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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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2
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Stastna M. Continuous flow electrophoretic separation - Recent developments and applications to biological sample analysis. Electrophoresis 2019; 41:36-55. [PMID: 31650578 DOI: 10.1002/elps.201900288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 01/23/2023]
Abstract
Continuous flow electrophoretic separation with continuous sample loading provides the advantage of processing volumes of any sizes, as well as the benefit of a real-time monitoring and optimization of the separation process. In addition, the spatial separation of the sample enables collecting multiple separated components simultaneously and in a continuous manner. The separation is usually performed in mild buffers without organic solvents and detergents (sample biological activity is retained) and it is carried out without usage of a solid support in the separation space preventing the interaction of the sample with it (high sample recovery). The method is used for the separation of proteins/peptides in proteomic applications, and its great applicability is to the separation of the cells, cellular organelles, vesicles, membrane fragments, and DNA. This review focuses on the electrophoretic separation performed in a continuous flow and it describes various electrophoretic modes and instrumental setups. Recent developments in methodology and instrumentation, the integration with other techniques, and the application to the biological sample analysis are discussed as well.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
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3
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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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4
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Torres SMF, Furrow E, Souza CP, Granick JL, de Jong EP, Griffin TJ, Wang X. Salivary proteomics of healthy dogs: An in depth catalog. PLoS One 2018; 13:e0191307. [PMID: 29329347 PMCID: PMC5766244 DOI: 10.1371/journal.pone.0191307] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/02/2018] [Indexed: 12/19/2022] Open
Abstract
Objective To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups. Methods 36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups). Saliva collected from dogs was pooled by phylogeny group and analyzed using nanoscale liquid chromatography-tandem mass spectrometry. Resulting tandem mass spectra were compared to databases for identification of endogenous peptides and inferred proteins. Results 2,491 proteins and endogenous peptides were found in the saliva of healthy dogs with no periodontal disease. All dog phylogeny groups’ saliva was rich in proteins and peptides with antimicrobial functions. The ancient breeds group was distinct in that it contained unique proteins and was missing many proteins and peptides present in the other groups. Conclusions and clinical relevance Using a sophisticated nanoscale liquid chromatography-tandem mass spectrometry, we were able to identify 10-fold more salivary proteins than previously reported in dogs. Seven of the top 10 most abundant proteins or peptides serve immune functions and many more with various antimicrobial mechanisms were found. This is the most comprehensive analysis of healthy canine saliva to date, and will provide the groundwork for future studies analyzing salivary proteins and endogenous peptides in disease states.
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Affiliation(s)
- Sheila M. F. Torres
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
| | - Eva Furrow
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Clarissa P. Souza
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
- Clinical Sciences Department, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jennifer L. Granick
- Veterinary Clinical Sciences Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Ebbing P. de Jong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biochemistry and Molecular Biochemistry, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Xiong Wang
- Department of Veterinary Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, United States of America
- Minnesota Department of Health, Saint Paul, Minnesota, United States of America
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5
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Kong F, Zhang M, Chen J, Fan L, Xiao H, Liu S, Cao C. Continuous protein concentration via free-flow moving reaction boundary electrophoresis. J Chromatogr A 2017; 1508:169-175. [DOI: 10.1016/j.chroma.2017.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
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6
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Ranjbar L, Foley JP, Breadmore MC. Multidimensional liquid-phase separations combining both chromatography and electrophoresis – A review. Anal Chim Acta 2017; 950:7-31. [DOI: 10.1016/j.aca.2016.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 01/31/2023]
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7
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Abstract
The human plasma proteome represents an important secreted sub-proteome. Proteomic analysis of blood plasma with mass spectrometry is a challenging task. The high complexity and wide dynamic range of proteins as well as the presence of several proteins at very high concentrations complicate the profiling of the human plasma proteome. The peptidome (or low-molecular-weight fraction, LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based markers of disease. Peptides are generated by active synthesis and proteolytic processing, often yielding proteolytic fragments that mediate a variety of physiological and pathological functions. As such, degradomic studies, investigating cleavage products via peptidomics and top-down proteomics in particular, have warranted significant research interest. However, due to their molecular weight, abundance, and solubility, issues with identifying specific cleavage sites and coverage of peptide fragments remain challenging. Peptidomics is currently focused toward comprehensively studying peptides cleaved from precursor proteins by endogenous proteases. This protocol outlines a standardized rapid and reproducible procedure for peptidomic profiling of human plasma using centrifugal ultrafiltration and mass spectrometry. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration (cellulose triacetate membrane) for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration, and temperature to facilitate recovery >95% and enrichment of the human plasma peptidome. This method serves as a comprehensive and facile process to enrich and identify a key, underrepresented sub-proteome of human blood plasma.
