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Doroudian M, Gailer J. Interaction of carbonic anhydrase I released from red blood cells with human plasma in vitro. Metallomics 2024; 16:mfae028. [PMID: 38811147 PMCID: PMC11188540 DOI: 10.1093/mtomcs/mfae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/28/2024] [Indexed: 05/31/2024]
Abstract
Red blood cells (RBCs) constitute ∼50% of the bloodstream and represent an important target for environmental pollutants and bacterial/viral infections, which can result in their rupture. In addition, diseases such as sickle cell anaemia and paroxysmal nocturnal haemoglobinuria can also result in the rupture of RBCs, which can be potentially life-threatening. With regard to the release of cytosolic metalloproteins from RBCs into the blood-organ system, the biochemical fate of haemoglobin is rather well understood, while comparatively little is known about another highly abundant Zn-metalloprotein, carbonic anhydrase (CA I). To gain insight into the interaction of CA I with human blood plasma constituents, we have employed a metallomics tool comprised of size-exclusion chromatography (SEC) coupled online with an inductively coupled plasma atomic emission spectrometer (ICP-AES), which allows to simultaneously observe all Cu, Fe, and Zn-metalloproteins. After the addition of CA I to human blood plasma incubated at 37°C, the SEC-ICP-AES analysis using phosphate buffered saline (pH 7.4) after 5 min, 1 h, and 2 h revealed that CA I eluted after all endogenous Zn-metalloproteins in the 30 kDa range. Matrix-assisted laser desorption-time of flight mass spectrometry analysis of the collected Zn-peak confirmed that CA I eluted from the column intact. Our in vitro results suggest that CA I released from RBCs to plasma remains free and may be actively involved in health-relevant adverse processes that unfold at the bloodstream-endothelial interface, including atherosclerosis and vision loss.
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Affiliation(s)
- Maryam Doroudian
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Jürgen Gailer
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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2
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Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically fluorescence two-dimensional difference gel electrophoresis (2D-DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, ProteoMiner, is the focus of this chapter. The ProteoMiner technology utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppresses the concentration of high-abundance proteins in subsequent analysis.
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Affiliation(s)
- Sandra Murphy
- Charles River Laboratories, Saffron Walden, Essex, United Kingdom
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Integrative Metallomics Studies of Toxic Metal(loid) Substances at the Blood Plasma–Red Blood Cell–Organ/Tumor Nexus. INORGANICS 2022. [DOI: 10.3390/inorganics10110200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Globally, an estimated 9 million deaths per year are caused by human exposure to environmental pollutants, including toxic metal(loid) species. Since pollution is underestimated in calculations of the global burden of disease, the actual number of pollution-related deaths per year is likely to be substantially greater. Conversely, anticancer metallodrugs are deliberately administered to cancer patients, but their often dose-limiting severe adverse side-effects necessitate the urgent development of more effective metallodrugs that offer fewer off-target effects. What these seemingly unrelated events have in common is our limited understanding of what happens when each of these toxic metal(loid) substances enter the human bloodstream. However, the bioinorganic chemistry that unfolds at the plasma/red blood cell interface is directly implicated in mediating organ/tumor damage and, therefore, is of immediate toxicological and pharmacological relevance. This perspective will provide a brief synopsis of the bioinorganic chemistry of AsIII, Cd2+, Hg2+, CH3Hg+ and the anticancer metallodrug cisplatin in the bloodstream. Probing these processes at near-physiological conditions and integrating the results with biochemical events within organs and/or tumors has the potential to causally link chronic human exposure to toxic metal(loid) species with disease etiology and to translate more novel anticancer metal complexes to clinical studies, which will significantly improve human health in the 21st century.
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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Chiaradia E, Miller I. In slow pace towards the proteome of equine body fluids. J Proteomics 2020; 225:103880. [PMID: 32569818 DOI: 10.1016/j.jprot.2020.103880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]
Abstract
Equine medicine represents a relevant field of veterinary science and the horse industry generates a significant economic impact. Horses can be involved in different sport disciplines, meat production, work and recreational purposes. Horses are also important for human health as they can be used as animal models for studying human diseases and in equine-assisted therapy. This review summarizes the data related to body fluids such as plasma/serum, urine, cerebrospinal fluid, synovial fluid, saliva, bronchoalveolar lavage fluid and peritoneal fluid obtained using proteomic analysis. Horse body fluid proteome analysis under various physiological and pathological conditions is a useful method for identifying new biomarkers for horse diseases which are still difficult to diagnose, but with serious consequences on equine health and welfare. The findings reported here reveal that further proteomic studies on equine body fluids collected from diseased animals are required. SIGNIFICANCE: Body fluids are sources of potential protein biomarkers for diagnosis and therapeutic target identification. Indeed, they contain proteins that play a crucial role in cell functions and whose presence or relative abundance are indicative of the health status of tissues/organs. The review reports the data on the equine body fluids obtained using proteomic analysis, including those which are commonly used to obtain a correct diagnosis and prognosis of horse diseases which still pose a significant challenge. For equine medicine, new biomarkers are needed to formulate early diagnosis and to distinguish among diseases with similar clinical signs.
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Affiliation(s)
- Elisabetta Chiaradia
- Laboratory of proteomics, Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, via San Costanzo, 4, 06126 Perugia, Italy.
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria.
