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Gobena S, Admassu B, Kinde MZ, Gessese AT. Proteomics and Its Current Application in Biomedical Area: Concise Review. ScientificWorldJournal 2024; 2024:4454744. [PMID: 38404932 PMCID: PMC10894052 DOI: 10.1155/2024/4454744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Biomedical researchers tirelessly seek cutting-edge technologies to advance disease diagnosis, drug discovery, and therapeutic interventions, all aimed at enhancing human and animal well-being. Within this realm, proteomics stands out as a pivotal technology, focusing on extensive studies of protein composition, structure, function, and interactions. Proteomics, with its subdivisions of expression, structural, and functional proteomics, plays a crucial role in unraveling the complexities of biological systems. Various sophisticated techniques are employed in proteomics, including polyacrylamide gel electrophoresis, mass spectrometry analysis, NMR spectroscopy, protein microarray, X-ray crystallography, and Edman sequencing. These methods collectively contribute to the comprehensive understanding of proteins and their roles in health and disease. In the biomedical field, proteomics finds widespread application in cancer research and diagnosis, stem cell studies, and the diagnosis and research of both infectious and noninfectious diseases. In addition, it plays a pivotal role in drug discovery and the emerging frontier of personalized medicine. The versatility of proteomics allows researchers to delve into the intricacies of molecular mechanisms, paving the way for innovative therapeutic approaches. As infectious and noninfectious diseases continue to emerge and the field of biomedical research expands, the significance of proteomics becomes increasingly evident. Keeping abreast of the latest developments in proteomics applications becomes paramount for the development of therapeutics, translational research, and study of diverse diseases. This review aims to provide a comprehensive overview of proteomics, offering a concise outline of its current applications in the biomedical domain. By doing so, it seeks to contribute to the understanding and advancement of proteomics, emphasizing its pivotal role in shaping the future of biomedical research and therapeutic interventions.
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Affiliation(s)
- Semira Gobena
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Bemrew Admassu
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Mebrie Zemene Kinde
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe Tesfaye Gessese
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
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Nisa MU, Farooq S, Ali S, Eachkoti R, Rehman MU, Hafiz S. Proteomics: A modern tool for identifying therapeutic targets in different types of carcinomas. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00013-4] [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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Li Y, Zhang S, Snyder MP, Meador KJ. Precision medicine in women with epilepsy: The challenge, systematic review, and future direction. Epilepsy Behav 2021; 118:107928. [PMID: 33774354 PMCID: PMC8653993 DOI: 10.1016/j.yebeh.2021.107928] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 11/29/2022]
Abstract
Epilepsy is one of the most prevalent neurologic conditions, affecting almost 70 million people worldwide. In the United States, 1.3 million women with epilepsy (WWE) are in their active reproductive years. Women with epilepsy (WWE) face gender-specific challenges such as pregnancy, seizure exacerbation with hormonal pattern fluctuations, contraception, fertility, and menopause. Precision medicine, which applies state-of-the art molecular profiling to diagnostic, prognostic, and therapeutic problems, has the potential to advance the care of WWE by precisely tailoring individualized management to each patient's needs. For example, antiseizure medications (ASMs) are among the most common teratogens prescribed to women of childbearing potential. Teratogens act in a dose-dependent manner on a susceptible genotype. However, the genotypes at risk for ASM-induced teratogenic deficits are unknown. Here we summarize current challenging issues for WWE, review the state-of-art tools for clinical precision medicine approaches, perform a systematic review of pharmacogenomic approaches in management for WWE, and discuss potential future directions in this field. We envision a future in which precision medicine enables a new practice style that puts focus on early detection, prediction, and targeted therapies for WWE.
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Affiliation(s)
- Yi Li
- Department of Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Sai Zhang
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford CA, 94305, USA
| | - Michael P. Snyder
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford CA, 94305, USA
| | - Kimford J. Meador
- Department of Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
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Rappold BA. Clinical Protein Analysis by Mass Spectrometry: A New Higher Order. Clin Chem 2021; 67:461-462. [PMID: 33532834 DOI: 10.1093/clinchem/hvaa335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 11/15/2022]
Affiliation(s)
- Brian A Rappold
- Integrated Genetics, Laboratory Corporation of America, Research Triangle Park, NC, USA
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Al-Lamki RS, Hudson NJ, Bradley JR, Warren AY, Eisen T, Welsh SJ, Riddick ACP, O’Mahony FC, Turnbull A, Powles T, Reverter A, Harrison DJ, Stewart GD. The Efficacy of Sunitinib Treatment of Renal Cancer Cells Is Associated with the Protein PHAX In Vitro. BIOLOGY 2020; 9:E74. [PMID: 32272660 PMCID: PMC7236799 DOI: 10.3390/biology9040074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 02/02/2023]
Abstract
Anti-angiogenic agents, such as the multi-tyrosine kinase inhibitor sunitinib, are key first line therapies for metastatic clear cell renal cell carcinoma (ccRCC), but their mechanism of action is not fully understood. Here, we take steps towards validating a computational prediction based on differential transcriptome network analysis that phosphorylated adapter RNA export protein (PHAX) is associated with sunitinib drug treatment. The regulatory impact factor differential network algorithm run on patient tissue samples suggests PHAX is likely an important regulator through changes in genome-wide network connectivity. Immunofluorescence staining of patient tumours showed strong localisation of PHAX to the microvasculature consistent with the anti-angiogenic effect of sunitinib. In normal kidney tissue, PHAX protein abundance was low but increased with tumour grade (G1 vs. G3/4; p < 0.01), consistent with a possible role in cancer progression. In organ culture, ccRCC cells had higher levels of PHAX protein expression than normal kidney cells, and sunitinib increased PHAX protein expression in a dose dependent manner (untreated vs. 100 µM; p < 0.05). PHAX knockdown in a ccRCC organ culture model impacted the ability of sunitinib to cause cancer cell death (p < 0.0001 untreated vs. treated), suggesting a role for PHAX in mediating the efficacy of sunitinib.
