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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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3
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Insight of low-abundance proteins in rice leaves under Cd stress using combinatorial peptide ligand library technology. Anal Bioanal Chem 2020; 412:5435-5446. [DOI: 10.1007/s00216-020-02760-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/18/2020] [Accepted: 06/05/2020] [Indexed: 01/22/2023]
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Teclemariam ET, Pergande MR, Cologna SM. Considerations for mass spectrometry-based multi-omic analysis of clinical samples. Expert Rev Proteomics 2020; 17:99-107. [PMID: 31996049 DOI: 10.1080/14789450.2020.1724540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
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Affiliation(s)
- Esei T Teclemariam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, USA
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Boschetti E, D'Amato A, Candiano G, Righetti PG. Protein biomarkers for early detection of diseases: The decisive contribution of combinatorial peptide ligand libraries. J Proteomics 2017; 188:1-14. [PMID: 28882677 DOI: 10.1016/j.jprot.2017.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/09/2017] [Accepted: 08/13/2017] [Indexed: 12/31/2022]
Abstract
The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications. Although panels of proteins have been presented, with robust evidence, as potential early-stage biomarkers in these different pathologies, their approval by FDA as novel biomarkers in routine clinical chemistry settings would require plenty of additional work and efforts from the pharma industry. The science environment in universities could simply not afford such heavy monetary investments. SIGNIFICANCE After more than 16years of search for novel biomarkers, to be used in a clinical chemistry set-up, via proteomic analysis (mostly in biological fluids) it was felt a critical review was due. In the present report, though, only papers reporting biomarker discovery via combinatorial peptide ligand libraries are listed and assessed, since this methodology seems to be the most advanced one for digging in depth into low-to very-low-abundance proteins, which might represent important biomarkers for the onset of pathologies. In particular, a large survey has been made for the following diseases, since they appear to have a large incidence on human population and/or represent fatal diseases: ovarian cancer, breast cancer, pancreatic cancer and hepatocellular carcinoma.
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Affiliation(s)
| | - Alfonsina D'Amato
- Quadram Institute of Bioscience, Norwich Research Park, NR4 7UA Norwich, UK
| | - Giovanni Candiano
- Nephrology, Dialysis, Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa, Italy
| | - Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, Milano 20131, Italy.
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Manfredi M, Barberis E, Gosetti F, Conte E, Gatti G, Mattu C, Robotti E, Zilberstein G, Koman I, Zilberstein S, Marengo E, Righetti PG. Method for Noninvasive Analysis of Proteins and Small Molecules from Ancient Objects. Anal Chem 2017; 89:3310-3317. [DOI: 10.1021/acs.analchem.6b03722] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcello Manfredi
- Dipartimento
di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy
- ISALIT, Via G. Bovio 6, 28100, Novara, Novara, Italy
| | - Elettra Barberis
- Dipartimento
di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy
- ISALIT, Via G. Bovio 6, 28100, Novara, Novara, Italy
| | - Fabio Gosetti
- Dipartimento
di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | | | - Giorgio Gatti
- Dipartimento
di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Clara Mattu
- Politecnico di Torino - sede di Alessandria, Viale T. Michel, 5 15121 Alessandria, Italy
| | - Elisa Robotti
- Dipartimento
di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | | | - Igor Koman
- Translational
Medicine Institute, Ariel University, Ariel, 40700 Israel
| | | | - Emilio Marengo
- Dipartimento
di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy
| | - Pier Giorgio Righetti
- Department
of Chemistry, Materials and Chemical Engineering “‘Giulio Natta”’, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
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The Aotus nancymaae erythrocyte proteome and its importance for biomedical research. J Proteomics 2016; 152:131-137. [PMID: 27989940 DOI: 10.1016/j.jprot.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022]
Abstract
The Aotus nancymaae species has been of great importance in researching the biology and pathogenesis of malaria, particularly for studying Plasmodium molecules for including them in effective vaccines against such microorganism. In spite of the forgoing, there has been no report to date describing the biology of parasite target cells in primates or their biomedical importance. This study was thus designed to analyse A. nancymaae erythrocyte protein composition using MS data collected during a previous study aimed at characterising the Plasmodium vivax proteome and published in the pertinent literature. Most peptides identified were similar to those belonging to 1189 Homo sapiens molecules; >95% of them had orthologues in New World primates. GO terms revealed a correlation between categories having the greatest amount of proteins and vital cell function. Integral membrane molecules were also identified which could be possible receptors facilitating interaction with Plasmodium species. The A. nancymaae erythrocyte proteome is described here for the first time, as a starting point for more in-depth/extensive studies. The data reported represents a source of invaluable information for laboratories interested in carrying out basic and applied biomedical investigation studies which involve using this primate. SIGNIFICANCE An understanding of the proteomics characteristics of A. nancymaae erythrocytes represents a fascinating area for research regarding the study of the pathogenesis of malaria since these are the main target for Plasmodium invasion. However, and even though Aotus is one of the non-human primate models considered most appropriate for biomedical research, knowledge of its proteome, particularly its erythrocytes, remains unknown. According to the above and bearing in mind the lack of information about the A. nancymaae species genome and transcriptome, this study involved a search for primate proteins for comparing their MS/MS spectra with the available information for Homo sapiens. The great similarity found between the primate's molecules and those for humans supported the use of the monkeys or their cells for continuing assays involved in studying malaria. Integral membrane receptors used by Plasmodium for invading cells were also found; this required timely characterisation for evaluating their therapeutic role. The list of erythrocyte protein composition reported here represents a useful source of basic knowledge for advancing biomedical investigation in this field.