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Peffers MJ, Smagul A, Anderson JR. Proteomic analysis of synovial fluid: current and potential uses to improve clinical outcomes. Expert Rev Proteomics 2019; 16:287-302. [PMID: 30793992 DOI: 10.1080/14789450.2019.1578214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Synovial fluid (SF) is in close proximity to tissues which are primarily altered during articular disease and has significant potential to better understand the underlying disease pathogeneses of articular pathologies and biomarker discovery. Although development of mass spectrometry-based methods has allowed faster and higher sensitivity techniques, interrogation of the SF proteome has been hindered by its large protein concentration dynamic range, impeding quantification of lower abundant proteins. Areas covered: Recent advances have developed methodologies to reduce the large protein concentration dynamic range of SF and subsequently allow deeper exploration of the SF proteome. This review concentrates on methods to overcome biofluid complexity, mass spectrometry proteomics methodologies, extracellular vesicles proteomics and the application of advances within the field in clinical disease, including osteoarthritis, rheumatoid arthritis, spondyloarthritis and juvenile arthritis. A narrative review was conducted with articles searched using PubMed, 1991-2018. Expert opinion: The SF proteomics field faces various challenges, including the requirement for rigorous and standardised methods of sample collection/storage, the sensitivity and specificity of proteomic assays, techniques to combat the large protein concentration dynamic range and comprehensive data analysis to reduce falsely identified markers. Additionally, there are challenges in developing multi 'omic' integration techniques, with computational integration enhancing analysis.
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Affiliation(s)
- Mandy Jayne Peffers
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - Aibek Smagul
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - James Ross Anderson
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
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Proteomics: Tools of the Trade. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:1-22. [DOI: 10.1007/978-3-030-12298-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Sarpong-Kumankomah S, Gibson MA, Gailer J. Organ damage by toxic metals is critically determined by the bloodstream. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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9
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Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically difference gel electrophoresis (DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, Proteominer, will be the focus of this chapter. The Proteominer technology a utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppressing the concentration of high-abundance proteins in subsequent analysis.
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10
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Proteins and bioactive peptides from donkey milk: The molecular basis for its reduced allergenic properties. Food Res Int 2017; 99:41-57. [PMID: 28784499 DOI: 10.1016/j.foodres.2017.07.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/29/2017] [Accepted: 07/02/2017] [Indexed: 12/18/2022]
Abstract
The legendary therapeutics properties of donkey milk have recently been supported by many clinical trials who have clearly demonstrated that, even if with adequate lipid integration, it may represent a valid natural substitute of cow milk for feeding allergic children. During the last decade many investigations by MS-based methods have been performed in order to obtain a better knowledge of donkey milk proteins. The knowledge about the primary structure of donkey milk proteins now may provide the basis for a more accurate comprehension of its potential benefits for human nutrition. In this aspect, experimental data today available clearly demonstrate that donkey milk proteins (especially casein components) are more closely related with the human homologues rather than cow counterparts. Moreover, the low allergenic properties of donkey milk with respect to cow one seem to be related to the low total protein content, the low ratio of caseins to whey fraction, and finally to the presence in almost all bovine IgE-binding linear epitopes of multiple amino acid differences with respect to the corresponding regions of donkey milk counterparts.
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11
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Gibson MA, Sarpong-Kumankomah S, Nehzati S, George GN, Gailer J. Remarkable differences in the biochemical fate of Cd2+, Hg2+, CH3Hg+ and thimerosal in red blood cell lysate. Metallomics 2017; 9:1060-1072. [DOI: 10.1039/c7mt00069c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The application of a metallomics method revealed that all investigated Hg species bound to hemoglobin and that these interactions are of toxicological significance.
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Affiliation(s)
| | | | - Susan Nehzati
- Molecular and Environmental Science Research Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | - Graham N. George
- Molecular and Environmental Science Research Group
- Department of Geological Sciences
- University of Saskatchewan
- Saskatoon
- Canada
| | - Jürgen Gailer
- Department of Chemistry
- University of Calgary
- Calgary
- Canada
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12
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Giorgianni F, Beranova-Giorgianni S. Phosphoproteome Discovery in Human Biological Fluids. Proteomes 2016; 4:proteomes4040037. [PMID: 28248247 PMCID: PMC5260970 DOI: 10.3390/proteomes4040037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 01/07/2023] Open
Abstract
Phosphorylation plays a critical role in regulating protein function and thus influences a vast spectrum of cellular processes. With the advent of modern bioanalytical technologies, examination of protein phosphorylation on a global scale has become one of the major research areas. Phosphoproteins are found in biological fluids and interrogation of the phosphoproteome in biological fluids presents an exciting opportunity for discoveries that hold great potential for novel mechanistic insights into protein function in health and disease, and for translation to improved diagnostic and therapeutic approaches for the clinical setting. This review focuses on phosphoproteome discovery in selected human biological fluids: serum/plasma, urine, cerebrospinal fluid, saliva, and bronchoalveolar lavage fluid. Bioanalytical workflows pertinent to phosphoproteomics of biological fluids are discussed with emphasis on mass spectrometry-based approaches, and summaries of studies on phosphoproteome discovery in major fluids are presented.