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Affiliation(s)
- Rafia S. Al-Lamki
- Department of Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (R.S.A.-L.); (J.R.B.)
| | - Nicholas J. Hudson
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD 4343, Australia;
| | - John R. Bradley
- Department of Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (R.S.A.-L.); (J.R.B.)
| | - Anne Y. Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Tim Eisen
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah J. Welsh
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Antony C. P. Riddick
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Fiach C. O’Mahony
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Arran Turnbull
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Thomas Powles
- Bart’s Cancer Institute, Charterhouse Square, London EC1M 6BE, UK;
| | - SCOTRRCC Collaborative
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia;
| | - David J. Harrison
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
- School of Medicine, University of St. Andrews, St. Andrews KY16 9TF, UK
| | - Grant D. Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
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Hernández-Pérez A, Zamora-Briseño JA, Ruiz-May E, Pereira-Santana A, Elizalde-Contreras JM, Pozos-González S, Torres-Irineo E, Hernández-López J, Gaxiola-Cortés MG, Rodríguez-Canul R. Proteomic profiling of the white shrimp Litopenaeus vannamei (Boone, 1931) hemocytes infected with white spot syndrome virus reveals the induction of allergy-related proteins. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 91:37-49. [PMID: 30336173 DOI: 10.1016/j.dci.2018.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
To elucidate the proteomic responses of shrimp hemocytes to white spot syndrome virus (WSSV) infection at the proteome level, a quantitative shotgun proteomic analysis was performed to detect differentially synthesized proteins in infected hemocytes of white shrimp (Litopenaeus vannamei). We identified 1528 proteins associated to 203 gene ontology (GO) categories. The most representative GO categories were regulation of cellular processes, organic substance metabolic processes and nitrogen compound metabolic processes. Most of the 83 detected up-regulated proteins are involved in DNA regulation and organization and cell signaling. In contrast, most of the 40 down-regulated proteins were related to immune defense processes, protein folding, and development. Differentially induced proteins were further analyzed at the transcript level by RT-qPCR to validate the results. This work provides new insights into the alterations of L. vannamei hemocytes at the protein level at 12 h post-infection with WSSV. Interestingly, several of the up-regulated proteins are allergy-related proteins in humans. Based on our results, we suggest a deeper analysis of the effects of this interaction on the regulation of allergy related-proteins as their up-regulation during WSSV could represent a threat to human health.
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Affiliation(s)
- Ariadne Hernández-Pérez
- Laboratorio de Inmunología y Biología Molecular, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, Mérida, Yucatán, CP 97310, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Laboratorio de Inmunología y Biología Molecular, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, Mérida, Yucatán, CP 97310, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Cluster Científico y Tecnológico BioMimic(®), El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico
| | - Alejandro Pereira-Santana
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, Mexico
| | - José Miguel Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Cluster Científico y Tecnológico BioMimic(®), El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico
| | - Sirenia Pozos-González
- Unidad de Microscopía Electrónica (LANSE), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Zacatenco, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo I. Madero, CP 07360, Ciudad de México, Mexico
| | - Edgar Torres-Irineo
- Unidad Multidisciplinaria de Docencia e Investigación (UMDI-Sisal), Facultad de Ciencias, Universidad Nacional Autónoma de México, Tablaje # 31262. Sierra Papacal, Yucatán, Mexico
| | - Jorge Hernández-López
- Centro de Investigaciones Biológicas del Noroeste, Hermosa # 101, Hermosillo, Sonora, 83000, Mexico
| | | | - Rossanna Rodríguez-Canul
- Laboratorio de Inmunología y Biología Molecular, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional-Unidad Mérida, Km 6 Antigua Carretera a Progreso, CORDEMEX, Mérida, Yucatán, CP 97310, Mexico.
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Goey CH, Alhuthali S, Kontoravdi C. Host cell protein removal from biopharmaceutical preparations: Towards the implementation of quality by design. Biotechnol Adv 2018; 36:1223-1237. [DOI: 10.1016/j.biotechadv.2018.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/12/2018] [Accepted: 03/29/2018] [Indexed: 01/05/2023]
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9
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Sundar S, Singh B. Understanding Leishmania parasites through proteomics and implications for the clinic. Expert Rev Proteomics 2018; 15:371-390. [PMID: 29717934 PMCID: PMC5970101 DOI: 10.1080/14789450.2018.1468754] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Leishmania spp. are causative agents of leishmaniasis, a broad-spectrum neglected vector-borne disease. Genomic and transcriptional studies are not capable of solving intricate biological mysteries, leading to the emergence of proteomics, which can provide insights into the field of parasite biology and its interactions with the host. Areas covered: The combination of genomics and informatics with high throughput proteomics may improve our understanding of parasite biology and pathogenesis. This review analyses the roles of diverse proteomic technologies that facilitate our understanding of global protein profiles and definition of parasite development, survival, virulence and drug resistance mechanisms for disease intervention. Additionally, recent innovations in proteomics have provided insights concerning the drawbacks associated with conventional chemotherapeutic approaches and Leishmania biology, host-parasite interactions and the development of new therapeutic approaches. Expert commentary: With progressive breakthroughs in the foreseeable future, proteome profiles could provide target molecules for vaccine development and therapeutic intervention. Furthermore, proteomics, in combination with genomics and informatics, could facilitate the elimination of several diseases. Taken together, this review provides an outlook on developments in Leishmania proteomics and their clinical implications.
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Affiliation(s)
- Shyam Sundar
- a Department of Medicine, Institute of Medical Sciences , Banaras Hindu University , Varanasi , India
| | - Bhawana Singh
- a Department of Medicine, Institute of Medical Sciences , Banaras Hindu University , Varanasi , India
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10
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Liang Y, Neta P, Yang X, Stein SE. Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:463-469. [PMID: 29143271 DOI: 10.1007/s13361-017-1842-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Yuxue Liang
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Pedatsur Neta
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Xiaoyu Yang
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Stephen E Stein
- Mass Spectrometry Data Center, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
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Brandi J, Manfredi M, Speziali G, Gosetti F, Marengo E, Cecconi D. Proteomic approaches to decipher cancer cell secretome. Semin Cell Dev Biol 2017; 78:93-101. [PMID: 28684183 DOI: 10.1016/j.semcdb.2017.06.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 01/17/2023]
Abstract
In this review, we give an overview of the actual proteomic approaches used in the study of cancer cells secretome. In particular, we describe the proteomic strategies to decipher cancer cell secretome initially focusing on the different aspects of sample preparation. We examine the issues related to the presence of low abundant proteins, the analysis of secreted proteins in the conditioned media with or without the removal of fetal bovine serum and strategies developed to reduce intracellular protein contamination. As regards the identification and quantification of secreted proteins, we described the different proteomic approaches used, i.e. gel-based, MS-based (label-based and label-free), and the antibody and array-based methods, together with some of the most recent applications in the field of cancer research. Moreover, we describe the bioinformatics tools developed for the in silico validation and characterization of cancer cells secretome. We also discuss the most important available tools for protein annotation and for prediction of classical and non-classical secreted proteins. In summary in this review advances, concerns and challenges in the field of cancer secretome analysis are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy; ISALIT S.r.l., Novara, Italy.