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8
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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Gianazza E, Miller I, Palazzolo L, Parravicini C, Eberini I. With or without you — Proteomics with or without major plasma/serum proteins. J Proteomics 2016; 140:62-80. [DOI: 10.1016/j.jprot.2016.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/26/2022]
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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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Abstract
One of the main challenges in proteomics investigation, protein biomarker research, and protein purity and contamination analysis is how to efficiently enrich and detect low-abundance proteins in biological samples. One approach that makes the detection of rare species possible is the treatment of biological samples with solid-phase combinatorial peptide ligand libraries, ProteoMiner. This method utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but remove most of the high-abundance proteins, therefore compresses the protein abundance range in the samples. This work describes optimized protocols and highlights on the successful application of ProteoMiner to protein identification and analysis.
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Affiliation(s)
- Lei Li
- Protein Technologies R&D, Life Science Group, Bio-Rad Laboratories, 1000 Alfred Nobel Drive, Hercules, CA, 94547, USA,
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12
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Righetti PG, Candiano G, Citterio A, Boschetti E. Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics. Anal Chem 2014; 87:293-305. [DOI: 10.1021/ac502171b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
| | - Giovanni Candiano
- Laboratory on Pathophysiology of Uremia
and Department of Nephrology, Istituto Giannina Gaslini, Genova, Italy
| | - Attilio Citterio
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
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13
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Decrease of dynamic range of proteins in human plasma by ampholine immobilized polymer microspheres. Anal Chim Acta 2014; 826:43-50. [DOI: 10.1016/j.aca.2014.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/28/2014] [Accepted: 04/03/2014] [Indexed: 12/25/2022]
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14
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Stoevesandt O, Taussig MJ. Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Rev Proteomics 2014; 9:401-14. [DOI: 10.1586/epr.12.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Barasa B, Slijper M. Challenges for red blood cell biomarker discovery through proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:1003-10. [PMID: 24129076 DOI: 10.1016/j.bbapap.2013.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/11/2013] [Accepted: 10/01/2013] [Indexed: 12/23/2022]
Abstract
Red blood cells are rather unique body cells, since they have lost all organelles when mature, which results in lack of potential to replace proteins that have lost their function. They maintain only a few pathways for obtaining energy and reducing power for the key functions they need to fulfill. This makes RBCs highly sensitive to any aberration. If so, these RBCs are quickly removed from circulation, but if the RBC levels reduce extremely fast, this results in hemolytic anemia. Several causes of HA exist, and proteome analysis is the most straightforward way to obtain deeper insight into RBC functioning under the stress of disease. This should result in discovery of biomarkers, typical for each source of anemia. In this review, several challenges to generate in-depth RBC proteomes are described, like to obtain pure RBCs, to overcome the wide dynamic range in protein expression, and to establish which of the identified/quantified proteins are active in RBCs. The final challenge is to acquire and validate suited biomarkers unique for the changes that occur for each of the clinical questions; in red blood cell aging (also important for transfusion medicine), for thalassemias or sickle cell disease. Biomarkers for other hemolytic anemias that are caused by dysfunction of RBC membrane proteins (the RBC membrane defects) or RBC cytosolic proteins (the enzymopathies) are sometimes even harder to discover, in particular for the patients with RBC rare diseases with unknown cause. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Benjamin Barasa
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, The Netherlands
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, The Netherlands.
