559277.ch140272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Victoria E. Hedrick
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Mercedes N. LaLand
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Ernesto S. Nakayasu
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Lake N. Paul
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
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37
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Proteotyping: Proteomic characterization, classification and identification of microorganisms--A prospectus. Syst Appl Microbiol 2015; 38:246-57. [PMID: 25933927 DOI: 10.1016/j.syapm.2015.03.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/23/2015] [Indexed: 12/13/2022]
Abstract
Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels.
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Hafiane A, Genest J. High density lipoproteins: Measurement techniques and potential biomarkers of cardiovascular risk. BBA CLINICAL 2015; 3:175-88. [PMID: 26674734 PMCID: PMC4661556 DOI: 10.1016/j.bbacli.2015.01.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/16/2015] [Accepted: 01/26/2015] [Indexed: 12/31/2022]
Abstract
Plasma high density lipoprotein cholesterol (HDL) comprises a heterogeneous family of lipoprotein species, differing in surface charge, size and lipid and protein compositions. While HDL cholesterol (C) mass is a strong, graded and coherent biomarker of cardiovascular risk, genetic and clinical trial data suggest that the simple measurement of HDL-C may not be causal in preventing atherosclerosis nor reflect HDL functionality. Indeed, the measurement of HDL-C may be a biomarker of cardiovascular health. To assess the issue of HDL function as a potential therapeutic target, robust and simple analytical methods are required. The complex pleiotropic effects of HDL make the development of a single measurement challenging. Development of laboratory assays that accurately HDL function must be developed validated and brought to high-throughput for clinical purposes. This review discusses the limitations of current laboratory technologies for methods that separate and quantify HDL and potential application to predict CVD, with an emphasis on emergent approaches as potential biomarkers in clinical practice.
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Key Words
- 2D-PAGGE, two dimensional polyacrylamide gradient gel electrophoresis
- ApoA-I, apolipoprotein A-I
- Apolipoprotein A-I
- Atherosclerosis
- Biomarkers of cardiovascular risk
- CHD, coronary heart disease
- CVD, cardiovascular disease
- Cellular cholesterol efflux
- Coronary artery disease
- HDL, high density lipoprotein
- HPLC, High Performance Liquid Chromatography
- High density lipoproteins
- LCAT, lecithin–cholesterol acyltransferase
- LDL, low density lipoprotein
- MALDI, matrix-assisted laser desorption/ionization
- MOP, myeloperoxidase
- MS/MS, tandem-mass spectrometry
- ND-PAGGE, non-denaturant polyacrylamide gradient gel electrophoresis
- NMR, nuclear magnetic resonance
- PEG, polyethylene glycol
- PON1, paraoxonase 1
- SELDI, surface enhanced laser desorption/ionization
- TOF, time-of-flight
- UTC, ultracentrifugation
- Vascular endothelial function
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Affiliation(s)
- Anouar Hafiane
- McGill University Health Center, Royal Victoria Hospital, 687 Avenue des Pins West, Montreal, QC H3A 1A1, Canada
| | - Jacques Genest
- McGill University Health Center, Royal Victoria Hospital, 687 Avenue des Pins West, Montreal, QC H3A 1A1, Canada
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Law HCH, Kong RPW, Szeto SSW, Zhao Y, Zhang Z, Wang Y, Li G, Quan Q, Lee SMY, Lam HC, Chu IK. A versatile reversed phase-strong cation exchange-reversed phase (RP–SCX–RP) multidimensional liquid chromatography platform for qualitative and quantitative shotgun proteomics. Analyst 2015; 140:1237-52. [DOI: 10.1039/c4an01893a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We developed a novel online MDLC platform that integrates a dual-trap configuration and two separation technologies into a single automated commercial platform.
