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Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery. Bioanalysis 2019; 11:1799-1812. [PMID: 31617391 DOI: 10.4155/bio-2019-0145] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
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Cangelosi D, Resaz R, Petretto A, Segalerba D, Ognibene M, Raggi F, Mastracci L, Grillo F, Bosco MC, Varesio L, Sica A, Colombo I, Eva A. A Proteomic Analysis of GSD-1a in Mouse Livers: Evidence for Metabolic Reprogramming, Inflammation, and Macrophage Polarization. J Proteome Res 2019; 18:2965-2978. [PMID: 31173686 DOI: 10.1021/acs.jproteome.9b00309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Davide Cangelosi
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Roberta Resaz
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Andrea Petretto
- Core Facilities-Proteomics Laboratory, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Daniela Segalerba
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Marzia Ognibene
- Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Federica Raggi
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences (DISC), Anatomic Pathology Unit, University of Genova, Viale Benedetto XV n. 6, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, National Cancer Research Institute, Largo Rosanna Benzi n. 10, 16132 Genova, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences (DISC), Anatomic Pathology Unit, University of Genova, Viale Benedetto XV n. 6, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, National Cancer Research Institute, Largo Rosanna Benzi n. 10, 16132 Genova, Italy
| | - Maria Carla Bosco
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Luigi Varesio
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
| | - Antonio Sica
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale “Amedeo Avogadro”, Largo Guido Donegani n. 2, 28100 Novara, Italy
- Humanitas Clinical and Research Center, Via Alessandro Manzoni n. 56, 20089 Rozzano, Italy
| | - Irma Colombo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti n. 9, 20133 Milano, Italy
| | - Alessandra Eva
- Laboratorio di Biologia Molecolare, IRCCS Istituto Giannina Gaslini, Via G. Gaslini n. 5, 16147 Genova, Italy
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Harpole M, Davis J, Espina V. Current state of the art for enhancing urine biomarker discovery. Expert Rev Proteomics 2017; 13:609-26. [PMID: 27232439 DOI: 10.1080/14789450.2016.1190651] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Urine is a highly desirable biospecimen for biomarker analysis because it can be collected recurrently by non-invasive techniques, in relatively large volumes. Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect, at a given time point, an individual's metabolic and pathophysiologic state. AREAS COVERED High-resolution mass spectrometry, coupled with state of the art fractionation systems are revealing the plethora of diagnostic/prognostic proteomic information existing within urinary exosomes, glycoproteins, and proteins. Affinity capture pre-processing techniques such as combinatorial peptide ligand libraries and biomarker harvesting hydrogel nanoparticles are enabling measurement/identification of previously undetectable urinary proteins. Expert commentary: Future challenges in the urinary proteomics field include a) defining either single or multiple, universally applicable data normalization methods for comparing results within and between individual patients/data sets, and b) defining expected urinary protein levels in healthy individuals.