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16
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Goodman SR, Daescu O, Kakhniashvili DG, Zivanic M. The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 2013; 238:509-18. [DOI: 10.1177/1535370213488474] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this minireview, we focus on advances in our knowledge of the human erythrocyte proteome and interactome that have occurred since our seminal review on the topic published in 2007. As will be explained, the number of unique proteins has grown from 751 in 2007 to 2289 as of today. We describe how proteomics and interactomics tools have been used to probe critical protein changes in disorders impacting the blood. The primary example used is the work done on sickle cell disease where biomarkers of severity have been identified, protein changes in the erythrocyte membranes identified, pharmacoproteomic impact of hydroxyurea studied and interactomics used to identify erythrocyte protein changes that are predicted to have the greatest impact on protein interaction networks.
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Affiliation(s)
- Steven R Goodman
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Ovidiu Daescu
- Department of Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA
| | - David G Kakhniashvili
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Marko Zivanic
- Department of Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA
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Zhu G, Zhao P, Deng N, Tao D, Sun L, Liang Z, Zhang L, Zhang Y. Single chain variable fragment displaying M13 phage library functionalized magnetic microsphere-based protein equalizer for human serum protein analysis. Anal Chem 2012; 84:7633-7. [PMID: 22909037 DOI: 10.1021/ac3017746] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Single chain variable fragment (scFv) displaying the M13 phage library was covalently immobilized on magnetic microspheres and used as a protein equalizer for the treatment of human serum. First, scFv displaying M13 phage library functionalized magnetic microspheres (scFv@M13@MM) was incubated with a human serum sample. Second, captured proteins on scFv@M13@MM were eluted with 2 M NaCl, 50 mM glycine-hydrochloric acid (Gly-HCl), and 20% (v/v) acetonitrile with 0.5% (v/v) trifluoroacetic acid in sequence. Finally, the tightly bonded proteins were released by the treatment with thrombin. The eluates were first analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with silver staining. Results indicated that the difference of protein concentration was reduced obviously in NaCl and Gly-HCl fractions compared with untreated human serum sample. The eluates were also digested with trypsin, followed by online 2D-strong cation exchange (SCX)-RPLC-ESI-MS/MS analysis. Results demonstrated that the number of proteins identified from an scFv@M13@MM treated human serum sample was improved 100% compared with that from the untreated sample. In addition, the spectral count of 10 high abundance proteins (serum albumin, serotransferrin, α-2-macroglobulin, α-1-antitrypsin, apolipoprotein B-100, Ig γ-2 chain C region, haptoglobin, hemopexin, α-1-acid glycoprotein 1, and α-2-HS-glycoprotein) decreased evidently after scFv@M13@MM treatment. All these results demonstrate that scFv@M13@MM could efficiently remove high-abundance proteins, reduce the protein concentration difference of human serum, and result in more protein identification.
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Affiliation(s)
- Guijie Zhu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. and A. Center, Dalian Institute of Chemical Physics, The Chinese Academy of Science, Dalian, China
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18
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Walpurgis K, Kohler M, Thomas A, Wenzel F, Geyer H, Schänzer W, Thevis M. Validated hemoglobin-depletion approach for red blood cell lysate proteome analysis by means of 2D PAGE and Orbitrap MS. Electrophoresis 2012; 33:2537-45. [DOI: 10.1002/elps.201200151] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Walpurgis
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Maxie Kohler
- Department of Medicine; Respiratory Medicine Unit; Karolinska Institute; Stockholm; Sweden
| | - Andreas Thomas
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Folker Wenzel
- Institute of Transplantation Diagnostics and Cell Therapeutics; University of Düsseldorf Medical School; Düsseldorf; Germany
| | - Hans Geyer