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Affiliation(s)
- Francesco Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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Rodríguez-Celma J, Ceballos-Laita L, Grusak MA, Abadía J, López-Millán AF. Plant fluid proteomics: Delving into the xylem sap, phloem sap and apoplastic fluid proteomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:991-1002. [PMID: 27033031 DOI: 10.1016/j.bbapap.2016.03.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 12/12/2022]
Abstract
The phloem sap, xylem sap and apoplastic fluid play key roles in long and short distance transport of signals and nutrients, and act as a barrier against local and systemic pathogen infection. Among other components, these plant fluids contain proteins which are likely to be important players in their functionalities. However, detailed information about their proteomes is only starting to arise due to the difficulties inherent to the collection methods. This review compiles the proteomic information available to date in these three plant fluids, and compares the proteomes obtained in different plant species in order to shed light into conserved functions in each plant fluid. Inter-species comparisons indicate that all these fluids contain the protein machinery for self-maintenance and defense, including proteins related to cell wall metabolism, pathogen defense, proteolysis, and redox response. These analyses also revealed that proteins may play more relevant roles in signaling in the phloem sap and apoplastic fluid than in the xylem sap. A comparison of the proteomes of the three fluids indicates that although functional categories are somewhat similar, proteins involved are likely to be fluid-specific, except for a small group of proteins present in the three fluids, which may have a universal role, especially in cell wall maintenance and defense. 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)
- Jorge Rodríguez-Celma
- University of East Anglia/John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Laura Ceballos-Laita
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 13034, E-50080 Zaragoza, Spain
| | - Michael A Grusak
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA
| | - Javier Abadía
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 13034, E-50080 Zaragoza, Spain
| | - Ana-Flor López-Millán
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 13034, E-50080 Zaragoza, Spain; USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA.
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Santucci L, Bruschi M, Candiano G, Lugani F, Petretto A, Bonanni A, Ghiggeri GM. Urine Proteome Biomarkers in Kidney Diseases. I. Limits, Perspectives, and First Focus on Normal Urine. Biomark Insights 2016; 11:41-8. [PMID: 26997865 PMCID: PMC4795486 DOI: 10.4137/bmi.s26229] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 11/05/2022] Open
Abstract
Urine proteome is a potential source of information in renal diseases, and it is considered a natural area of investigation for biomarkers. Technology developments have markedly increased the power analysis on urinary proteins, and it is time to confront methodologies and results of major studies on the topics. This is a first part of a series of reviews that will focus on the urine proteome as a site for detecting biomarkers of renal diseases; the theme of the first review concerns methodological aspects applied to normal urine. Main issues are techniques for urine pretreatment, separation of exosomes, use of combinatorial peptide ligand libraries, mass spectrometry approaches, and analysis of data sets. Available studies show important differences, suggesting a major confounding effect of the technologies utilized for analysis. The objective is to obtain consensus about which approaches should be utilized for studying urine proteome in renal diseases.
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Affiliation(s)
- Laura Santucci
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Maurizio Bruschi
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Candiano
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Francesca Lugani
- Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Petretto
- Laboratory of Mass Spectrometry - Core Facility, Istituto Giannina Gaslini, Genova, Italy
| | - Alice Bonanni
- Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genova, Italy
| | - Gian Marco Ghiggeri
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy.; Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genova, Italy
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Comparative proteomics dataset of skimmed milk samples from Holstein and Jersey dairy cattle. Data Brief 2016; 6:843-6. [PMID: 26937459 PMCID: PMC4749939 DOI: 10.1016/j.dib.2016.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/11/2015] [Accepted: 01/20/2016] [Indexed: 11/21/2022] Open
Abstract
Milk samples were collected from Holstein and Jersey breeds of dairy cattle maintained under the same management practices and environmental conditions over a seven-day period. Milk samples were collected twice daily from six cows of each breed as previously described (Tacoma et al., 2016) [1]. Samples were composited within individual cow over the experimental period and skimmed to remove the fat layer. Skimmed milk samples were fractionated using CaCl2 precipitation, ultracentrifugation and ProteoMiner treatment to remove the high abundance milk proteins. Separation of the low abundance proteins was achieved using SDS-PAGE. Differential protein abundances were analyzed by mass spectrometry-based proteomic approaches followed by statistical analyses of the peptide count data. The complete list of low-abundance proteins identified in both breeds is provided in the dataset as well as the total number of distinct sequenced peptides and gene ontology functions for each protein. The relative abundance of a select few proteins is depicted using the SIEVE software.
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Nguyen-Kim H, San Clemente H, Balliau T, Zivy M, Dunand C, Albenne C, Jamet E. Arabidopsis thaliana
root cell wall proteomics: Increasing the proteome coverage using a combinatorial peptide ligand library and description of unexpected Hyp in peroxidase amino acid sequences. Proteomics 2016; 16:491-503. [DOI: 10.1002/pmic.201500129] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/07/2015] [Accepted: 11/10/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Huan Nguyen-Kim
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Thierry Balliau
- CNRS; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
- INRA; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
| | - Michel Zivy
- CNRS; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
- INRA; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Cécile Albenne
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
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Chakrabarti A, Halder S, Karmakar S. Erythrocyte and platelet proteomics in hematological disorders. Proteomics Clin Appl 2016; 10:403-14. [PMID: 26611378 DOI: 10.1002/prca.201500080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/26/2015] [Accepted: 11/19/2015] [Indexed: 12/20/2022]
Abstract
Erythrocytes undergo ineffective erythropoesis, hemolysis, and premature eryptosis in sickle cell disease and thalassemia. Abnormal hemoglobin variants associated with hemoglobinopathy lead to vesiculation, membrane instability, and loss of membrane asymmetry with exposal of phosphatidylserine. This potentiates thrombin generation resulting in activation of the coagulation cascade responsible for subclinical phenotypes. Platelet activation also results in the release of microparticles, which express and transfer functional receptors from platelet membrane, playing key roles in vascular reactivity and activation of intracellular signaling pathways. Over the last decade, proteomics had proven to be an important field of research in studies of blood and blood diseases. Blood cells and its fluidic components have been proven to be easy systems for studying differential expressions of proteins in hematological diseases encompassing hemoglobinopathies, different types of anemias, myeloproliferative disorders, and coagulopathies. Proteomic studies of erythrocytes and platelets reported from several groups have highlighted various factors that intersect the signaling networks in these anucleate systems. In this review, we have elaborated on the current scenario of anucleate blood cell proteomes in normal and diseased individuals and the cross-talk between the two major constituent cell types of circulating blood.