| | - Giulia Speziali
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
| | - Fabio Gosetti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Daniela Cecconi
- Department of Biotechnology, Proteomics and Mass Spectrometry Lab, University of Verona, Strada le Grazie 15, 37135, Verona, Italy
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Salehi-Reyhani A, Ces O, Elani Y. Artificial cell mimics as simplified models for the study of cell biology. Exp Biol Med (Maywood) 2017; 242:1309-1317. [PMID: 28580796 PMCID: PMC5528198 DOI: 10.1177/1535370217711441] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Living cells are hugely complex chemical systems composed of a milieu of distinct chemical species (including DNA, proteins, lipids, and metabolites) interconnected with one another through a vast web of interactions: this complexity renders the study of cell biology in a quantitative and systematic manner a difficult task. There has been an increasing drive towards the utilization of artificial cells as cell mimics to alleviate this, a development that has been aided by recent advances in artificial cell construction. Cell mimics are simplified cell-like structures, composed from the bottom-up with precisely defined and tunable compositions. They allow specific facets of cell biology to be studied in isolation, in a simplified environment where control of variables can be achieved without interference from a living and responsive cell. This mini-review outlines the core principles of this approach and surveys recent key investigations that use cell mimics to address a wide range of biological questions. It will also place the field in the context of emerging trends, discuss the associated limitations, and outline future directions of the field. Impact statement Recent years have seen an increasing drive to construct cell mimics and use them as simplified experimental models to replicate and understand biological phenomena in a well-defined and controlled system. By summarizing the advances in this burgeoning field, and using case studies as a basis for discussion on the limitations and future directions of this approach, it is hoped that this minireview will spur others in the experimental biology community to use artificial cells as simplified models with which to probe biological systems.
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Affiliation(s)
| | - Oscar Ces
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Yuval Elani
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
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Gómez-Cardona EE, Hernández-Domínguez EE, Velarde-Salcedo AJ, Pacheco AB, Diaz-Gois A, De León-Rodríguez A, Barba de la Rosa AP. 2D-DIGE as a strategy to identify serum biomarkers in Mexican patients with Type-2 diabetes with different body mass index. Sci Rep 2017; 7:46536. [PMID: 28425473 PMCID: PMC5397846 DOI: 10.1038/srep46536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/22/2017] [Indexed: 12/11/2022] Open
Abstract
Obesity and type 2 diabetes(T2D) are the most prevalent and serious metabolic diseases affecting people worldwide. However racial and ethnic disparities seems to be a risk factor for their development. Mexico has been named as one of the largest populations with the highest prevalence of diabetes and obesity. The aim of this study was to identify novel T2D-associated proteins in Mexican patients. Blood samples were collected from 62 Mexican patients with T2D and they were grouped according to their body mass index(BMI). A panel of 10 diabetes and obesity serum markers was determined using MAGPIX. A comparative proteomics study was performed using two-dimensional difference in-gel electrophoresis(2D-DIGE) followed by mass spectrometry(LC-MS/MS). We detected 113 spots differentially accumulated, in which 64 unique proteins were identified, proteins that were involved in metabolism pathways, molecular transport, and cellular signalling. Four proteins(14-3-3, ApoH, ZAG, and OTO3) showing diabetes-related variation and also changes in relation to obesity were selected for further validation by western blotting. Our results reveal new diabetes related proteins present in the Mexican population. These could provide additional insight into the understanding of diabetes development in Mexican population and may also be useful candidate biomarkers.
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Affiliation(s)
- Erik E Gómez-Cardona
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San Jose No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216, Mexico
| | - Eric E Hernández-Domínguez
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San Jose No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216, Mexico
| | - Aída J Velarde-Salcedo
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San Jose No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216, Mexico
| | - Alberto-Barrera- Pacheco
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San Jose No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216, Mexico
| | - Agustín Diaz-Gois
- Juridiscción Sanitaria No. 1, Centros de Salud San Luis Potosi, San Luis Potosi, Mexico
| | - Antonio De León-Rodríguez
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San Jose No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216, Mexico.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ana P Barba de la Rosa
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C. Camino a la Presa San Jose No. 2055, Lomas 4a sección, San Luis Potosí, San Luis Potosí, 78216, Mexico
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Chaurand P, Schwartz SA, Reyzer ML, Caprioli RM. Imaging Mass Spectrometry: Principles and Potentials. Toxicol Pathol 2016; 33:92-101. [PMID: 15805060 DOI: 10.1080/01926230590881862] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Direct tissue profiling and imaging mass spectrometry (MS) allow for detailed mapping of the complex protein pattern across a tissue sample. Utilization of these tools provides spatial information across a tissue section for target protein expression and can be used to correlate changes in expression levels with specific disease states or drug response. Protein patterns can be directly correlated to known histological regions within the tissue, allowing for the direct monitoring of proteins specific for morphological regions within a tissue sample. Profiling and imaging MS have been used to characterize multiple tissues, including human gliomas and lung cancers, as well as tumor response to specific therapeutics, suggesting the use of proteomic information in assessing disease progression as well as predicting patient response to specific treatments. This article discusses both the technology and methods involved in analyzing proteins directly from tissue samples as well as several MS applications, including profiling human tumors, characterizing protein differences between tumor grades, and monitoring protein changes due to drug therapy.
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Affiliation(s)
- Pierre Chaurand
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
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15
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Li X, Jackson A, Xie M, Wu D, Tsai WC, Zhang S. Proteomic insights into floral biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1050-60. [PMID: 26945514 DOI: 10.1016/j.bbapap.2016.02.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/25/2016] [Accepted: 02/24/2016] [Indexed: 12/17/2022]
Abstract
The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, Hangzhou 310021, PR China; International Atomic Energy Agency Collaborating Center, Zhejiang University, Hangzhou 310029, PR China.
| | | | - Ming Xie
- Zhejiang Academy of Agricultural Sciences, Shiqiao Road 139, Hangzhou 310021, PR China.