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Affiliation(s)
- Henry C. H. Law
- Department of Chemistry
- the University of Hong Kong
- Hong Kong
- China
| | - Ricky P. W. Kong
- 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
- Jinan University College of Pharmacy
- Guangzhou 510632
- China
| | - Yuqiang Wang
- Institute of New Drug Research
- Jinan University College of Pharmacy
- Guangzhou 510632
- China
| | - Guohui Li
- Department of Chemistry
- the University of Hong Kong
- Hong Kong
- China
- Institute of Chinese Medical Sciences
| | - Quan Quan
- Department of Chemistry
- the University of Hong Kong
- Hong Kong
- China
| | - Simon M. Y. Lee
- Institute of Chinese Medical Sciences
- University of Macau
- Macau
- China
| | - Herman C. Lam
- Department of Chemistry
- the University of Hong Kong
- Hong Kong
- China
| | - Ivan K. Chu
- Department of Chemistry
- the University of Hong Kong
- Hong Kong
- China
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40
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Link AJ, Washburn MP. Analysis of protein composition using multidimensional chromatography and mass spectrometry. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2014; 78:23.1.1-23.1.25. [PMID: 25367006 DOI: 10.1002/0471140864.ps2301s78] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multidimensional liquid chromatography of peptides produced by protease digestion of complex protein mixtures followed by tandem mass spectrometry can be coupled with automated database searching to identify large numbers of proteins in complex samples. These methods avoid the limitations of gel electrophoresis and in-gel digestions by directly identifying protein mixtures in solution. One method used extensively is named Multidimensional Protein Identification Technology (MudPIT), where reversed-phase chromatography and strong cation-exchange chromatography are coupled directly in a microcapillary column. This column is then placed in line between an HPLC and a mass spectrometer for complex mixture analysis. MudPIT remains a powerful approach for analyzing complex mixtures like whole proteomes and protein complexes. MudPIT is used for quantitative proteomic analysis of complex mixtures to generate novel biological insights.
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Affiliation(s)
- Andrew J Link
- Vanderbilt University School of Medicine Nashville, Tennessee
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41
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Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2014; 108:10.21.1-10.21.30. [PMID: 25271712 DOI: 10.1002/0471142727.mb1021s108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
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Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York
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42
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Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in food proteomics: a tutorial. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:768-784. [PMID: 25230173 DOI: 10.1002/jms.3374] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 06/03/2023]
Abstract
In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed.
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Affiliation(s)
- Vincenzo Cunsolo
- Department of Chemical Sciences, University of Catania, Viale A. Doria, 6, I-95125, Catania, Italy
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43
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Braga MS, Neves LX, Campos JM, Roatt BM, de Oliveira Aguiar Soares RD, Braga SL, de Melo Resende D, Reis AB, Castro-Borges W. Shotgun proteomics to unravel the complexity of the Leishmania infantum exoproteome and the relative abundance of its constituents. Mol Biochem Parasitol 2014; 195:43-53. [PMID: 25017697 DOI: 10.1016/j.molbiopara.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 01/27/2023]
Abstract
The exoproteome of some Leishmania species has revealed important insights into host-parasite interaction, paving the way for the proposal of novel disease-oriented interventions. The focus of the present investigation constituted the molecular profile of the L. infantum exoproteome revealed by a shotgun proteomic approach. Promastigotes under logarithmic phase of growth were obtained and harvested by centrifugation at different time points. Cell integrity was evaluated through the counting of viable parasites using propidium iodide labeling, followed by flow cytometry analysis. The 6h culture supernatant, operationally defined here as exoproteome, was then conditioned to in solution digestion and the resulting peptides submitted to mass spectrometry. A total of 102 proteins were identified and categorized according to their cellular function. Their relative abundance index (emPAI) allowed inference that the L. infantum exoproteome is a complex mixture dominated by molecules particularly involved in nucleotide metabolism and antioxidant activity. Bioinformatic analyses support that approximately 60% of the identified proteins are secreted, of which, 85% possibly reach the extracellular milieu by means of non-classic pathways. At last, sera from naturally infected animals, carriers of differing clinical forms of Canine Visceral Leishmaniasis (CVL), were used to test the immunogenicity associated to the L. infantum exoproteome. Western blotting experiments revealed that this sub-proteome was useful at discriminating symptomatic animals from those exhibiting other clinical forms of the disease. Collectively, the molecular characterization of the L. infantum exoproteome and the preliminary immunoproteomic assays opened up new research avenues related to treatment, prognosis and diagnosis of CVL.
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Affiliation(s)
- Micheline Soares Braga
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Leandro Xavier Neves
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Jonatan Marques Campos
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Bruno Mendes Roatt
- Laboratório de Imunopatologia, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | | | - Samuel Leôncio Braga
- Laboratório de Imunopatologia, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Daniela de Melo Resende
- Laboratório de Pesquisas Clínicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil; Grupo Informática de Biossistemas, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Alexandre Barbosa Reis
- Laboratório de Imunopatologia, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil; Laboratório de Pesquisas Clínicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - William Castro-Borges
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.