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8
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Reciprocating free-flow isoelectric focusing device for preparative separation of proteins. J Chromatogr A 2015; 1422:318-324. [DOI: 10.1016/j.chroma.2015.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022]
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9
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Chandrashekaran IR, Mohanty B, Linossi EM, Dagley LF, Leung EWW, Murphy JM, Babon JJ, Nicholson SE, Norton RS. Structure and Functional Characterization of the Conserved JAK Interaction Region in the Intrinsically Disordered N-Terminus of SOCS5. Biochemistry 2015; 54:4672-82. [PMID: 26173083 DOI: 10.1021/acs.biochem.5b00619] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
SOCS5 can negatively regulate both JAK/STAT and EGF-receptor pathways and has therefore been implicated in regulating both the immune response and tumorigenesis. Understanding the molecular basis for SOCS5 activity may reveal novel ways to target key components of these signaling pathways. The N-terminal region of SOCS5 coordinates critical protein interactions involved in inhibition of JAK/STAT signaling, and a conserved region within the N-terminus of SOCS5 mediates direct binding to the JAK kinase domain. Here we have characterized the solution conformation of this conserved JAK interaction region (JIR) within the largely disordered N-terminus of SOCS5. Using nuclear magnetic resonance (NMR) chemical shift analysis, relaxation measurements, and NOE analysis, we demonstrate the presence of preformed structural elements in the JIR of mouse SOCS5 (mSOCS5175-244), consisting of an α-helix encompassing residues 224-233, preceded by a turn and an extended structure. We have identified a phosphorylation site (Ser211) within the JIR of mSOCS5 and have investigated the role of phosphorylation in modulating JAK binding using site-directed mutagenesis.
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Affiliation(s)
- Indu R Chandrashekaran
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Biswaranjan Mohanty
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Edmond M Linossi
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Laura F Dagley
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Eleanor W W Leung
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - James M Murphy
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jeffrey J Babon
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Sandra E Nicholson
- §The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Raymond S Norton
- †Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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10
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Abstract
The technique of proteolytically digesting a sample and identifying its protein components by liquid chromatography followed by mass spectrometry (LC-MS) is a widely used analytical tool. Prior fractionation by isoelectric focusing (IEF) may be performed to increase the depth of proteome coverage. Here, we describe a method for in-gel IEF separation of a proteolytic digest that utilizes commercially available immobilized pH gradient (IPG) strips and a widely used IEF instrument.
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11
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Moreda-Piñeiro A, García-Otero N, Bermejo-Barrera P. A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment. Anal Chim Acta 2014; 836:1-17. [PMID: 24974865 DOI: 10.1016/j.aca.2014.04.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS) techniques are commonly used for protein identification and further analysis of selected protein spots after high resolution 2-D electrophoresis. Complementary gel-free approaches have been developed during the last few years and have shown to be useful tools in modern proteomics. The development and application of various gel-free electrophoresis devices for performing protein fractionation according to the pI differences is therefore a topic of interest. This review describes the current state of isoelectric focusing (IEF) gel-free electrophoresis based on the Agilent offgel 3100 fractionator. The review includes, therefore, (i) an overview on IEF as well as other previous IEF gel-free electrophoresis developments; (ii) offgel fundamentals and future trends; (iii) advantages and disadvantages of current offgel procedures; (iv) requirements of isolated protein pellets for further offgel fractionation; (v) offgel fraction requirements to perform the second dimensional analysis by advance electrophoresis and chromatographic techniques; and (vi) effect of the offgel operating conditions on the stability of metal-protein complexes.