| | - Dianxing Wu
- International Atomic Energy Agency Collaborating Center, Zhejiang University, Hangzhou 310029, PR China
| | - Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Cornell University, New York 14853, USA
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Bracewell DG, Francis R, Smales CM. The future of host cell protein (HCP) identification during process development and manufacturing linked to a risk-based management for their control. Biotechnol Bioeng 2015; 112:1727-37. [PMID: 25998019 PMCID: PMC4973824 DOI: 10.1002/bit.25628] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 03/04/2015] [Accepted: 04/21/2015] [Indexed: 12/14/2022]
Abstract
The use of biological systems to synthesize complex therapeutic products has been a remarkable success. However, during product development, great attention must be devoted to defining acceptable levels of impurities that derive from that biological system, heading this list are host cell proteins (HCPs). Recent advances in proteomic analytics have shown how diverse this class of impurities is; as such knowledge and capability grows inevitable questions have arisen about how thorough current approaches to measuring HCPs are. The fundamental issue is how to adequately measure (and in turn monitor and control) such a large number of protein species (potentially thousands of components) to ensure safe and efficacious products. A rather elegant solution is to use an immunoassay (enzyme-linked immunosorbent assay [ELISA]) based on polyclonal antibodies raised to the host cell (biological system) used to synthesize a particular therapeutic product. However, the measurement is entirely dependent on the antibody serum used, which dictates the sensitivity of the assay and the degree of coverage of the HCP spectrum. It provides one summed analog value for HCP amount; a positive if all HCP components can be considered equal, a negative in the more likely event one associates greater risk with certain components of the HCP proteome. In a thorough risk-based approach, one would wish to be able to account for this. These issues have led to the investigation of orthogonal analytical methods; most prominently mass spectrometry. These techniques can potentially both identify and quantify HCPs. The ability to measure and monitor thousands of proteins proportionally increases the amount of data acquired. Significant benefits exist if the information can be used to determine critical HCPs and thereby create an improved basis for risk management. We describe a nascent approach to risk assessment of HCPs based upon such data, drawing attention to timeliness in relation to biosimilar initiatives. The development of such an approach requires databases based on cumulative knowledge of multiple risk factors that would require national and international regulators, standards authorities (e.g., NIST and NIBSC), industry and academia to all be involved in shaping what is the best approach to the adoption of the latest bioanalytical technology to this area, which is vital to delivering safe efficacious biological medicines of all types.
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Affiliation(s)
- Daniel G Bracewell
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK.
| | | | - C Mark Smales
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury, Kent, UK, CT2 7NJ
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Wang X, Guo T, Peng F, Long Y, Mu Y, Yang H, Ye N, Li X, Zhan X. Proteomic and functional profiles of a follicle-stimulating hormone positive human nonfunctional pituitary adenoma. Electrophoresis 2015; 36:1289-304. [PMID: 25809007 DOI: 10.1002/elps.201500006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Xiaowei Wang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Tianyao Guo
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Fang Peng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Ying Long
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Yun Mu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Haiyan Yang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Department of Lung Cancer and Gastroenterology; Hunan Cancer Hospital; Changsha Hunan P. R. China
| | - Ningrong Ye
- Department of Neurosurgery; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Xuejun Li
- Department of Neurosurgery; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital; Central South University; Changsha Hunan P. R. China
- State Key Laboratory of Medical Genetics; Central South University; Changsha Hunan P. R. China
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Yuk IH, Nishihara J, Walker D, Huang E, Gunawan F, Subramanian J, Pynn AFJ, Yu XC, Zhu-Shimoni J, Vanderlaan M, Krawitz DC. More similar than different: Host cell protein production using three null CHO cell lines. Biotechnol Bioeng 2015; 112:2068-83. [PMID: 25894672 DOI: 10.1002/bit.25615] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/03/2015] [Accepted: 04/09/2015] [Indexed: 12/25/2022]
Abstract
To understand the diversity in the cell culture harvest (i.e., feedstock) provided for downstream processing, we compared host cell protein (HCP) profiles using three Chinese Hamster Ovary (CHO) cell lines in null runs which did not generate any recombinant product. Despite differences in CHO lineage, upstream process, and culture performance, the cell lines yielded similar cell-specific productivities for immunogenic HCPs. To compare the dynamics of HCP production, we searched for correlations between the time-course profiles of HCP (as measured by multi-analyte ELISA) and those of two intracellular HCP species, phospholipase B-like 2 (PLBL2) and lactate dehydrogenase (LDH). Across the cell lines, proteins in the day 14 supernatants analyzed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) showed different spot patterns. However, subsequent analysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) indicated otherwise: the total number of peptides and proteins identified were comparable, and 80% of the top 1,000 proteins identified were common to all three lines. Finally, to assess the impact of culture viability on extracellular HCP profiles, we analyzed supernatants from a cell line whose viability dropped after day 10. The amounts of HCP and PLBL2 (quantified by their respective ELISAs) as well as the numbers and major populations of HCPs (identified by LC-MS/MS) were similar across days 10, 14, and 17, during which viabilities declined from ∼80% to <20% and extracellular LDH levels increased several-fold. Our findings indicate that the CHO-derived HCPs in the feedstock for downstream processing may not be as diverse across cell lines and upstream processes, or change as dramatically upon viability decline as originally expected. In addition, our findings show that high density CHO cultures (>10(7) cells/mL)-operated in fed-batch mode and exhibiting high viabilities (>70%) throughout the culture duration-can accumulate a considerable amount of immunogenic HCP (∼1-2 g/L) in the extracellular environment at the time of harvest (day 14). This work also demonstrates the potential of using LC-MS/MS to overcome the limitations associated with ELISA and 2D-PAGE for HCP analysis.
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Affiliation(s)
- Inn H Yuk
- Early Stage Cell Culture, Genentech, 1 DNA Way, South San Francisco, California, 94080.
| | - Julie Nishihara
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Donald Walker
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Eric Huang
- Early Stage Cell Culture, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Feny Gunawan
- Analytical Operations, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Jayashree Subramanian
- Early Stage Cell Culture, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Abigail F J Pynn
- Early Stage Cell Culture, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - X Christopher Yu
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Judith Zhu-Shimoni
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Martin Vanderlaan
- Analytical Operations, Genentech, 1 DNA Way, South San Francisco, California, 94080
| | - Denise C Krawitz
- Analytical Operations, Genentech, 1 DNA Way, South San Francisco, California, 94080
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Gu H, Stokes MP, Silva JC. Proteomic Analysis of Posttranslational Modifications in Neurobiology. ANALYSIS OF POST-TRANSLATIONAL MODIFICATIONS AND PROTEOLYSIS IN NEUROSCIENCE 2015. [DOI: 10.1007/7657_2015_99] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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20
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Kailasa SK, Wu HF. Proteomic profiling by nanomaterials-based matrix-assisted laser desorption/ionization mass spectrometry for high-resolution data and novel protein information directly from biological samples. Methods Mol Biol 2015; 1295:479-496. [PMID: 25820742 DOI: 10.1007/978-1-4939-2550-6_34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Qualitative and quantitative analyses of global proteome samples derived from biocomplex mixtures are very important to understand the cellular functions in cell biology. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)-based proteomics has recently become one of the most informative and attractive core technologies in proteomics. Particularly, nanomaterials-based MALDI mass spectrometric methods are quickly becoming a critical miniaturized bioanalytical tool for detecting and discerning proteins from biocomplex samples. These MALDI-developed strategies allow high-throughput identification of proteins from highly complex mixtures including accurate mass measurement of peptides derived from total proteome digests and peptides/proteins separations from various samples. The nanomaterials-integrated MALDI-MS technologies in protein arrays hold much promise for interrogating the diverse and immense proteome in cell biology. As a result, nanomaterials-assisted MALDI-MS-based proteomic workflow, including sample preparation, information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins and their analysis, should make the technology more easily available to a broad community and turn it into a powerful methodology for bioanalysts.