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Wilhelm Schänzer
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Mario Thevis
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
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19
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Righetti PG, Boschetti E, Candiano G. Mark Twain: How to fathom the depth of your pet proteome. J Proteomics 2012; 75:4783-91. [DOI: 10.1016/j.jprot.2012.05.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 05/28/2012] [Accepted: 05/30/2012] [Indexed: 02/06/2023]
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20
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Zelenak C, Eberhard M, Jilani K, Qadri SM, Macek B, Lang F. Protein kinase CK1α regulates erythrocyte survival. Cell Physiol Biochem 2012; 29:171-80. [PMID: 22415086 DOI: 10.1159/000337598] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2012] [Indexed: 01/14/2023] Open
Abstract
Protein kinase CK1 (casein kinase 1) isoforms are involved in the regulation of various physiological functions including apoptosis. The specific CK1 inhibitor D4476 may either inhibit or foster apoptosis. Similar to apoptosis of nucleated cells, eryptosis, the suicidal death of erythrocytes, is paralleled by cell shrinkage and cell membrane scrambling with phosphatidylserine exposure at the cell surface. Triggers of eryptosis include increase of cytosolic Ca(2+) activity following energy depletion (removal of glucose) or oxidative stress (exposure to the oxidant tert-butyl hydroperoxide [TBOOH]). Western blotting was utilized to verify that erythrocytes express the protein kinase CK1α, and FACS analysis to determine whether the CK1 inhibitor D4476 and CK1α activator pyrvinium pamoate modify forward scatter (reflecting cell volume), annexin V binding (reflecting phosphatidylserine exposure), and Fluo3 fluorescence (reflecting cytosolic Ca(2+) activity). As a result, both, human and murine erythrocytes express CK1 isoform α. Glucose depletion (48 hours) and exposure to 0.3 mM TBOOH (30 minutes) both decreased forward scatter, increased annexin V binding and increased Fluo3 fluorescence. CK1 inhibitor D4476 (10 μM) significantly blunted the decrease in forward scatter, the increase in annexin V binding and the increase in Fluo 3 fluorescence. (R)-DRF053, another CK1 inhibitor, similarly blunted the increase in annexin V binding upon glucose depletion. The CK1α specific activator pyrvinium pamoate (10 μM) significantly enhanced the increase in annexin V binding and Fluo3 fluorescence upon glucose depletion and TBOOH exposure. In the presence of glucose, pyrvinium pamoate slightly but significantly increased Fluo3 fluorescence. In conclusion, CK1 isoform α participates in the regulation of erythrocyte programmed cell death by modulating cytosolic Ca(2+) activity.
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Boschetti E, Righetti P. Mixed Beds. ADVANCES IN CHROMATOGRAPHY 2012. [DOI: 10.1201/b11636-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Santucci L, Candiano G, Bruschi M, D'Ambrosio C, Petretto A, Scaloni A, Urbani A, Righetti PG, Ghiggeri GM. Combinatorial peptide ligand libraries for the analysis of low-expression proteins: Validation for normal urine and definition of a first protein MAP. Proteomics 2012; 12:509-15. [DOI: 10.1002/pmic.201100404] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/19/2011] [Accepted: 10/25/2011] [Indexed: 11/10/2022]
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23
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Selvaraju S, Rassi ZE. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis--an update covering the period 2008-2011. Electrophoresis 2012; 33:74-88. [PMID: 22125262 PMCID: PMC3516880 DOI: 10.1002/elps.201100431] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 11/08/2022]
Abstract
This review article expands on the previous one (Jmeian, Y. and El Rassi, Z. Electrophoresis 2009, 30, 249-261) by reviewing pertinent literature in the period extending from early 2008 to the present. Similar to the previous review article, the present one is concerned with proteomic sample preparation (e.g. depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article differs from the first version published in Electrophoresis 2009, 30, 249-261 by expanding on capturing/enriching subglycoproteomics by lectin affinity chromatography. Ninety-eight articles published in the period extending from early 2008 to the present have been reviewed. By no means is this review article exhaustive: its aim is to give a concise report on the latest developments in the field.