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Affiliation(s)
- Antonio Moreda-Piñeiro
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain.
| | - Natalia García-Otero
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
| | - Pilar Bermejo-Barrera
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
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12
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Geiger M, Frost NW, Bowser MT. Comprehensive Multidimensional Separations of Peptides Using Nano-Liquid Chromatography Coupled with Micro Free Flow Electrophoresis. Anal Chem 2014; 86:5136-42. [DOI: 10.1021/ac500939q] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew Geiger
- Department of Chemistry, University of Minnesota, 207 Pleasant
Street SE, Minneapolis, Minnesota 55455, United States
| | - Nicholas W. Frost
- Department of Chemistry, University of Minnesota, 207 Pleasant
Street SE, Minneapolis, Minnesota 55455, United States
| | - Michael T. Bowser
- Department of Chemistry, University of Minnesota, 207 Pleasant
Street SE, Minneapolis, Minnesota 55455, United States
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13
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Skandarajah AR, Moritz RL, Tjandra JJ, Simpson RJ. Proteomic analysis of colorectal cancer: discovering novel biomarkers. Expert Rev Proteomics 2014; 2:681-92. [PMID: 16209648 DOI: 10.1586/14789450.2.5.681] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Colorectal cancer is one of the most common cancers in the Western world. When detected at an early stage, the majority of cancers can be cured with current treatment modalities. However, most cancers present at an intermediate stage. The discovery of sensitive and specific biomarkers has the potential to improve preclinical diagnosis of primary and recurrent colorectal cancer, and holds the promise of prognostic and therapeutic application. Current biomarkers such as carcinoembryonic antigen lack sensitivity and specificity for general population screening. This review aims to highlight the role of current proteomic technologies in the discovery and validation of potential biomarkers with a view to translation to the clinic.
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Affiliation(s)
- Anita R Skandarajah
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Grattan Street, Parkville 3050, Victoria, Australia.
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14
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Wang Y, Balgley BM, Lee CS. Tissue proteomics using capillary isoelectric focusing-based multidimensional separations. Expert Rev Proteomics 2014; 2:659-67. [PMID: 16209646 DOI: 10.1586/14789450.2.5.659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The capabilities of capillary isoelectric focusing-based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. In this article, recent advances in online integration of capillary isoelectric focusing with nano-reversed phase liquid chromatography for achieving high-resolution peptide and protein separations prior to mass spectrometry analysis are reviewed, along with its potential application to tissue proteomics. These proteome technological advances combined with recently developed tissue microdissection techniques, provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.
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Affiliation(s)
- Yueju Wang
- Calibrant Biosystems, Gaithersburg, MD 20878, USA.
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15
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The potential of electrophoretic sample pretreatment techniques and new instrumentation for bioanalysis, with a focus on peptidomics and metabolomics. Bioanalysis 2013; 5:2785-801. [DOI: 10.4155/bio.13.254] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This Review highlights the potential of new electromigration-based sample pretreatment techniques for bioanalysis. Sample pretreatment is a challenging part of the analytical workflow, especially in the fields of peptidomics and metabolomics, where the analytes are very diverse, both in physicochemical properties and in endogenous concentration. Electromigration-based techniques have several strengths, such as fast selective analyte concentration and that complementary information on the content of a sample can be obtained when compared with more conventional (chromatography-based) techniques. In the past decade, various new electromigration-based sample pretreatment techniques have been developed, and importantly, new instrumental setups. In this Review, we provide an introduction on electromigration and its strengths. Then, selected examples of electromigration-based sample pretreatment techniques and instrumentation are discussed, namely free-flow electrophoresis, isoelectric focusing, isotachophoresis, electrodialysis, electromembrane extraction and electroextraction. Finally, the promising perspectives of electromigration-based sample pretreatment techniques are outlined.
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16
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Abstract
Prostate cancer (PCa), a highly heterogeneous disease, is the one of the leading cause of morbidity and mortality in the developed countries. Historically used biomarkers such as prostatic acid phosphatase (PAP), serum prostate-specific antigen (PSA), and its precursor have not stood the challenge of sensitivity and specificity. At present, there is need to re-evaluate the approach to diagnose and monitor PCa. To this end, molecular markers that can accurately identify men with PCa at an early stage, and those who would benefit from early therapeutic intervention, are the need of the hour. There has been unprecedented progress in the development of new PCa biomarkers through advancements in proteomics, tissue DNA and protein/RNA microarray, identification of microRNA, isolation of circulating tumor cells, and tumor immunohistochemistry. This review will examine the current status of prostate cancer biomarkers with emphasis on emerging biomarkers by evaluating their diagnostic and prognostic potentials.