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Affiliation(s)
- Suresh Kumar Kailasa
- Department of Applied Chemistry, S. V. National Institute of Technology, Surat, 395007, Gujarat, India
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Shao S, Guo T, Aebersold R. Mass spectrometry-based proteomic quest for diabetes biomarkers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:519-27. [PMID: 25556002 DOI: 10.1016/j.bbapap.2014.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/06/2014] [Accepted: 12/10/2014] [Indexed: 12/22/2022]
Abstract
Diabetes mellitus (DM) is a metabolic disorder characterized by chronic hyperglycemia, which affects hundreds of millions of individuals worldwide. Early diagnosis and complication prevention of DM are helpful for disease treatment. However, currently available DM diagnostic markers fail to achieve the goals. Identification of new diabetic biomarkers assisted by mass spectrometry (MS)-based proteomics may offer solution for the clinical challenges. Here, we review the current status of biomarker discovery in DM, and describe the pressure cycling technology (PCT)-Sequential Window Acquisition of all Theoretical fragment-ion (SWATH) workflow for sample-processing, biomarker discovery and validation, which may accelerate the current quest for DM biomarkers. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Shiying Shao
- Division of Endocrinology, Tongji Hospital, Huazhong University of Science & Technology, Wuhan 430030, PR China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str. 16, 8093, Switzerland.
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str. 16, 8093, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str. 16, 8093, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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22
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Wang X, Lu F, Zhang C, Lu Y, Bie X, Xie Y, Lu Z. Effects of recombinated Anabaena sp. lipoxygenase on the protein component and dough property of wheat flour. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9885-9892. [PMID: 25247399 DOI: 10.1021/jf503238h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The improvement effect of recombinated Anabaena sp. lipoxygenase (ana-rLOX) on the rheological property of dough was investigated with a farinograph and an extensograph. When 30 U/g ana-rLOX was added to wheat flour, the dough stability time extended from 7 to 9.5 min, the degree of softening increased about 31.1%, and the farinograph index also ascended. The dough with added ana-rLOX showed stronger resistance to extension throughout 135 min of resting time as compared to the dough without ana-rLOX. In addition, the protein component in the dough was varied with ana-rLOX. The glutenin in the dough was increased, whereas the gliadin, albumin, and globulin were decreased after the additino of ana-rLOX to the flours. Ana-rLOX could make globulin-3A, globulin 1a, and S48186 grain softness protein cross-link with gliadin and low-molecular-weight (LMW) glutenin, leading to the formation of the protein polymer. These results based on proteomic analysis might provide evidence that ana-rLOX could affect the gluten protein component and explain why it improved the farinograph and extensograph parameters of wheat flour.
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Affiliation(s)
- Xiaoming Wang
- College of Food Science and Technology, Nanjing Agriculture University , Nanjing 210095, China
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23
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Pei J, Moon KS, Pan S, Lee KH, Ryu HH, Jung TY, Kim IY, Jang WY, Jung CH, Jung S. Proteomic Analysis between U87MG and U343MG-A Cell Lines: Searching for Candidate Proteins for Glioma Invasion. Brain Tumor Res Treat 2014; 2:22-8. [PMID: 24926468 PMCID: PMC4049555 DOI: 10.14791/btrt.2014.2.1.22] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/29/2014] [Accepted: 03/07/2014] [Indexed: 11/30/2022] Open
Abstract
Background To investigate the molecular basis for invasion of malignant gliomas, proteomic analysis approach was carried out using two human glioma cell lines, U87MG and U343MG-A that demonstrate different motility and invasiveness in in vitro experiments. Methods High-resolution two-dimensional gel electrophoresis and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry analysis were performed. Results Nine distinct protein spots that were recognized with significant alteration between the two cell lines. Five of these protein spots were up-regulated in U87MG and four were up-regulated in U343MG-A. Conclusion Among these proteins, cathepsin D was shown to be one of the important proteins which are related with glioma invasion. However, further studies are necessary to reveal the exact role and mechanism of cathepsin D in glioma invasion.
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Affiliation(s)
- Jian Pei
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea. ; Department of Neurosurgery, Worker's Hospital of Tangshan, Tangshan City, China
| | - Kyung-Sub Moon
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - SangO Pan
- Department of Chemistry, College of Life Science, Chonnam National University, Gwangju, Korea
| | - Kyung-Hwa Lee
- Brain Tumor Research Laboratory, Department of Pathology, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Hyang-Hwa Ryu
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Tae-Young Jung
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - In-Young Kim
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Woo-Yeol Jang
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Chae-Hun Jung
- Department of Chemistry, College of Life Science, Chonnam National University, Gwangju, Korea
| | - Shin Jung
- Brain Tumor Research Laboratory, Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
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Recent developments in nanoparticle-based MALDI mass spectrometric analysis of phosphoproteomes. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1191-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ahmed FE. Mining the oncoproteome and studying molecular interactions for biomarker development by 2DE, ChIP and SPR technologies. Expert Rev Proteomics 2014; 5:469-96. [DOI: 10.1586/14789450.5.3.469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Chen G, Pramanik BN. LC-MS for protein characterization: current capabilities and future trends. Expert Rev Proteomics 2014; 5:435-44. [DOI: 10.1586/14789450.5.3.435] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Seibel J, König S, Göhler A, Doose S, Memmel E, Bertleff N, Sauer M. Investigating infection processes with a workflow from organic chemistry to biophysics: the combination of metabolic glycoengineering, super-resolution fluorescence imaging and proteomics. Expert Rev Proteomics 2014; 10:25-31. [DOI: 10.1586/epr.12.72] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Godovac-Zimmermann J. 8th Siena Meeting. From Genome to Proteome: Integration and Proteome Completion. Expert Rev Proteomics 2014; 5:769-73. [DOI: 10.1586/14789450.5.6.769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Grover HS, Kapoor S, Saksena N. Periodontal proteomics: wonders never cease! INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:850235. [PMID: 24490073 PMCID: PMC3893808 DOI: 10.1155/2013/850235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/05/2013] [Accepted: 12/05/2013] [Indexed: 02/07/2023]
Abstract
Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. The ongoing research to understand the signalling pathways that allow cells to divide, differentiate, and die in controlled manner has brought us to the era of proteomics. Proteomics is defined as the study of all proteins including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Its application to periodontal science can be used to monitor health status, disease onset, treatment response, and outcome. Proteomics can offer answers to critical, unresolved questions such as the biological basis for the heterogeneity in gingival, alveolar bone, and cemental cell populations.