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Affiliation(s)
- Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Suchismita Halder
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Shilpita Karmakar
- Biophysics and Structural Genomics Division, Saha institute of Nuclear Physics, Kolkata, India
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Comparison of serum fractionation methods by data independent label-free proteomics. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Tacoma R, Fields J, Ebenstein DB, Lam YW, Greenwood SL. Characterization of the bovine milk proteome in early-lactation Holstein and Jersey breeds of dairy cows. J Proteomics 2015; 130:200-10. [PMID: 26391770 DOI: 10.1016/j.jprot.2015.09.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/15/2015] [Accepted: 09/17/2015] [Indexed: 12/25/2022]
Abstract
UNLABELLED Milk is a highly nutritious natural product that provides not only a rich source of amino acids to the consumer but also hundreds of bioactive peptides and proteins known to elicit health-benefitting activities. We investigated the milk protein profile produced by Holstein and Jersey dairy cows maintained under the same diet, management and environmental conditions using proteomic approaches that optimize protein extraction and characterization of the low abundance proteins within the skim milk fraction of bovine milk. In total, 935 low abundance proteins were identified. Gene ontology classified all proteins identified into various cellular localization and function categories. A total of 43 low abundance proteins were differentially expressed between the two dairy breeds. Bioactive proteins involved in host-defense, including lactotransferrin (P=0.0026) and complement C2 protein (P=0.0001), were differentially expressed by the two breeds, whereas others such as osteopontin (P=0.1788) and lactoperoxidase (P=0.2973) were not. This work is the first to outline the protein profile produced by two important breeds of dairy cattle maintained under the same diet, environment and management conditions in order to observe likely true breed differences. This research now allows us to better understand and contrast further research examining the bovine proteome that includes these different breeds. BIOLOGICAL SIGNIFICANCE Within the last decade, the amount of research characterizing the bovine milk proteome has increased due to growing interest in the bioactive proteins that are present in milk. Proteomic analysis of low abundance whey proteins has mainly focused on human breast milk; however, previous research has highlighted the presence of bioactive proteins in bovine milk. Recent publications outlining the cross-reactivity of bovine bioactive proteins on human biological function highlight the need for further investigation into the bovine milk proteome. The rationale behind this study is to characterize and compare the low abundance protein profile in the skim milk fraction produced from Holstein and Jersey breeds of dairy cattle, which are two major dairy cattle breeds in the USA. A combination of fractionation strategies was used to efficiently enrich the low abundance proteins from bovine skim milk for proteomic profiling. A total of 935 low abundance proteins were identified and compared between the two bovine breeds. The results from this study provide insight into breed differences and similarities in the milk proteome profile produced by two breeds of dairy cattle.
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Affiliation(s)
- Rinske Tacoma
- The University of Vermont, Department of Animal & Veterinary Sciences, 570 Main Street, Burlington, VT 05405, United States
| | - Julia Fields
- The University of Vermont, Vermont Genetics Network Proteomics Facility, 109 Carrigan Drive, Burlington, VT 05405, United States
| | - David B Ebenstein
- The University of Vermont, Department of Animal & Veterinary Sciences, 570 Main Street, Burlington, VT 05405, United States
| | - Ying-Wai Lam
- The University of Vermont, Vermont Genetics Network Proteomics Facility, 109 Carrigan Drive, Burlington, VT 05405, United States
| | - Sabrina L Greenwood
- The University of Vermont, Department of Animal & Veterinary Sciences, 570 Main Street, Burlington, VT 05405, United States.
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20
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Rosal-Vela A, García-Rodríguez S, Postigo J, Iglesias M, Longobardo V, Lario A, Merino J, Merino R, Zubiaur M, Sancho J. Distinct serum proteome profiles associated with collagen-induced arthritis and complete Freund's adjuvant-induced inflammation in CD38−/−
mice: The discriminative power of protein species or proteoforms. Proteomics 2015; 15:3382-93. [DOI: 10.1002/pmic.201400536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 04/25/2015] [Accepted: 07/10/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Antonio Rosal-Vela
- Departamento de Biología Celular e Inmunología; Instituto de Parasitología y Biomedicina López Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada; Granada Spain
| | - Sonia García-Rodríguez
- Departamento de Biología Celular e Inmunología; Instituto de Parasitología y Biomedicina López Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada; Granada Spain
| | - Jorge Postigo
- Departamento de Biología Molecular; Instituto de Formación e Investigación Marqués de Valdecilla, Universidad de Cantabria; Cantabria Spain
| | - Marcos Iglesias
- Departamento de Biología Molecular; Instituto de Formación e Investigación Marqués de Valdecilla, Universidad de Cantabria; Cantabria Spain
| | - Victoria Longobardo
- Unidad de Proteómica; Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada; Granada Spain
| | - Antonio Lario
- Unidad de Proteómica; Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada; Granada Spain
| | - Jesús Merino
- Departamento de Biología Molecular; Instituto de Formación e Investigación Marqués de Valdecilla, Universidad de Cantabria; Cantabria Spain
| | - Ramón Merino
- Instituto de Biomedicina y Biotecnología de Cantabria/CSIC-Universidad de Cantabria-SODERCAN; Cantabria Spain
| | - Mercedes Zubiaur
- Departamento de Biología Celular e Inmunología; Instituto de Parasitología y Biomedicina López Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada; Granada Spain
| | - Jaime Sancho
- Departamento de Biología Celular e Inmunología; Instituto de Parasitología y Biomedicina López Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), PTS Granada; Granada Spain
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21
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Filip S, Vougas K, Zoidakis J, Latosinska A, Mullen W, Spasovski G, Mischak H, Vlahou A, Jankowski J. Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine. PLoS One 2015. [PMID: 26208298 PMCID: PMC4514849 DOI: 10.1371/journal.pone.0133773] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.