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Affiliation(s)
- Tapan Bhavsar
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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17
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Swearingen KE, Moritz RL. High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics. Expert Rev Proteomics 2013. [PMID: 23194268 DOI: 10.1586/epr.12.50] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that separates gas-phase ions by their behavior in strong and weak electric fields. FAIMS is easily interfaced with electrospray ionization and has been implemented as an additional separation mode between liquid chromatography (LC) and mass spectrometry (MS) in proteomic studies. FAIMS separation is orthogonal to both LC and MS and is used as a means of on-line fractionation to improve the detection of peptides in complex samples. FAIMS improves dynamic range and concomitantly the detection limits of ions by filtering out chemical noise. FAIMS can also be used to remove interfering ion species and to select peptide charge states optimal for identification by tandem MS. Here, the authors review recent developments in LC-FAIMS-MS and its application to MS-based proteomics.
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18
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 970] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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19
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Millioni R, Franchin C, Tessari P, Polati R, Cecconi D, Arrigoni G. Pros and cons of peptide isolectric focusing in shotgun proteomics. J Chromatogr A 2013; 1293:1-9. [PMID: 23639126 DOI: 10.1016/j.chroma.2013.03.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 02/03/2023]
Abstract
In shotgun proteomics, protein mixtures are proteolytically digested before tandem mass spectrometry (MS/MS) analysis. Biological samples are generally characterized by a very high complexity, therefore a step of peptides fractionation before the MS analysis is essential. This passage reduces the sample complexity and increases its compatibility with the sampling performance of the instrument. Among all the existing approaches for peptide fractionation, isoelectric focusing has several peculiarities that are theoretically known but practically rarely exploited by the proteomics community. The main aim of this review is to draw the readers' attention to these unique qualities, which are not accessible with other common approaches, and that represent important tools to increase confidence in the identification of proteins and some post-translational modifications. The general characteristics of different methods to perform peptide isoelectric focusing with natural and artificial pH gradients, the existing instrumentation, and the informatics tools available for isoelectric point calculation are also critically described. Finally, we give some general conclusions on this strategy, underlying its principal limitations.
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Affiliation(s)
- Renato Millioni
- Department of Medicine, University of Padova, Via Giustiniani 2, 35121 Padova, Italy; Proteomics Center of Padova University, VIMM and Padova University Hospital, Via G. Orus 2/B, 35129 Padova, Italy.
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20
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Choi YS. Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome. Arch Pharm Res 2012; 35:1861-70. [PMID: 23212627 DOI: 10.1007/s12272-012-1102-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/30/2012] [Accepted: 08/21/2012] [Indexed: 11/24/2022]
Abstract
In the last decade, there has been a dramatic progress in separation techniques, mass spectrometry, and bioinformatics, and this progress has significantly improved the techniques on protein analysis. However, the analysis of low-abundance proteins is still challenging because of the limited performance in the method of choice compared to the complexity and the vast dynamic range of biological samples. Since this issue is a big obstacle in most proteomics investigations, great interest has been paid recently to various techniques, such as multi-dimensional analysis, specific peptide selection, high-abundance protein depletion, ligand library treatment, to address this challenge. Therefore, here, the author reviews recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome, mainly focusing on their methods and perspectives.
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Affiliation(s)
- Yong Seok Choi
- College of Pharmacy, Dankook University, Cheonan 330-714, Korea.
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21
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Gaillard G, Trezzi JP, Betsou F. Validation of free flow electrophoresis as a novel plasma and serum processing and fractionation method in biobanking. Biopreserv Biobank 2012; 10:349-56. [PMID: 24849883 DOI: 10.1089/bio.2012.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Free flow electrophoresis (FFE) is a fractionation method, based on isoelectric focusing (IEF). We validate the reproducibility of the method and show that it can be applied by biobanks in order to fractionate fluid biospecimens efficiently and reproducibly and to facilitate downstream proteomic applications. We also propose a simple method allowing researchers to assess the reproducibility of each FFE run.