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Affiliation(s)
- Harpreet Singh Grover
- Department of Periodontology, Faculty of Dental Sciences, SGT University, Budhera, Gurgaon, Haryana 122505, India
| | - Shalini Kapoor
- Department of Periodontology, Faculty of Dental Sciences, SGT University, Budhera, Gurgaon, Haryana 122505, India
| | - Neha Saksena
- Department of Periodontology, Faculty of Dental Sciences, SGT University, Budhera, Gurgaon, Haryana 122505, India
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Musharraf SG, Mazhar S, Siddiqui AJ, Choudhary MI, Atta-ur-Rahman. Metabolite profiling of human plasma by different extraction methods through gas chromatography–mass spectrometry—An objective comparison. Anal Chim Acta 2013; 804:180-9. [DOI: 10.1016/j.aca.2013.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 10/26/2022]
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31
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Wu CC, Han CC, Chang HC. Applications of Surface-Functionalized Diamond Nanoparticles for Mass-Spectrometry-Based Proteomics. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Ellis SR, Jungmann JH, Smith DF, Soltwisch J, Heeren RMA. Enhanced detection of high-mass proteins by using an active pixel detector. Angew Chem Int Ed Engl 2013; 52:11261-4. [PMID: 24039122 DOI: 10.1002/anie.201305501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Indexed: 11/07/2022]
Abstract
Flying high: Application of an active pixel detector with high charge sensitivity to a linear time-of-flight mass spectrometer results in enhanced detection of high-mass proteins (such as Immunoglobulin G; IgG) using a conventional microchannel plate detection system. This technique thus provides a means to extend the mass range of such detectors as well as allowing direct visualization of mass-dependent ion-focusing phenomena.
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Affiliation(s)
- Shane R Ellis
- Biomolecular Imaging Mass Spectrometry, FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (The Netherlands)
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Ellis SR, Jungmann JH, Smith DF, Soltwisch J, Heeren RMA. Enhanced Detection of High-Mass Proteins by Using an Active Pixel Detector. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Tscheliessnig AL, Konrath J, Bates R, Jungbauer A. Host cell protein analysis in therapeutic protein bioprocessing - methods and applications. Biotechnol J 2013; 8:655-70. [DOI: 10.1002/biot.201200018] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/22/2012] [Accepted: 01/04/2013] [Indexed: 01/18/2023]
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Bianco G, Labella C, Pepe A, Cataldi TRI. Scrambling of autoinducing precursor peptides investigated by infrared multiphoton dissociation with electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry. Anal Bioanal Chem 2012. [PMID: 23208287 DOI: 10.1007/s00216-012-6583-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Two synthetic precursor peptides, H(2)N-CVGIW and H(2)N-LVMCCVGIW, involved in the quorum sensing of Lactobacillus plantarum WCFS1, were characterized by mass spectrometry (MS) with electrospray ionization and 7-T Fourier transform ion cyclotron resonance (ESI-FTICR) instrument. Cell-free bacterial supernatant solutions were analyzed by reversed-phase liquid chromatography with ESI-FTICR MS to verify the occurrence of both pentapeptide and nonapeptide in the bacterial broth. The structural characterization of both protonated peptides was performed by infrared multiphoton dissociation using a continuous CO(2) laser source at a wavelength of 10.6 μm. As their fragmentation behavior cannot be directly derived from the primary peptide structure, all anomalous fragments were interpreted as neutral loss of amino acids from the interior of both peptides, i.e., loss of V, G, VG and M, MC, V, CC, from H(2)N-CVGIW and H(2)N-LVMCCVGIW, respectively. Mechanisms of this scrambling are proposed. FTICR MS provides accurate masses of all fragment ions with very low absolute mass errors (<1.6 ppm), which facilitated the reliable assignment of their elemental compositions. The resolving power was more than sufficient to resolve closely isobaric product ions with routine subparts per million mass accuracies. Only the occurrence of pentapeptide was found in the cell-free culture of L. plantarum, grown in Waymouth's medium broth, with a low content of 5.2 ± 2.6 μM by external calibration. Most of it was present as oxidized H(2)N-CVGIW, that is, the soluble disulfide pentapeptide with a level tenfold higher (i.e., 50 ± 4 μM, n = 3).
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Affiliation(s)
- Giuliana Bianco
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
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Characterization of Heat-Labile toxin-subunit B from Escherichia coli by liquid chromatography–electrospray ionization-mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Food Chem Toxicol 2012; 50:3886-91. [DOI: 10.1016/j.fct.2012.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 07/30/2012] [Accepted: 08/07/2012] [Indexed: 11/21/2022]
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Mass spectrometry imaging is moving toward drug protein co-localization. Trends Biotechnol 2012; 30:466-74. [DOI: 10.1016/j.tibtech.2012.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/23/2012] [Accepted: 05/24/2012] [Indexed: 12/20/2022]
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Abstract
The metabolome is the terminal downstream product of the genome and consists of the total complement of all the low-molecular-weight molecules (metabolites) in a cell, tissue, or organism. Metabolomics aims to measure a wide breadth of small molecules in the context of physiological stimuli or disease states. Metabolomics methodologies fall into two distinct groups: untargeted metabolomics, an intended comprehensive analysis of all the measurable analytes in a sample including chemical unknowns, and targeted metabolomics, the measurement of defined groups of chemically characterized and biochemically annotated metabolites. The methodologies considered in this unit focus on the processes of conducting targeted metabolomics experiments, and the advantages of this general approach are highlighted herein. This unit outlines procedures for extracting nitrogenous metabolites (including amino acids), lipids, and intermediary metabolites (including TCA cycle oxoacids) from blood plasma. Specifically, protocols are described for analyzing these metabolites using targeted metabolomics experiments based on liquid chromatography-mass spectrometry.