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Affiliation(s)
- Szymon Filip
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantinos Vougas
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Agnieszka Latosinska
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - William Mullen
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - Goce Spasovski
- Ss. Cyril and Methodius University in Skopje, Nephrology Department, Skopje, Former Yugoslav Republic of Macedonia
| | - Harald Mischak
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Joachim Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research, Aachen, Germany
- * E-mail:
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22
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Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3415-31. [DOI: 10.1021/pr5013009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Péter Horvatovich
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Emma K. Lundberg
- Science
for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Fuchu He
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Edouard C. Nice
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. Goode
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Simon Yu
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Shoba Ranganathan
- Department
of Chemistry and Biomolecular Sciences and ARC Centre of Excellence
in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark S. Baker
- Australian
School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Gilberto B. Domont
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Erika Velasquez
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Dong Li
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Siqi Liu
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- BGI Shenzhen, Beishan Road, Yantian District, Shenzhen, 518083, China
| | - Quanhui Wang
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein
Research of Guangdong
Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Rajasree Menon
- Department of Computational Medicine & Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Yuanfang Guan
- Departments of Computational Medicine & Bioinformatics and Computer Sciences, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Fernando J. Corrales
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Victor Segura
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - J. Ignacio Casal
- Department
of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | | | - Juan P. Albar
- Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Manuel Fuentes
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Maria Gonzalez-Gonzalez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Paula Diez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Rosa M. Degano
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Andrea Urbani
- Proteomics
and Metabonomic, Laboratory, Fondazione Santa Lucia, Rome, Italy
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessio Soggiu
- Department
of Veterinary Science and Public Health (DIVET), University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Tadashi Yamamoto
- Institute
of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | | | | | - Andrey Lisitsa
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Cheryl F. Lichti
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Ekaterina Mostovenko
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Roger A. Kroes
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, Northwestern University, 1801 Maple Ave., Suite 4300, Evanston, Illinois 60201, United States
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Juan Antonio Vizcaíno
- European Molecular
Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, United Kingdom
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department
of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carol L. Nilsson
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Seul-Ki Jeong
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Jong-Sun Lim
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Young-Ki Paik
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - William S. Hancock
- The
Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
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23
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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24
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Bruschi M, Candiano G, Santucci L, D'Ambrosio C, Scaloni A, Bonsano M, Ghiggeri GM, Verrina E. Combinatorial Peptide Ligand Library and two dimensional electrophoresis: New frontiers in the study of peritoneal dialysis effluent in pediatric patients. J Proteomics 2015; 116:68-80. [DOI: 10.1016/j.jprot.2015.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/22/2014] [Accepted: 01/04/2015] [Indexed: 12/28/2022]
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25
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Bladergroen MR, van der Burgt YEM. Solid-phase extraction strategies to surmount body fluid sample complexity in high-throughput mass spectrometry-based proteomics. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:250131. [PMID: 25692071 PMCID: PMC4322654 DOI: 10.1155/2015/250131] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 05/08/2023]
Abstract
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential. Here we present high-throughput sample preparation solutions for balancing the speed of current MS-acquisitions and the time needed for analytical workup of body fluids. The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches. Various sample preparation methods that involve solid-phase extraction (SPE) including affinity enrichment strategies have been automated. Obtained peptide and protein fractions can be mass analyzed by direct infusion into an electrospray ionization (ESI) source or by means of matrix-assisted laser desorption ionization (MALDI) without further need of time-consuming liquid chromatography (LC) separations.
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Affiliation(s)
- Marco R. Bladergroen
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
- *Yuri E. M. van der Burgt:
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26
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Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in food proteomics: a tutorial. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:768-784. [PMID: 25230173 DOI: 10.1002/jms.3374] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 06/03/2023]
Abstract
In the last decades, the continuous and rapid evolution of proteomic approaches has provided an efficient platform for the characterization of food-derived proteins. Particularly, the impressive increasing in performance and versatility of the MS instrumentation has contributed to the development of new analytical strategies for proteins, evidencing how MS arguably represents an indispensable tool in food proteomics. Investigation of protein composition in foodstuffs is helpful for understanding the relationship between the protein content and the nutritional and technological properties of foods, the production of methods for food traceability, the assessment of food quality and safety, including the detection of allergens and microbial contaminants in foods, or even the characterization of genetically modified products. Given the high variety of the food-derived proteins and considering their differences in chemical and physical properties, a single proteomic strategy for all purposes does not exist. Rather, proteomic approaches need to be adapted to each analytical problem, and development of new strategies is necessary in order to obtain always the best results. In this tutorial, the most relevant aspects of MS-based methodologies in food proteomics will be examined, and their advantages and drawbacks will be discussed.
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Affiliation(s)
- Vincenzo Cunsolo
- Department of Chemical Sciences, University of Catania, Viale A. Doria, 6, I-95125, Catania, Italy
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27
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Di Girolamo F, D'Amato A, Lante I, Signore F, Muraca M, Putignani L. Farm animal serum proteomics and impact on human health. Int J Mol Sci 2014; 15:15396-411. [PMID: 25257521 PMCID: PMC4200749 DOI: 10.3390/ijms150915396] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/22/2014] [Accepted: 08/25/2014] [Indexed: 01/19/2023] Open
Abstract
Due to the incompleteness of animal genome sequencing, the analysis and characterization of serum proteomes of most farm animals are still in their infancy, compared to the already well-documented human serum proteome. This review focuses on the implications of the farm animal serum proteomics in order to identify novel biomarkers for animal welfare, early diagnosis, prognosis and monitoring of infectious disease treatment, and develop new vaccines, aiming at determining the reciprocal benefits for humans and animals.