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22
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Duša F, Křenková J, Moravcová D, Kahle V, Šlais K. Divergent-flow isoelectric focusing for separation and preparative analysis of peptides. Electrophoresis 2012; 33:1687-94. [DOI: 10.1002/elps.201100587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jana Křenková
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Vladislav Kahle
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
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23
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Doucette AA, Tran JC, Wall MJ, Fitzsimmons S. Intact proteome fractionation strategies compatible with mass spectrometry. Expert Rev Proteomics 2012; 8:787-800. [PMID: 22087661 DOI: 10.1586/epr.11.67] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Proteome fractionation refers to separation at the level of intact proteins. Proteome fractionation may precede sample digestion and subsequent peptide-level separation and detection (i.e., bottom-up mass spectrometry [MS]). For top-down MS, proteome fractionation acts as a stand-alone separation platform, since intact proteins are directly analyzed by the mass spectrometer. Regardless of the MS identification strategy, separation of intact proteins has clear benefits as a result of decreasing sample complexity. However, this stage of the workflow also creates considerable challenges, which are generally absent from the counterpart peptide separation experiment. For example, maintaining protein solubility is a key concern before, during and after separation. To this end, surfactants such as sodium dodecyl sulfate may be employed during fractionation, so long as they are eliminated prior to MS. In this article, current strategies for proteome fractionation in a MS-compatible format are reviewed, illustrating the challenges and outlooks on this important aspect of proteomics.
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Affiliation(s)
- Alan A Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada.
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Rafalko A, Dai S, Hancock WS, Karger BL, Hincapie M. Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma. J Proteome Res 2012; 11:808-17. [PMID: 22098410 PMCID: PMC3656385 DOI: 10.1021/pr2006704] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an important tool for biomarker verification studies in highly complex biological samples. Analyte enrichment or sample fractionation is often necessary to reduce sample complexity and improve sensitivity of SRM for quantitation of clinically relevant biomarker candidates present at the low ng/mL range in blood. In this paper, we describe an alternative method for sample preparation for LC-SRM MS, which does not rely on availability of antibodies. This new platform is based on selective enrichment of proteotypic peptides from complex biological peptide mixtures via isoelectric focusing (IEF) on a digital ProteomeChip (dPC) for SRM quantitation using a triple quadrupole (QQQ) instrument with an LC-Chip (Chip/Chip/SRM). To demonstrate the value of this approach, the optimization of the Chip/Chip/SRM platform was performed using prostate specific antigen (PSA) added to female plasma as a model system. The combination of immunodepletion of albumin and IgG with peptide fractionation on the dPC, followed by SRM analysis, resulted in a limit of quantitation of PSA added to female plasma at the level of ∼1-2.5 ng/mL with a CV of ∼13%. The optimized platform was applied to measure levels of PSA in plasma of a small cohort of male patients with prostate cancer (PCa) and healthy matched controls with concentrations ranging from 1.5 to 25 ng/mL. A good correlation (r(2) = 0.9459) was observed between standard clinical ELISA tests and the SRM-based assay. Our data demonstrate that the combination of IEF on the dPC and SRM (Chip/Chip/SRM) can be successfully applied for verification of low abundance protein biomarkers in complex samples.
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Affiliation(s)
- Agnes Rafalko
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Shujia Dai
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - William S. Hancock
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Barry L. Karger
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Marina Hincapie
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology Northeastern University, 360 Huntington Avenue, Boston, MA 02115
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Stastna M, Van Eyk JE. Investigating the secretome: lessons about the cells that comprise the heart. CIRCULATION. CARDIOVASCULAR GENETICS 2012; 5:o8-o18. [PMID: 22337932 PMCID: PMC3282018 DOI: 10.1161/circgenetics.111.960187] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cell/environment interface is composed of the proteins of plasma membrane which face the extracellular space and by the proteins secreted directly by the cell of origin or by neighboring cells. The secreted proteins can act as extracellular matrix proteins and/or autocrine/paracrine proteins. This report discusses the technical aspects involved in the identification and characterization of the secreted proteins of specific cell types that comprise the heart. These aspects include the culturing of the cells, cell co-culturing and quantitative labeling, conditioned media collection and dealing with high abundant serum proteins, post-translational modification enrichment, the use of protein separation methods and mass spectrometry, protein identification and validation and the incorporation of pathway analysis to better understand the novel discovery on the background of already known experimental biological systems. The proteomic methods have the solid emplacement in cardiovascular research and the identification of proteins secreted by cardiac cells has been used in various applications such as determination the specificity between secretomes of different cell types, e.g. cardiac stem cells and cardiac myocytes, for the global secretome screening of e.g. human arterial smooth muscle cells, for the mapping of the beneficial effect of conditioned medium of one cell type on the other cell type, e.g. conditioned medium of human mesenchymal stem cells on cardiac myocytes, and for the searching the candidate paracrine factors and potential biomarkers.