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Affiliation(s)
- Lee D Roberts
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Maiolica A, Jünger MA, Ezkurdia I, Aebersold R. Targeted proteome investigation via selected reaction monitoring mass spectrometry. J Proteomics 2012; 75:3495-513. [PMID: 22579752 DOI: 10.1016/j.jprot.2012.04.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 04/27/2012] [Accepted: 04/29/2012] [Indexed: 12/20/2022]
Abstract
Due to the enormous complexity of proteomes which constitute the entirety of protein species expressed by a certain cell or tissue, proteome-wide studies performed in discovery mode are still limited in their ability to reproducibly identify and quantify all proteins present in complex biological samples. Therefore, the targeted analysis of informative subsets of the proteome has been beneficial to generate reproducible data sets across multiple samples. Here we review the repertoire of antibody- and mass spectrometry (MS) -based analytical tools which is currently available for the directed analysis of predefined sets of proteins. The topics of emphasis for this review are Selected Reaction Monitoring (SRM) mass spectrometry, emerging tools to control error rates in targeted proteomic experiments, and some representative examples of applications. The ability to cost- and time-efficiently generate specific and quantitative assays for large numbers of proteins and posttranslational modifications has the potential to greatly expand the range of targeted proteomic coverage in biological studies. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
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Affiliation(s)
- Alessio Maiolica
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
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An overview of human protein databases and their application to functional proteomics in health and disease. SCIENCE CHINA-LIFE SCIENCES 2011; 54:988-98. [PMID: 22173304 DOI: 10.1007/s11427-011-4247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Accepted: 11/23/2011] [Indexed: 02/02/2023]
Abstract
Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs. In recent years, a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery. In addition to being used to annotate the proteome, these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease. Here, we present a comprehensive review of the major human protein bioinformatics databases. We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.
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The Role of Proteomics in the Diagnosis and Treatment of Women's Cancers: Current Trends in Technology and Future Opportunities. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011. [PMID: 21886869 PMCID: PMC3163496 DOI: 10.1155/2011/373584] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Technological and scientific innovations over the last decade have greatly contributed to improved diagnostics, predictive models, and prognosis among cancers affecting women. In fact, an explosion of information in these areas has almost assured future generations that outcomes in cancer will continue to improve. Herein we discuss the current status of breast, cervical, and ovarian cancers as it relates to screening, disease diagnosis, and treatment options. Among the differences in these cancers, it is striking that breast cancer has multiple predictive tests based upon tumor biomarkers and sophisticated, individualized options for prescription therapeutics while ovarian cancer lacks these tools. In addition, cervical cancer leads the way in innovative, cancer-preventative vaccines and multiple screening options to prevent disease progression. For each of these malignancies, emerging proteomic technologies based upon mass spectrometry, stable isotope labeling with amino acids, high-throughput ELISA, tissue or protein microarray techniques, and click chemistry in the pursuit of activity-based profiling can pioneer the next generation of discovery. We will discuss six of the latest techniques to understand proteomics in cancer and highlight research utilizing these techniques with the goal of improvement in the management of women's cancers.
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Functional proteomics: application of mass spectrometry to the study of enzymology in complex mixtures. Anal Bioanal Chem 2011; 402:625-45. [PMID: 21769551 DOI: 10.1007/s00216-011-5236-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/30/2011] [Accepted: 07/04/2011] [Indexed: 12/19/2022]
Abstract
This review covers recent developments in mass spectrometry-based applications dealing with functional proteomics with special emphasis on enzymology. The introduction of mass spectrometry into this research field has led to an enormous increase in knowledge in recent years. A major challenge is the identification of "biologically active substances" in complex mixtures. These biologically active substances are, on the one hand, potential regulators of enzymes. Elucidation of function and identity of those regulators may be accomplished by different strategies, which are discussed in this review. The most promising approach thereby seems to be the one-step procedure, because it enables identification of the functionality and identity of biologically active substances in parallel and thus avoids misinterpretation. On the other hand, besides the detection of regulators, the identification of endogenous substrates for known enzymes is an emerging research field, but in this case studies are quite rare. Moreover, the term biologically active substances may also encompass proteins with diverse biological functions. Elucidation of the functionality of those-so far unknown-proteins in complex mixtures is another branch of functional proteomics and those investigations will also be discussed in this review.
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Vestal ML. The future of biological mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:953-959. [PMID: 21953036 DOI: 10.1007/s13361-011-0108-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/15/2011] [Indexed: 05/31/2023]
Abstract
Biological applications of mass spectrometry have grown exponentially since the discovery of MALDI and electrospray ionization techniques. This growth has been further fueled by the massive volume of DNA sequence information that is now available. An ambitious goal of some of this research is to monitor the level and modification of all proteins and metabolites in a biological sample such as plasma. A major research effort in mass spectrometry and related disciplines has been expended over the past several years toward reaching this and other less ambitious goals, and considerable progress has been made; but the presently available tools are clearly not sufficient for these very difficult tasks. In this "critical insight" discussion we suggest that recent advances in time-of-flight (TOF) technology with MALDI ionization may provide some important new tools for achieving the goals of biological research.
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Colucci-D'Amato L, Farina A, Vissers JPC, Chambery A. Quantitative neuroproteomics: classical and novel tools for studying neural differentiation and function. Stem Cell Rev Rep 2011; 7:77-93. [PMID: 20352529 DOI: 10.1007/s12015-010-9136-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience ("neuroproteomics") are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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Sospedra I, Soler C, Mañes J, Soriano JM. Analysis of staphylococcal enterotoxin A in milk by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Anal Bioanal Chem 2011; 400:1525-31. [PMID: 21442364 DOI: 10.1007/s00216-011-4906-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/11/2011] [Accepted: 03/12/2011] [Indexed: 11/30/2022]
Abstract
Staphylococcal enterotoxin A (SEA) is an exotoxin excreted mainly by Staphylococcus aureus and nowadays is the most prevalent compound in staphylococcal food poisoning worldwide. SEA is highly heat-resistant, and usual cooking times and temperatures are unlikely to completely inactivate it. A procedure for extraction of this toxin based on protein precipitation with a mixture of dichloromethane and acidified water was used before SDS-PAGE separation of soluble proteins. Finally, bands of interest were excised from the gel and in-gel enzymatic digestion was done. SEA from pasteurized milk was detected with matrix-assisted laser-desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. Nineteen peptides (range 800-2400 Da) were identified as products of trypsin cleavage of the SEA standard with a score of 204 and 73% coverage of the protein sequence, whereas thirteen peptides were revealed for SEA extracted from milk with a score of 148 and 58% sequence coverage obtained. This procedure has been applied successfully for identification of SEA in milk.
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Affiliation(s)
- Isabel Sospedra
- Department of Preventive Medicine and Public Health, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n, 46100 Burjassot, Spain.