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Affiliation(s)
| | - Ziad El Rassi
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071
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24
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Fernández C, Santos HM, Ruíz-Romero C, Blanco FJ, Capelo-Martínez JL. A comparison of depletion versus equalization for reducing high-abundance proteins in human serum. Electrophoresis 2011; 32:2966-74. [DOI: 10.1002/elps.201100183] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 05/28/2011] [Accepted: 06/13/2011] [Indexed: 11/10/2022]
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25
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Tu C, Li J, Young R, Page BJ, Engler F, Halfon MS, Canty JM, Qu J. Combinatorial peptide ligand library treatment followed by a dual-enzyme, dual-activation approach on a nanoflow liquid chromatography/orbitrap/electron transfer dissociation system for comprehensive analysis of swine plasma proteome. Anal Chem 2011; 83:4802-13. [PMID: 21491903 DOI: 10.1021/ac200376m] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plasma proteome holds enormous clinical potential, yet an in-depth analysis of the plasma proteome remains a daunting challenge due to its high complexity and the extremely wide dynamic range in protein concentrations. Furthermore, existing antibody-based approaches for depleting high-abundance proteins are not adaptable to the analysis of the animal plasma proteome, which is often essential for experimental pathology/pharmacology. Here we describe a highly comprehensive method for the investigation of the animal plasma proteome which employs an optimized combinatorial peptide ligand library (CPLL) treatment to reduce the protein concentration dynamic range and a dual-enzyme, dual-activation strategy to achieve high proteomic coverage. The CPLL treatment enriched the lower abundance proteins by >100-fold when the samples were loaded in moderately denaturing conditions with multiple loading-washing cycles. The native and the CPLL-treated plasma were digested in parallel by two enzymes (trypsin and GluC) carrying orthogonal specificities. By performing this differential proteolysis, the proteome coverage is improved where peptides produced by only one enzyme are poorly detectable. Digests were fractionated with high-resolution strong cation exchange chromatography and then resolved on a long, heated nano liquid chromatography column. MS analysis was performed on a linear triple quadrupole/orbitrap with two complementary activation methods (collisionally induced dissociation (CID) and electron transfer dissociation). We applied this optimized strategy to investigate the plasma proteome from swine, a prominent animal model for cardiovascular diseases (CVDs). This large-scale analysis results in identification of a total of 3421 unique proteins, spanning a concentration range of 9-10 orders of magnitude. The proteins were identified under a set of commonly accepted criteria, including a precursor mass error of <15 ppm, Xcorr cutoffs, and ≥2 unique peptides at a peptide probability of ≥95% and a protein probability of ≥99%, and the peptide false-positive rate of the data set was 1.8% as estimated by searching the reversed database. CPLL treatment resulted in 55% more identified proteins over those from native plasma; moreover, compared with using only trypsin and CID, the dual-enzyme/activation approach enabled the identification of 2.6-fold more proteins and substantially higher sequence coverage for most individual proteins. Further analysis revealed 657 proteins as significantly associated with CVDs (p < 0.05), which constitute five CVD-related pathways. This study represents the first in-depth investigation of a nonhuman plasma proteome, and the strategy developed here is adaptable to the comprehensive analysis of other highly complex proteomes.
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Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, New York 14260, USA
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26
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Righetti PG, Fasoli E, Boschetti E. Combinatorial peptide ligand libraries: The conquest of the ‘hidden proteome’ advances at great strides. Electrophoresis 2011; 32:960-6. [DOI: 10.1002/elps.201000589] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 11/21/2010] [Accepted: 11/21/2010] [Indexed: 12/27/2022]
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27
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Deep insights into the plant proteome by pretreatment with combinatorial hexapeptide ligand libraries. J Proteomics 2011; 74:1182-9. [PMID: 21354349 DOI: 10.1016/j.jprot.2011.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/11/2011] [Accepted: 02/16/2011] [Indexed: 01/21/2023]
Abstract
Proteome analyses suffer from the large complexity of even small proteomes. Additionally, in many protein samples a few highly abundant proteins are hindering detailed proteomic studies, since they mask low abundant proteins. Recently, a new technology has emerged, which reduces dynamic range of protein concentrations within a given sample using combinatorial hexapeptide ligand libraries (CPLLs). This technique has been widely used in the microbial, animal and human fields and is now going to enter plant research. It can be a useful tool for fractionation of protein samples and might help to get a deeper insight into specific plant proteomes. In this review we describe the CPLL protein fractionation, summarize its possible applications in the plant field and discuss the limitations of this method.
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Righetti PG, Boschetti E, Kravchuk AV, Fasoli E. The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries. Expert Rev Proteomics 2010; 7:373-85. [PMID: 20536309 DOI: 10.1586/epr.10.25] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The latest advances in combinatorial peptide ligand libraries, with their unique performance in discovering low-abundance species in proteomes, are reviewed here. Explanations of mechanism, potential applications, capture of proteomes at different pH values to enhance the total catch and quantitative elutions, such as boiling in the presence of 5% sodium dodecyl sulfate and 3% dithiothreitol are included. The reproducibility of protein capture among different experiments with the same batch of beads or with different batches is also reported to be very high, with coefficient of variations in the order of 10-20%. Miniaturized operations, consisting of capture with as little as 20 or even 5 microl of peptide beads are reported, thus demonstrating that the described technology could be exploited for routine biomarker discovery in a biomedical environment. Finally, it is shown that the signal of captured proteins is linear over approximately three orders of magnitude, ranging from nM to microM, thus ensuring that differential quantitative proteomics for biomarker discovery can be fully implemented, providing species do not saturate their ligands.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Via Mancinelli 7, Politecnico di Milano, Milano, Italy.