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Affiliation(s)
- Michael Harpole
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin Davis
- b Department of Chemistry/Biochemistry , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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Cunsolo V, Fasoli E, Saletti R, Muccilli V, Gallina S, Righetti PG, Foti S. Zeus, Aesculapius, Amalthea and the proteome of goat milk. J Proteomics 2015; 128:69-82. [DOI: 10.1016/j.jprot.2015.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
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Candiano G, Santucci L, Petretto A, Lavarello C, Inglese E, Bruschi M, Ghiggeri GM, Boschetti E, Righetti PG. Widening and Diversifying the Proteome Capture by Combinatorial Peptide Ligand Libraries via Alcian Blue Dye Binding. Anal Chem 2015; 87:4814-20. [DOI: 10.1021/acs.analchem.5b00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Giovanni Candiano
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Laura Santucci
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Andrea Petretto
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Chiara Lavarello
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Elvira Inglese
- Core Facilities—Proteomics
Laboratory, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Maurizio Bruschi
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, Italy
| | - Gian Marco Ghiggeri
- Nephrology, Dialysis,
Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa 16148, 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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Wiśniewski JR, Koepsell H, Gizak A, Rakus D. Absolute protein quantification allows differentiation of cell-specific metabolic routes and functions. Proteomics 2015; 15:1316-25. [DOI: 10.1002/pmic.201400456] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 10/29/2014] [Accepted: 11/27/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Jacek R. Wiśniewski
- Biochemical Proteomics Group; Department of Proteomics and Signal Transduction; Max Planck Institute of Biochemistry; Martinsried Germany
| | - Hermann Koepsell
- Department of Molecular Plant Physiology and Biophysics; Julius von Sachs Institute; University of Würzburg; Würzburg Germany
| | - Agnieszka Gizak
- Department of Animal Molecular Physiology; Wroclaw University; Wroclaw Poland
| | - Dariusz Rakus
- Department of Animal Molecular Physiology; Wroclaw University; Wroclaw Poland
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Boschetti E, Righetti PG. Mixed-bed affinity chromatography: principles and methods. Methods Mol Biol 2015; 1286:131-158. [PMID: 25749952 DOI: 10.1007/978-1-4939-2447-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mixed-bed chromatography is far from being a well-established technology within the panoply of bioseparation tools. Composed of an assembly of distinct sorbents that are mixed in a single bed, they have been mostly developed in the last decade for the reduction of dynamic concentration range where they allowed discovering many low-copy proteins within very complex proteomes. Other interesting preparative applications of mixed-bed chromatography have since been developed. In this chapter the basic concepts first and then detailed application recipes are described for (1) the reduction of protein dynamic concentration range, (2) the removal of impurity traces at the last stage of a biopurification process, and (3) the selection and use of sorbents as mixed bed in protein purification.
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Affiliation(s)
- Egisto Boschetti
- JAM-Conseil, 9-11 rue Boutard, 92200, Neuilly sur Seine, France,
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8
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Righetti PG, Boschetti E. Sample treatment methods involving combinatorial peptide ligand libraries for improved proteomes analyses. Methods Mol Biol 2015; 1243:55-82. [PMID: 25384740 DOI: 10.1007/978-1-4939-1872-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians. Orientations for optional routes are also given according to the objective of the experimental investigations. This covers different approaches to capture proteins of very low abundance. Total protein harvestings to prevent partial losses are also described such as single exhaustive desorption and fractionated elutions for more detailed analyses. Documented results are also reported demonstrating the capability of the technology well beyond what is the common assumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
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Wang H, Sun S, Zhang Y, Chen S, Liu P, Liu B. An off-line high pH reversed-phase fractionation and nano-liquid chromatography–mass spectrometry method for global proteomic profiling of cell lines. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 974:90-5. [DOI: 10.1016/j.jchromb.2014.10.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/30/2022]
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10
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Santucci L, Bruschi M, Ghiggeri GM, Candiano G. The latest advancements in proteomic two-dimensional gel electrophoresis analysis applied to biological samples. Methods Mol Biol 2015; 1243:103-125. [PMID: 25384742 DOI: 10.1007/978-1-4939-1872-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two-dimensional gel electrophoresis (2DE) is one of the fundamental approaches in proteomics for the separation and visualization of complex protein mixtures. Proteins can be analyzed by 2DE using isoelectric focusing (IEF) in the first dimension, combined to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, gel staining (silver and Coomassie), image analysis, and 2DE gel database. High-resolution 2DE can resolve up to 5,000 different proteins simultaneously (∼2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Here, we describe the latest developments for a more complete analysis of biological fluids.
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Affiliation(s)
- Laura Santucci
- Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Largo G. Gaslini 5, Genoa, Italy
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11
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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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12
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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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13
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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14
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Optimized sample treatment protocol by solid-phase peptide libraries to enrich for protein traces. Amino Acids 2013; 45:1431-42. [DOI: 10.1007/s00726-013-1596-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/12/2013] [Indexed: 12/11/2022]
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