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Affiliation(s)
- Miroslava Stastna
- Johns Hopkins Bayview Proteomics Center, Department of Medicine, Division of Cardiology, School of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA.
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26
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Petriz BA, Gomes CP, Rocha LAO, Rezende TMB, Franco OL. Proteomics applied to exercise physiology: A cutting-edge technology. J Cell Physiol 2011; 227:885-98. [DOI: 10.1002/jcp.22809] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Zhou H, Ning Z, E. Starr A, Abu-Farha M, Figeys D. Advancements in Top-Down Proteomics. Anal Chem 2011; 84:720-34. [DOI: 10.1021/ac202882y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Zhibing Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
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Walowski B, Hüttner W, Wackerbarth H. Generation of a miniaturized free-flow electrophoresis chip based on a multi-lamination technique—isoelectric focusing of proteins and a single-stranded DNA fragment. Anal Bioanal Chem 2011; 401:2465-71. [DOI: 10.1007/s00216-011-5353-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 12/01/2022]
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Abstract
Micro free flow electrophoresis (micro-FFE) is a continuous micro-separation or preparation technique, which has been applied in the analysis of biomolecules, such as cells, sub cell organics and proteins. In this review, the recent progresses in micro FFE are summarized, with emphasis on the design of microchips, the separation modes and the applications of micro-FFE. Furthermore, the further developments of micro-FFE are prospected.
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Affiliation(s)
- Pingli Wang
- National Chromatographic R. & A. Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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30
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Greening DW, Simpson RJ. Low-molecular weight plasma proteome analysis using centrifugal ultrafiltration. Methods Mol Biol 2011; 728:109-124. [PMID: 21468943 DOI: 10.1007/978-1-61779-068-3_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The low-molecular weight fraction (LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based biomarkers of disease. This protocol outlines a standardized procedure for the rapid/reproducible LMF profiling of human plasma samples using centrifugal ultrafiltration fractionation, followed by 1D-SDS-PAGE separation and nano-LC-MS/MS. Ultrafiltration is a convective process that uses anisotropic semipermeable membranes to separate macromolecular species on the basis of size. We have optimized centrifugal ultrafiltration for plasma fractionation with respect to buffer and solvent composition, centrifugal force, duration and temperature to facilitate >95% recovery, and enrichment of low-M (r) components from human plasma. Using this protocol, >260 unique peptides can be identified from a single plasma profiling experiment using 100 μL of plasma (Greening and Simpson, J Proteomics 73:637-648, 2010). The efficacy of this method is demonstrated by the identification, for the first time, of several plasma proteins (e.g., protein KIAA0649 (Q9Y4D3), rheumatoid factor D5, serine protease inhibitor A3, and transmembrane adapter protein PAG) previously not reported in extant high-confidence Human Proteome Organization Plasma Proteome Project datasets.
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Affiliation(s)
- David W Greening
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Australia
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31
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Moritz RL, Skandarajah AR, Ji H, Simpson RJ. Proteomic analysis of colorectal cancer: prefractionation strategies using two-dimensional free-flow electrophoresis. Comp Funct Genomics 2010; 6:236-43. [PMID: 18629191 PMCID: PMC2447484 DOI: 10.1002/cfg.477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 03/16/2005] [Accepted: 03/17/2005] [Indexed: 01/21/2023] Open
Abstract
This review deals with the application of a new prefractionation tool, free-flow
electrophoresis (FFE), for proteomic analysis of colorectal cancer (CRC). CRC is a
leading cause of cancer death in the Western world. Early detection is the single most
important factor influencing outcome of CRC patients. If identified while the disease
is still localized, CRC is treatable. To improve outcomes for CRC patients there
is a pressing need to identify biomarkers for early detection (diagnostic markers),
prognosis (prognostic indicators), tumour responses (predictive markers) and disease
recurrence (monitoring markers). Despite recent advances in the use of genomic
analysis for risk assessment, in the area of biomarker identification genomic methods
alone have yet to produce reliable candidate markers for CRC. For this reason,
attention is being directed towards proteomics as a complementary analytical tool
for biomarker identification. Here we describe a proteomics separation tool, which
uses a combination of continuous FFE, a liquid-based isoelectric focusing technique, in
the first dimension, followed by rapid reversed-phase HPLC (1–6 min/analysis) in the
second dimension. We have optimized imaging software to present the FFE/RP-HPLC
data in a virtual 2D gel-like format. The advantage of this liquid based fractionation
system over traditional gel-based fractionation systems is the ability to fractionate
large quantity protein samples. Unlike 2D gels, the method is applicable to both
high-Mr proteins and small peptides, which are difficult to separate, and in the case
of peptides, are not retained in standard 2D gels.