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29
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Pasini EM, Mann M, Thomas AW. Red blood cell proteomics. Transfus Clin Biol 2010; 17:151-64. [PMID: 20655788 DOI: 10.1016/j.tracli.2010.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 05/21/2010] [Indexed: 12/23/2022]
Abstract
Since its discovery in the 17th century, the red blood cell, recognized in time as the critical cell component for survival, has been the focus of much attention. Its unique role in gas exchange (oxygen/CO(2) transport) and its distinct characteristics (absence of nucleus; biconcave cell shape) together with an - in essence - unlimited supply lead to extensive targeted biochemical, molecular and structural studies. A quick PubMed query with the word "erythrocyte" results in 198 013 scientific articles of which 162 are red blood cell proteomics studies, indicating that this new technique has been only recently applied to the red blood cell and related fields. Standard and comparative proteomics have been widely used to study different blood components. A growing body of proteomics literature has since developed, which deals with the characterization of red blood cells in health and disease. The possibility offered by proteomics to obtain a global snapshot of the whole red blood cell protein make-up, has provided unique insights to many fields including transfusion medicine, anaemia studies, intra-red blood cell parasite biology and translational research. While the contribution of proteomics is beyond doubt, a full red blood cell understanding will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. In this review we will briefly discuss the methodology and limitations of proteomics, the contribution it made to the understanding of the erythrocyte and the advances in red blood cell-related fields brought about by comparative proteomics.
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Affiliation(s)
- E M Pasini
- Biomedical Primate Research Centre, Lange Kleiweg 139, 2288 GJ Rijswijk, The Netherlands
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30
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31
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Proteomics for quality-control processes in transfusion medicine. Anal Bioanal Chem 2010; 398:111-24. [DOI: 10.1007/s00216-010-3799-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/24/2010] [Accepted: 04/27/2010] [Indexed: 12/23/2022]
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32
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In-depth exploration of Hevea brasiliensis latex proteome and “hidden allergens” via combinatorial peptide ligand libraries. J Proteomics 2010; 73:1368-80. [DOI: 10.1016/j.jprot.2010.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/02/2010] [Accepted: 03/04/2010] [Indexed: 11/18/2022]
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33
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Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis. Talanta 2010; 82:245-54. [PMID: 20685463 DOI: 10.1016/j.talanta.2010.04.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Revised: 03/31/2010] [Accepted: 04/16/2010] [Indexed: 11/23/2022]
Abstract
In most diseases, the clinical need for serum/plasma markers has never been so crucial, not only for diagnosis, but also for the selection of the most efficient therapies, as well as exclusion of ineffective or toxic treatment. Due to the high sample complexity, prefractionation is essential for exploring the deep proteome and finding specific markers. In this study, three different sample preparation methods (i.e., highly abundant protein precipitation, restricted access materials (RAM) combined with IMAC chromatography and peptide ligand affinity beads) were investigated in order to select the best fractionation step for further differential proteomic experiments focusing on the LMW proteome (MW inferior to 40,000 Da). Indeed, the aim was not to cover the entire plasma/serum proteome, but to enrich potentially interesting tissue leakage proteins. These three methods were evaluated on their reproducibility, on the SELDI-TOF-MS peptide/protein peaks generated after fractionation and on the information supplied. The studied methods appeared to give complementary information and presented good reproducibility (below 20%). Peptide ligand affinity beads were found to provide efficient depletion of HMW proteins and peak enrichment in protein/peptide profiles.