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Affiliation(s)
- Francesco Di Girolamo
- Department of Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome 00165, Italy.
| | - Alfonsina D'Amato
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy.
| | - Isabella Lante
- Department of Laboratory Medicine, San Camillo Hospital, Viale Vittorio Veneto 18, Treviso 31100, Italy.
| | - Fabrizio Signore
- Department of Obstetrics and Gynaecology, San Camillo Forlanini Hospital, Circonvallazione Gianicolense, 87, Rome 00151, Italy.
| | - Marta Muraca
- Department of Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome 00165, Italy.
| | - Lorenza Putignani
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome 00165, Italy.
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28
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Lerma-García MJ, D’Amato A, Fasoli E, Simó-Alfonso EF, Righetti PG. According to the CPLL proteome sheriffs, not all aperitifs are created equal! BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1493-9. [DOI: 10.1016/j.bbapap.2014.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/24/2014] [Accepted: 04/28/2014] [Indexed: 12/01/2022]
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29
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From hundreds to thousands: Widening the normal human Urinome (1). J Proteomics 2014; 112:53-62. [PMID: 25123350 DOI: 10.1016/j.jprot.2014.07.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
UNLABELLED It is currently unknown how many proteins can be detected in urine. Improving the analytical approach would increase their number and potentially strengthen their predictive potential in diseases. We developed a combination of analytical procedures for maximizing sensitivity and reproducibility of normal human urinary proteome analysis based on ultracentrifugation, vesicles separation, combinatorial peptide ligand libraries (CPLL) and solvent removal of pigments. Proteins were identified by an Orbitrap Velos Mass Spectrometry. Overall, 3429 proteins were characterized: most components (1615) were contained in vesicles while the remaining 1794 were equally distributed among CPLL and butanol insoluble fractions. Several proteins were detected exclusively in one of the phases of the procedure, suggesting that each step is crucial in the fractionation strategy. Many (1724) proteins are described here whose presence in urine has never been reported and represents a potential source of information considering that urine is the unique site of excretion of products of interaction of metabolic processes. Improving the characterization of normal urinary proteome would also represent the basis for the analysis of urine biomarkers in human diseases. BIOLOGICAL SIGNIFICANCE Sub-fractionating normal urine by successive steps (vesicle separation, CPLL and solvent treatments) allowed the identification of 3429 proteins, a relevant part (1724) being detected for the first time in urine. Several proteins of new description have been implicated in physiology pathways and in pathologies thus representing a potential source of new information on both metabolic processes and diseases.
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Ma Y, Sun Z, de Matos R, Zhang J, Odunsi K, Lin B. Towards an animal model of ovarian cancer: cataloging chicken blood proteins using combinatorial peptide ligand libraries coupled with shotgun proteomic analysis for translational research. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:280-97. [PMID: 24660652 DOI: 10.1089/omi.2013.0164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Epithelial ovarian cancer is the most deadly gynecological cancer around the world, with high morbidity in industrialized countries. Early diagnosis is key in reducing its morbidity rate. Yet, robust biomarkers, diagnostics, and animal models are still limited for ovarian cancer. This calls for broader omics and systems science oriented diagnostics strategies. In this vein, the domestic chicken has been used as an ovarian cancer animal model, owing to its high rate of developing spontaneous epithelial ovarian tumors. Chicken blood has thus been considered a surrogate reservoir from which cancer biomarkers can be identified. However, the presence of highly abundant proteins in chicken blood has compromised the applicability of proteomics tools to study chicken blood owing to a lack of immunodepletion methods. Here, we demonstrate that a combinatorial peptide ligand library (CPLL) can efficiently remove highly abundant proteins from chicken blood samples, consequently doubling the number of identified proteins. Using an integrated CPLL-1DGE-LC-MSMS workflow, we identified a catalog of 264 unique proteins. Functional analyses further suggested that most proteins were coagulation and complement factors, blood transport and binding proteins, immune- and defense-related proteins, proteases, protease inhibitors, cellular enzymes, or cell structure and adhesion proteins. Semiquantitative spectral counting analysis identified 10 potential biomarkers from the present chicken ovarian cancer model. Additionally, many human homologs of chicken blood proteins we have identified have been independently suggested as diagnostic biomarkers for ovarian cancer, further triangulating our novel observations reported here. In conclusion, the CPLL-assisted proteomic workflow using the chicken ovarian cancer model provides a feasible platform for translational research to identify ovarian cancer biomarkers and understand ovarian cancer biology. To the best of our knowledge, we report here the most comprehensive survey of the chicken blood proteome to date.