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Affiliation(s)
- Robert L Moritz
- Joint Proteomics Laboratory Ludwig Institute for Cancer Research (Melbourne Branch), The Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
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Wang P, Zhang L, Shan Y, Cong Y, Liang Y, Han B, Liang Z, Zhang Y. Protein separation using free-flow electrophoresis microchip etched in a single step. J Sep Sci 2010; 33:2039-44. [DOI: 10.1002/jssc.201000162] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Islinger M, Eckerskorn C, Völkl A. Free-flow electrophoresis in the proteomic era: A technique in flux. Electrophoresis 2010; 31:1754-63. [DOI: 10.1002/elps.200900771] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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Meert CD, Brady LJ, Guo A, Balland A. Characterization of Antibody Charge Heterogeneity Resolved by Preparative Immobilized pH Gradients. Anal Chem 2010; 82:3510-8. [PMID: 20364842 DOI: 10.1021/ac902408r] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Charlie D. Meert
- Amgen Inc., Analytical and Formulation Sciences, 1201 Amgen Court West, Seattle, Washington 98119
| | - Lowell J. Brady
- Amgen Inc., Analytical and Formulation Sciences, 1201 Amgen Court West, Seattle, Washington 98119
| | - Amy Guo
- Amgen Inc., Analytical and Formulation Sciences, 1201 Amgen Court West, Seattle, Washington 98119
| | - Alain Balland
- Amgen Inc., Analytical and Formulation Sciences, 1201 Amgen Court West, Seattle, Washington 98119
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35
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Moseley FL, Bicknell KA, Marber MS, Brooks G. The use of proteomics to identify novel therapeutic targets for the treatment of disease. J Pharm Pharmacol 2010; 59:609-28. [PMID: 17524226 DOI: 10.1211/jpp.59.5.0001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Abstract
The completion of the Human Genome Project has revealed a multitude of potential avenues for the identification of therapeutic targets. Extensive sequence information enables the identification of novel genes but does not facilitate a thorough understanding of how changes in gene expression control the molecular mechanisms underlying the development and regulation of a cell or the progression of disease. Proteomics encompasses the study of proteins expressed by a population of cells, and evaluates changes in protein expression, post-translational modifications, protein interactions, protein structure and splice variants, all of which are imperative for a complete understanding of protein function within the cell. From the outset, proteomics has been used to compare the protein profiles of cells in healthy and diseased states and as such can be used to identify proteins associated with disease development and progression. These candidate proteins might provide novel targets for new therapeutic agents or aid the development of assays for disease biomarkers. This review provides an overview of the current proteomic techniques available and focuses on their application in the search for novel therapeutic targets for the treatment of disease.
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Affiliation(s)
- Fleur L Moseley
- School of Pharmacy, The University of Reading, Whiteknights, Reading, Berkshire, RG6 6AP, UK
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36
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Foucher AL, Craft DR, Gelfand CA. Application of free flow electrophoresis to the analysis of the urine proteome. Methods Mol Biol 2010; 641:27-45. [PMID: 20407940 DOI: 10.1007/978-1-60761-711-2_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Urine is a complex fluid, which is thought to contain valuable diagnostic information regarding general health. In particular, there is great diagnostic potential in the peptide and/or protein content of urine, but the information is present in low abundance. Most traditional proteomic techniques lack sufficient sensitivity/dynamic range, especially for dilute and/or complex samples. However, orthogonal separation methods can be applied prior to protein/peptide analysis to increase the success rate of urine proteomic studies and access this potentially valuable information. In this chapter, we describe isoelectric focusing (IEF) of intact urine proteins, via free flow electrophoresis (FFE), prior to typical peptide-based mass spectrometry analysis, facilitating the deep analysis of urine protein detection and identification, for biomarker discovery. Our work demonstrates that such an approach can be used as a preprocessing step and can be integrated into a workflow for the successful identification of protein components (biomarkers) from urine.