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du Plessis SS, Kashou AH, Benjamin DJ, Yadav SP, Agarwal A. Proteomics: a subcellular look at spermatozoa. Reprod Biol Endocrinol 2011; 9:36. [PMID: 21426553 PMCID: PMC3071316 DOI: 10.1186/1477-7827-9-36] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/22/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting. METHODS Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry. RESULTS Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome. CONCLUSION Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites which can act as biomarkers in the detection of sperm impairments and to potentially develop treatment for infertile couples.Further comprehensive studies on sperm-specific proteome, mechanisms of protein function and its proteolytic regulation, biomarkers and functional pathways, such as oxidative-stress induced mechanisms, will provide better insight into physiological functions of the spermatozoa. Large-scale proteomic studies using purified protein assays will eventually lead to the development of novel biomarkers that may allow for detection of disease states, genetic abnormalities, and risk factors for male infertility. Ultimately, these biomarkers will allow for a better diagnosis of sperm dysfunction and aid in drug development.
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Affiliation(s)
- Stefan S du Plessis
- Division of Medical Physiology, Stellenbosch University, Tygerberg, South Africa
| | - Anthony H Kashou
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - David J Benjamin
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Satya P Yadav
- Molecular Biotechnology Core Laboratory, The Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Ashok Agarwal
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, Ohio, USA
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Jones AW, Cooper HJ. Dissociation techniques in mass spectrometry-based proteomics. Analyst 2011; 136:3419-29. [DOI: 10.1039/c0an01011a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Hasan N, Wu HF, Li YH, Nawaz M. Two-step on-particle ionization/enrichment via a washing- and separation-free approach: multifunctional TiO2 nanoparticles as desalting, accelerating, and affinity probes for microwave-assisted tryptic digestion of phosphoproteins in ESI-MS and MALDI-MS: comparison with microscale TiO2. Anal Bioanal Chem 2010; 396:2909-19. [PMID: 20232060 DOI: 10.1007/s00216-010-3573-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 02/08/2010] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
We introduce a simplified sample preparation method using bare TiO(2) nanoparticles (NPs) to serve as multifunctional nanoprobes (desalting, accelerating, and affinity probes) for effective enrichment of phosphopeptides from microwave-assisted tryptic digestion of phosphoproteins (alpha-casein, beta-casein and milk) in Electrospray Ionization Mass Spectrometry (ESI-MS) and Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS). The results demonstrate that TiO(2) NPs can effectively enrich and accelerate the digestion reactions of phosphoproteins in aqueous solutions and also from complex real samples. After the microwave experiments, we directly injected the resulting solutions into the ESI-MS and MALDI-MS systems for analysis, and excellent sensitivity was achieved without the need for any washing procedure or separation process. The reasons are attributed to the high binding affinity and selectivity of TiO(2) NPs toward phosphopeptides. Thus, phosphopeptides can be adsorbed onto the TiO(2) NP surface. The digested or partially digested phosphoproteins can be concentrated onto the TiO(2) NP surface. This results in the effective or complete digestion of phosphoproteins in a short period of time (45 s). In addition, high sensitivity and sequence coverage of phosphopeptide can be obtained using TiO(2) NPs as microwave absorbers and affinity probes in MALDI-MS and ESI-MS. This is due to the photocatalytic nature of the TiO(2) NPs because the absorption of microwave radiation that can accelerate the activation of trypsin for efficient digestion of phosphoproteins and enhances the ionization of phosphopeptides. The lowest concentrations detected for ESI-MS and MALDI-MS were 0.1 microM and 10 fmol, respectively, for alpha-casein. Comparing the two-step approach of TiO(2) NPs with microscale TiO(2) particles, the microscale TiO(2) particles shows no effect on the microwave-assisted tryptic digestion of phosphoproteins. The current approach offers multiple advantages, such as great simplicity, high sensitivity and selectivity, straightforward and separation/washing-free technique for phosphopeptide enrichment analysis.
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Affiliation(s)
- Nazim Hasan
- Department of Chemistry, National Sun Yat-Sen University, 70, Lien-Hai Road, Kaohsiung 80424, Taiwan
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Chandramouli K, Qian PY. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. HUMAN GENOMICS AND PROTEOMICS : HGP 2009; 2009. [PMID: 20948568 PMCID: PMC2950283 DOI: 10.4061/2009/239204] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 08/28/2009] [Indexed: 01/12/2023]
Abstract
Proteomics is the large-scale study of the structure and function of proteins in complex biological sample. Such an approach has the potential value to understand the complex nature of the organism. Current proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. Advances in protein fractionation and labeling techniques have improved protein identification to include the least abundant proteins. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. However, the major limitation of proteomic investigations remains the complexity of biological structures and physiological processes, rendering the path of exploration paved with various difficulties and pitfalls. The quantity of data that is acquired with new techniques places new challenges on data processing and analysis. This article provides a brief overview of currently available proteomic techniques and their applications, followed by detailed description of advantages and technical challenges. Some solutions to circumvent technical difficulties are proposed.
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Abstract
Various methods of protein footprinting use hydrogen peroxide as an oxidant. Its removal by various solid-phase desalting methods, catalase treatment, or freeze drying after the footprinting is critical to ensure no uncontrolled oxidation. Although catalase treatment removes hydrogen peroxide with little loss of protein or additional protein oxidation, we discovered that freeze drying or freezing of the protein in a peroxide solution does lead to protein oxidation. Interestingly, the oxidation is not a result of freeze or thaw processes but is dependent on the temperature and length of time for incubation. After 2 h, apomyoglobin undergoes almost-complete single oxidation at -80 degrees C and double oxidation at -15 degrees C. Minimal oxidation is observed at 4 and 22 degrees C, compared to oxidation at -80 or -15 degrees C. The concentration of hydrogen peroxide is critical; 75 mM (0.2%) is required to oxidize >50% of the protein at -15 degrees C and 100 mM (0.3%) is required at -80 degrees C. In addition to Met, approximately 5% of the tryptophan and tyrosine residues are oxidized, as well as lower amounts of His and Phe. Oxidation of Val 68 and Val 17 (a buried residue) also occurs, with the oxidation of Val 17 likely occurring by electron transfer from one of two of the oxidized aromatic residues that are in contact with Val 17. Here, we describe the need to remove the hydrogen peroxide prior to cold storage of proteins, and we also report some preliminary results pertaining to the mechanism of cold, solid-state oxidation.
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Affiliation(s)
- David M Hambly
- Department of Chemistry, Washington University in St. Louis, Missouri 63130, USA
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