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34
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Plucking, pillaging and plundering proteomes with combinatorial peptide ligand libraries. J Chromatogr A 2010; 1217:893-900. [DOI: 10.1016/j.chroma.2009.08.070] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 08/19/2009] [Accepted: 08/27/2009] [Indexed: 11/23/2022]
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35
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Fasoli E, Farinazzo A, Sun CJ, Kravchuk AV, Guerrier L, Fortis F, Boschetti E, Righetti PG. Interaction among proteins and peptide libraries in proteome analysis: pH involvement for a larger capture of species. J Proteomics 2010; 73:733-42. [DOI: 10.1016/j.jprot.2009.10.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 10/05/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
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36
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Mouton-Barbosa E, Roux-Dalvai F, Bouyssié D, Berger F, Schmidt E, Righetti PG, Guerrier L, Boschetti E, Burlet-Schiltz O, Monsarrat B, Gonzalez de Peredo A. In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. Mol Cell Proteomics 2010; 9:1006-21. [PMID: 20093276 DOI: 10.1074/mcp.m900513-mcp200] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cerebrospinal fluid (CSF) is the biological fluid in closest contact with the brain and thus contains proteins of neural cell origin. Hence, CSF is a biochemical window into the brain and is particularly attractive for the search for biomarkers of neurological diseases. However, as in the case of other biological fluids, one of the main analytical challenges in proteomic characterization of the CSF is the very wide concentration range of proteins, largely exceeding the dynamic range of current analytical approaches. Here, we used the combinatorial peptide ligand library technology (ProteoMiner) to reduce the dynamic range of protein concentration in CSF and unmask previously undetected proteins by nano-LC-MS/MS analysis on an LTQ-Orbitrap mass spectrometer. This method was first applied on a large pool of CSF from different sources with the aim to better characterize the protein content of this fluid, especially for the low abundance components. We were able to identify 1212 proteins in CSF, and among these, 745 were only detected after peptide library treatment. However, additional difficulties for clinical studies of CSF are the low protein concentration of this fluid and the low volumes typically obtained after lumbar puncture, precluding the conventional use of ProteoMiner with large volume columns for treatment of patient samples. The method has thus been optimized to be compatible with low volume samples. We could show that the treatment is still efficient with this miniaturized protocol and that the dynamic range of protein concentration is actually reduced even with small amounts of beads, leading to an increase of more than 100% of the number of identified proteins in one LC-MS/MS run. Moreover, using a dedicated bioinformatics analytical work flow, we found that the method is reproducible and applicable for label-free quantification of series of samples processed in parallel.
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Affiliation(s)
- Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, 31077 Toulouse, France
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37
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Lion N, Crettaz D, Rubin O, Tissot JD. Stored red blood cells: a changing universe waiting for its map(s). J Proteomics 2009; 73:374-85. [PMID: 19931659 DOI: 10.1016/j.jprot.2009.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 11/03/2009] [Accepted: 11/04/2009] [Indexed: 12/11/2022]
Abstract
The availability of stored red blood cells (RBCs) for transfusion remains an important aspect of the treatment of polytrauma, acute anemia or major bleedings. RBCs are prepared by blood banks from whole blood donations and stored in the cold in additive solutions for typically six weeks. These far from physiological storage conditions result in the so-called red cell storage lesion that is of importance both to blood bankers and to clinical practitioners. Here we review the current state of knowledge about the red cell storage lesion from a proteomic perspective. In particular, we describe the current models accounting for RBC aging and response to lethal stresses, review the published proteomic studies carried out to uncover the molecular basis of the RBC storage lesion, and conclude by suggesting a few possible proteomic studies that would provide further knowledge of the molecular alterations carried by RBCs stored in the cold for six weeks.
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Affiliation(s)
- Niels Lion
- Service Régional Vaudois de Transfusion Sanguine, Lausanne, Switzerland.
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D’Alessandro A, Righetti PG, Zolla L. The Red Blood Cell Proteome and Interactome: An Update. J Proteome Res 2009; 9:144-63. [DOI: 10.1021/pr900831f] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Angelo D’Alessandro
- Department of Environmental Sciences, University of Tuscia, Viterbo, Italy, and Department of Chemistry, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
| | - Pier Giorgio Righetti
- Department of Environmental Sciences, University of Tuscia, Viterbo, Italy, and Department of Chemistry, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
| | - Lello Zolla
- Department of Environmental Sciences, University of Tuscia, Viterbo, Italy, and Department of Chemistry, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
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39
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D’Amato A, Bachi A, Fasoli E, Boschetti E, Peltre G, Sénéchal H, Righetti PG. In-Depth Exploration of Cow’s Whey Proteome via Combinatorial Peptide Ligand Libraries. J Proteome Res 2009; 8:3925-36. [DOI: 10.1021/pr900221x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alfonsina D’Amato
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Angela Bachi
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Elisa Fasoli
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Egisto Boschetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Gabriel Peltre
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Helène Sénéchal
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Pier Giorgio Righetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
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40
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Searching for specific motifs in affinity capture in proteome analysis. J Proteomics 2009; 72:791-802. [DOI: 10.1016/j.jprot.2009.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 03/20/2009] [Accepted: 04/07/2009] [Indexed: 11/18/2022]
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41
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Blood-related proteomics. J Proteomics 2009; 73:483-507. [PMID: 19567275 DOI: 10.1016/j.jprot.2009.06.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 12/12/2022]
Abstract
Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew.