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Affiliation(s)
- Yingying Ma
- 1 System Biology Division, Zhejiang-California International Nanosystem Institute (ZCNI), Zhejiang University , Hangzhou, China
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González-Iglesias H, Álvarez L, García M, Escribano J, Rodríguez-Calvo PP, Fernández-Vega L, Coca-Prados M. Comparative proteomic study in serum of patients with primary open-angle glaucoma and pseudoexfoliation glaucoma. J Proteomics 2014; 98:65-78. [DOI: 10.1016/j.jprot.2013.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/02/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022]
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32
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Manley SA, Gailer J. Analysis of the plasma metalloproteome by SEC–ICP-AES: bridging proteomics and metabolomics. Expert Rev Proteomics 2014; 6:251-65. [DOI: 10.1586/epr.09.44] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Smejkal GB. Genomics and proteomics: of hares, tortoises and the complexity of tortoises. Expert Rev Proteomics 2014. [DOI: 10.1586/epr.12.48] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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34
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Smejkal GB, Poinar GO, Righetti PG. Will amber inclusions provide the first glimpse of a Mesozoic proteome? Expert Rev Proteomics 2014; 6:1-4. [DOI: 10.1586/14789450.6.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Panfoli I, Calzia D, Santucci L, Ravera S, Bruschi M, Candiano G. A blue dive: from ‘blue fingers’ to ‘blue silver’. A comparative overview of staining methods for in-gel proteomics. Expert Rev Proteomics 2014; 9:627-34. [DOI: 10.1586/epr.12.63] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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36
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The Monkey King: a personal view of the long journey towards a proteomic Nirvana. J Proteomics 2013; 107:39-49. [PMID: 24316443 DOI: 10.1016/j.jprot.2013.11.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 11/22/2022]
Abstract
UNLABELLED The review covers about fifty years of progress in "proteome" analysis, starting from primitive two-dimensional (2D) map attempts in the early sixties of last century. The polar star in 2D mapping arose in 1975 with the classic paper by O'Farrell in J Biol. Chem. It became the compass for all proteome navigators. Perfection came, though, only with the introduction of immobilized pH gradients, which fixed the polypeptide spots in the 2D plane. Great impetus in proteome analysis came with the introduction of informatic tools and creating databases, among which Swiss Prot remains the site of excellence. Towards the end of the nineties, 2D chromatography, epitomized by coupling strong cation exchangers with C18 resins, began to be a serious challenge to electrophoretic 2D mapping, although up to the present both techniques are still much in vogue and appear to give complementary results. Yet the migration of "proteomics" into the third millennium was made possible only by mass spectrometry (MS), which today represents the standard analytical tool in any lab dealing with proteomic analysis. Another major improvement has been the introduction of combinatorial peptide ligand libraries (CPLL), which, when properly used, enhance the visibility of low-abundance species by 3 to 4 orders of magnitude. Coupling MS to CPLLs permits the exploration of at least 8 orders of magnitude in dynamic range on any proteome. BIOLOGICAL SIGNIFICANCE The present review is a personal recollection highlighting the developments that led to present-day proteomics on a long march that lasted about 50years. It is meant to give to young scientists an overview on how science grows, which ones are the quantum jumps in science and which research is of particular significance in general and in the field of proteomics in particular. It also gives some real-life episodes of greater-than-life figures. As such, it can be viewed as a tutorial to stimulate the young generation to be creative (and use their imagination too!).This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Fasoli E, Righetti PG. The peel and pulp of mango fruit: A proteomic samba. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2539-45. [DOI: 10.1016/j.bbapap.2013.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 09/10/2013] [Indexed: 12/31/2022]
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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40
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Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring. J Proteomics 2013; 89:215-26. [DOI: 10.1016/j.jprot.2013.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/03/2013] [Accepted: 05/29/2013] [Indexed: 11/18/2022]
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41
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Fasoli E, Colzani M, Aldini G, Citterio A, Righetti PG. Lemon peel and Limoncello liqueur: A proteomic duet. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1484-91. [DOI: 10.1016/j.bbapap.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/23/2022]
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42
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Di Girolamo F, Del Chierico F, Caenaro G, Lante I, Muraca M, Putignani L. Human serum proteome analysis: new source of markers in metabolic disorders. Biomark Med 2013; 6:759-73. [PMID: 23227840 DOI: 10.2217/bmm.12.92] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The prevalence of metabolic disorders (MDs), especially diabetes, is rapidly increasing worldwide, leading to an increasing risk of cardiovascular and other socially relevant complications. To boost MD biomarker discovery, advanced proteomics can harmonize metabolomics. Indeed, the rapid development of mass spectrometry (MS) has designated proteomics as an emerging platform to interrogate the plasma/serum proteome for the discovery of next-generation biomarkers exploitable for risk assessment, early detection and prognosis of MDs. Preanalytical plasma/serum treatment, such as combinatorial peptide ligand libraries with nano-liquid chromatography coupled with tandem MS or selected reaction monitoring coupled to triple-quadrupole time-of-flight instruments, are proven clinical laboratory techniques for quantitative analyses. New strategies, such as SWATH™ MS, which allows us to systematically characterize and quantify query sample sets of 'any protein of interest' in complex biological samples, may dramatically improve next-generation MD biomarkers, especially considering the plethora of candidates coming from the 'bioreactor' gut microbiota affecting MD onset and progression.
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Affiliation(s)
- Francesco Di Girolamo
- Parasitology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
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Combinatorial ligand libraries as a two-dimensional method for proteome analysis. J Chromatogr A 2013; 1297:106-12. [PMID: 23726082 DOI: 10.1016/j.chroma.2013.04.065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/19/2013] [Accepted: 04/23/2013] [Indexed: 12/17/2022]
Abstract
The present report tries to assess the possibility of performing capture of proteomes via combinatorial peptide ligand libraries (CPLL) in a two-dimensional (2D) mode, i.e. via orthogonal complementarity in the capture phase. To that aim, serum proteins are captured at physiological pH either at low ionic strength (25mM NaCl) or at high concentrations of lyotropic salts of the Hofmeister series (1M ammonium sulphate) favouring hydrophobic interaction. Indeed such 2D mechanisms seems to be operative, since 52% of the captured proteins are common to the two capture modes, 20% are specific only of the "ionic" interaction mode and 28% are found only in the "hydrophobically" driven interaction. As an additional bonus, losses of protein species from the initial sample, one of the major drawbacks of CPLLs, are diminished to about 5% and are found only in the ionic capture, whereas the hydrophobically engendered capture is loss-free.