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44
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Colombo G, Clerici M, Giustarini D, Portinaro NM, Aldini G, Rossi R, Milzani A, Dalle-Donne I. Pathophysiology of tobacco smoke exposure: recent insights from comparative and redox proteomics. MASS SPECTROMETRY REVIEWS 2014; 33:183-218. [PMID: 24272816 DOI: 10.1002/mas.21392] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 05/23/2013] [Accepted: 05/23/2013] [Indexed: 06/02/2023]
Abstract
First-hand and second-hand tobacco smoke are causally linked to a huge number of deaths and are responsible for a broad spectrum of pathologies such as cancer, cardiovascular, respiratory, and eye diseases as well as adverse effects on female reproductive function. Cigarette smoke is a complex mixture of thousands of different chemical species, which exert their negative effects on macromolecules and biochemical pathways, both directly and indirectly. Many compounds can act as oxidants, pro-inflammatory agents, carcinogens, or a combination of these. The redox behavior of cigarette smoke has many implications for smoke related diseases. Reactive oxygen and nitrogen species (both radicals and non-radicals), reactive carbonyl compounds, and other species may induce oxidative damage in almost all the biological macromolecules, compromising their structure and/or function. Different quantitative and redox proteomic approaches have been applied in vitro and in vivo to evaluate, respectively, changes in protein expression and specific oxidative protein modifications induced by exposure to cigarette smoke and are overviewed in this review. Many gel-based and gel-free proteomic techniques have already been used successfully to obtain clues about smoke effects on different proteins in cell cultures, animal models, and humans. The further implementation with other sensitive screening techniques could be useful to integrate the comprehension of cigarette smoke effects on human health. In particular, the redox proteomic approach may also help identify biomarkers of exposure to tobacco smoke useful for preventing these effects or potentially predictive of the onset and/or progression of smoking-induced diseases as well as potential targets for therapeutic strategies.
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Affiliation(s)
- Graziano Colombo
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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45
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Ghosh D, Xu J. Abiotic stress responses in plant roots: a proteomics perspective. FRONTIERS IN PLANT SCIENCE 2014; 5:6. [PMID: 24478786 PMCID: PMC3900766 DOI: 10.3389/fpls.2014.00006] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/06/2014] [Indexed: 05/18/2023]
Abstract
Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abundance that can be best explored through proteomics. This review summarizes comparative proteomic studies conducted with roots of various plant species subjected to different abiotic stresses especially drought, salinity, flood, and cold. The main purpose of this article is to highlight and classify the protein level changes in abiotic stress response pathways specifically in plant roots. Shared as well as stressor-specific proteome signatures and adaptive mechanism(s) are simultaneously described. Such a comprehensive account will facilitate the design of genetic engineering strategies that enable the development of broad-spectrum abiotic stress-tolerant crops.
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Affiliation(s)
- Dipanjana Ghosh
- Department of Biological Sciences, NUS Centre for BioImaging Sciences, National University of SingaporeSingapore
| | - Jian Xu
- Department of Biological Sciences, NUS Centre for BioImaging Sciences, National University of SingaporeSingapore
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46
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Garbis SD, Townsend PA. Proteomics of human prostate cancer biospecimens: the global, systems-wide perspective for Protein markers with potential clinical utility. Expert Rev Proteomics 2014; 10:337-54. [DOI: 10.1586/14789450.2013.827408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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47
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Gao M, Qi D, Zhang P, Deng C, Zhang X. Development of multidimensional liquid chromatography and application in proteomic analysis. Expert Rev Proteomics 2014; 7:665-78. [DOI: 10.1586/epr.10.49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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48
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Marino F, Cristobal A, Binai NA, Bache N, Heck AJR, Mohammed S. Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system. Analyst 2014; 139:6520-8. [DOI: 10.1039/c4an01568a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The EASY-spray technology can now be implemented as a simple online 2D SCX-RP ultra-high pressure system, which allows one to reach deep proteome coverages.
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Affiliation(s)
- Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Alba Cristobal
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Nadine A. Binai
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | | | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics
- Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
- University of Utrecht
- 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre
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49
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Liu Q, Wang L, Zhou Z, Wang Q, Yan L, Zhang B. Toward rapid preparation of capillary columns for electrochromatography use. Electrophoresis 2013; 35:836-9. [DOI: 10.1002/elps.201300503] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/15/2013] [Accepted: 11/25/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Qing Liu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen P.R. China
| | - Lin Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen P.R. China
| | - Zhuoheng Zhou
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen P.R. China
| | - Qiuquan Wang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen P.R. China
| | - Lijuan Yan
- Xiamen Entry-Exit Inspection and Quarantine Bureau; Xiamen P.R. China
| | - Bo Zhang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen P.R. China
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50
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Jha MK, Seo M, Kim JH, Kim BG, Cho JY, Suk K. The secretome signature of reactive glial cells and its pathological implications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2418-28. [PMID: 23269363 DOI: 10.1016/j.bbapap.2012.12.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/23/2012] [Accepted: 12/12/2012] [Indexed: 12/12/2022]
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