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42
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Antonioli P, Bachi A, Fasoli E, Righetti PG. Efficient removal of DNA from proteomic samples prior to two-dimensional map analysis. J Chromatogr A 2009; 1216:3606-12. [DOI: 10.1016/j.chroma.2008.11.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 11/18/2008] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
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43
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Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 2009; 9:1492-510. [DOI: 10.1002/pmic.200800389] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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44
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Jmeian Y, El Rassi Z. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids for in-depth proteomics analysis. Electrophoresis 2009; 30:249-61. [DOI: 10.1002/elps.200800639] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Righetti PG, Boschetti E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. MASS SPECTROMETRY REVIEWS 2008; 27:596-608. [PMID: 18481254 DOI: 10.1002/mas.20178] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The present review covers modern aspects of combinatorial peptide ligand libraries (CPLL), as used to analyze the "low-abundance proteome" in association with mass spectrometry. First, the capturing properties of baits of different lengths (from single amino acid to hexa-peptides) are described to show that a plateau is rapidly reached above a tetra-peptide in length, thus confirming the validity of having adopted hexapeptides for the considered application. The mechanism of interaction with proteins from very complex proteomes and the ability to decrease the dynamic concentration range is demonstrated with the help of mass spectrometry analysis. Examples are given on how treatment with CPLLs dramatically improves the detectability of peptides in mass spectrometry analysis, permitting detection of a very large number of proteins as compared with control, untreated samples. The use of complementary libraries is discussed with the aim to discover additional low-abundance species that escaped the first library. A discussion on the possibility to discover extremely rare gene products, and the quantitative aspect of the technology when associated with mass spectrometry is also provided. Some insights on the applications for hidden, low-abundance biomarkers are also presented.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Polytechnic of Milano, 20131 Milan, Italy.
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Boschetti E, Righetti PG. The ProteoMiner in the proteomic arena: A non-depleting tool for discovering low-abundance species. J Proteomics 2008; 71:255-64. [DOI: 10.1016/j.jprot.2008.05.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 05/20/2008] [Accepted: 05/22/2008] [Indexed: 10/22/2022]
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Fang X, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J Proteomics 2008; 71:284-303. [PMID: 18619565 DOI: 10.1016/j.jprot.2008.06.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/24/2008] [Accepted: 06/24/2008] [Indexed: 12/24/2022]
Abstract
Protein separation or enrichment is one of the rate-limiting steps in proteomic studies. Specific capture and removal of highly-abundant proteins (HAP) with large sample-handling capacities are in great demand for enabling detection and analysis of low-abundant proteins (LAP). How to grasp and enrich these specific proteins or LAP in complex protein mixtures is also an outstanding challenge for biomarker discovery and validation. In response to these needs, various approaches for removal of HAP or capture of LAP in biological fluids, particularly in plasma or serum, have been developed. Among them, immunoaffinity subtraction methods based upon polyclonal IgY or IgG antibodies have shown to possess unique advantages for proteomic analysis of plasma, serum and other biological samples. In addition, other affinity methods that use recombinant proteins, lectins, peptides, or chemical ligands have also been developed and applied to LAP capture or enrichment. This review discusses in detail the need to put technologies and methods in affinity subtraction or enrichment into a context of proteomic and systems biology as "Separomics" and provides a prospective of affinity-mediated proteomics. Specific products, along with their features, advantages, and disadvantages will also be discussed.
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Bachi A, Simó C, Restuccia U, Guerrier L, Fortis F, Boschetti E, Masseroli M, Righetti PG. Performance of Combinatorial Peptide Libraries in Capturing the Low-Abundance Proteome of Red Blood Cells. 2. Behavior of Resins Containing Individual Amino Acids. Anal Chem 2008; 80:3557-65. [DOI: 10.1021/ac8001353] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Angela Bachi
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Carolina Simó
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Umberto Restuccia
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Luc Guerrier
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Frederic Fortis
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Egisto Boschetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Marco Masseroli
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
| | - Pier Giorgio Righetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Polytechnic of Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Department of Electronics and Informatics, Polytechnic of Milano, 20133 Milano, Italy
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