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44
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Righetti PG. Bioanalysis: Heri, hodie, cras. Electrophoresis 2013; 34:1442-51. [DOI: 10.1002/elps.201300001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/09/2013] [Indexed: 12/11/2022]
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45
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Agrawal GK, Timperio AM, Zolla L, Bansal V, Shukla R, Rakwal R. Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics. J Proteomics 2013; 93:74-92. [PMID: 23619387 DOI: 10.1016/j.jprot.2013.04.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 03/17/2013] [Accepted: 04/01/2013] [Indexed: 12/18/2022]
Abstract
Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal.
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46
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Boggess MV, Lippolis JD, Hurkman WJ, Fagerquist CK, Briggs SP, Gomes AV, Righetti PG, Bala K. The need for agriculture phenotyping: "moving from genotype to phenotype". J Proteomics 2013; 93:20-39. [PMID: 23563084 DOI: 10.1016/j.jprot.2013.03.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Abstract
UNLABELLED Increase in the world population has called for the increased demand for agricultural productivity. Traditional methods to augment crop and animal production are facing exacerbating pressures in keeping up with population growth. This challenge has in turn led to the transformational change in the use of biotechnology tools to meet increased productivity for both plant and animal systems. Although many challenges exist, the use of proteomic techniques to understand agricultural problems is steadily increasing. This review discusses the impact of genomics, proteomics, metabolomics and phenotypes on plant, animal and bacterial systems to achieve global food security and safety and we highlight examples of intra and extra mural research work that is currently being done to increase agricultural productivity. BIOLOGICAL SIGNIFICANCE This review focuses on the global demand for increased agricultural productivity arising from population growth and how we can address this challenge using biotechnology. With a population well above seven billion humans, in a very unbalanced nutritional state (20% overweight, 20% risking starvation) drastic measures have to be taken at the political, infrastructure and scientific levels. While we cannot influence politics, it is our duty as scientists to see what can be done to feed humanity. Hence we highlight the transformational change in the use of biotechnology tools over traditional methods to increase agricultural productivity (plant and animal). Specifically, this review deals at length on how a three-pronged attack, namely combined genomics, proteomics and metabolomics, can help to ensure global food security and safety. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Mark V Boggess
- Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
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Orrù S, Di Nicola P, Giuliani F, Fabris C, Conti A, Coscia A, Bertino E. Detection of Bovine Alpha-S1-Casein in Term and Preterm Human Colostrum with Proteomic Techniques. Int J Immunopathol Pharmacol 2013; 26:435-44. [DOI: 10.1177/039463201302600216] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Due to increased social awareness of allergens and population hyper-sensitization, the reported incidence of allergic reactions to food allergens has increased over the past two decades. Cow's milk proteins (CMPs) are among the most common food allergens. The aim of this study was to use proteomics techniques to investigate cow's milk allergens in both full-term human colostrum and in preterm newborns' mothers - where both groups showed no prior allergen detection – in order to understand whether cow's milk allergens could be a cause of sensitization established through lactation. The most relevant finding was the detection of the intact bovine alpha-S1-casein in both term and preterm colostrum. Using techniques detailed in this paper and which allowed for direct protein identification, β-lactoglobulin was not detected in any of the colostrum samples. According to our results, bovine alpha 1 casein is considered a major cow's milk allergen, is readily secreted in human milk, and so could be considered a possible cause of sensitization in exclusively breastfed infants.
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Affiliation(s)
- S. Orrù
- CNR, Institute of Science of Food Production, Turin, Italy
| | | | | | - C. Fabris
- Neonatal Unit, University of Turin, Italy
| | - A. Conti
- CNR, Institute of Science of Food Production, Turin, Italy
| | - A. Coscia
- Neonatal Unit, University of Turin, Italy
| | - E. Bertino
- Neonatal Unit, University of Turin, Italy
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Artichoke and Cynar liqueur: Two (not quite) entangled proteomes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:119-26. [DOI: 10.1016/j.bbapap.2012.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 01/13/2023]
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49
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Rodríguez-Suárez E, Whetton AD. The application of quantification techniques in proteomics for biomedical research. MASS SPECTROMETRY REVIEWS 2013; 32:1-26. [PMID: 22847841 DOI: 10.1002/mas.21347] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 06/01/2023]
Abstract
The systematic analysis of biological processes requires an understanding of the quantitative expression patterns of proteins, their interacting partners and their subcellular localization. This information was formerly difficult to accrue as the relative quantification of proteins relied on antibody-based methods and other approaches with low throughput. The advent of soft ionization techniques in mass spectrometry plus advances in separation technologies has aligned protein systems biology with messenger RNA, DNA, and microarray technologies to provide data on systems as opposed to singular protein entities. Another aspect of quantitative proteomics that increases its importance for the coming few years is the significant technical developments underway both for high pressure liquid chromatography and mass spectrum devices. Hence, robustness, reproducibility and mass accuracy are still improving with every new generation of instruments. Nonetheless, the methods employed require validation and comparison to design fit for purpose experiments in advanced protein analyses. This review considers the newly developed systematic protein investigation methods and their value from the standpoint that relative or absolute protein quantification is required de rigueur in biomedical research.
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Rolland A, Lavigne R, Dauly C, Calvel P, Kervarrec C, Freour T, Evrard B, Rioux-Leclercq N, Auger J, Pineau C. Identification of genital tract markers in the human seminal plasma using an integrative genomics approach. Hum Reprod 2012; 28:199-209. [DOI: 10.1093/humrep/des360] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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