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37
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You J, Cozzi P, Walsh B, Willcox M, Kearsley J, Russell P, Li Y. Innovative biomarkers for prostate cancer early diagnosis and progression. Crit Rev Oncol Hematol 2010; 73:10-22. [DOI: 10.1016/j.critrevonc.2009.02.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 02/05/2009] [Accepted: 02/25/2009] [Indexed: 02/07/2023] Open
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Neustadt M, Costina V, Kupfahl C, Buchheidt D, Eckerskorn C, Neumaier M, Findeisen P. Characterization and identification of proteases secreted by Aspergillus fumigatus using free flow electrophoresis and MS. Electrophoresis 2009; 30:2142-50. [PMID: 19582717 DOI: 10.1002/elps.200800700] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of life-threatening invasive aspergillosis in neutropenic patients remains challenging because current laboratory methods have limited diagnostic sensitivity and/or specificity. Aspergillus species are known to secrete various pathogenetically relevant proteases and the monitoring of their protease activity in serum specimens might serve as a new diagnostic approach.For the characterization and identification of secreted proteases, the culture supernatant of Aspergillus fumigatus was fractionated using free flow electrophoresis (Becton Dickinson). Protease activity of separated fractions was measured using fluorescently labeled reporter peptides. Fractions were also co-incubated in parallel with various protease inhibitors that specifically inhibit a distinct class of proteases e.g. metallo- or cysteine-proteases. Those fractions with high protease activity were further subjected to LC-MS/MS analysis for protease identification. The highest protease activity was measured in fractions with an acidic pH range. The results of the 'inhibitor-panel' gave a clear indication that it is mainly metallo- and serine-proteases that are involved in the degradation of reporter peptides. Furthermore, several proteases were identified that facilitate the optimization of reporter peptides for functional protease profiling as a diagnostic tool for invasive aspergillosis.
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Affiliation(s)
- Madlen Neustadt
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
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Abstract
We review microfluidic devices designed for multidimensional sample analysis, with a primer on relevant theory, an emphasis on protein analysis, and an eye towards future improvements and challenges to the field. Image shows results of an on-chip IEF-CE separation of a protein mixture; unpublished surface plot data from A. E. Herr.
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Affiliation(s)
- Samuel Tia
- Department of Bioengineering, University of California, Berkeley, 308B Stanley Hall, MC # 1762 Berkeley, CA 94720-1762, USA
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40
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Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
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Kasicka V. From micro to macro: conversion of capillary electrophoretic separations of biomolecules and bioparticles to preparative free-flow electrophoresis scale. Electrophoresis 2009; 30 Suppl 1:S40-52. [PMID: 19517515 DOI: 10.1002/elps.200900156] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This invited contribution in the special issue of Electrophoresis published in celebration of the 30th Anniversary of this journal reflects the impact of our milestone paper [Prusík, Z., Kasicka, V., Mudra, P., Stepánek, J., Smékal, O., Hlavácek, J., Electrophoresis 1990, 11, 932-936] in the area of conversion of microscale analytical and micropreparative CE separations of biomolecules and bioparticles into (macro)preparative free-flow electrophoresis (FFE) scale on the basis of a correlation between CE and FFE methods. In addition to the survey of advances in the relatively narrow field of CE-FFE correlation and CE-FFE conversion, a comprehensive review of the recent developments of micropreparative CE and (macro)preparative FFE techniques is also presented and applications of these techniques to micro- and (macro)preparative separations and purifications of biomolecules and bioparticles are demonstrated. The review covers the period since the year of publication of the above paper, i.e. ca. the last 20 years.
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Affiliation(s)
- Václav Kasicka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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42
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Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci 2009; 32:771-98. [PMID: 19219839 DOI: 10.1002/jssc.200800622] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine at East Carolina University, Greenville, NC, USA.
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43
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Abstract
Membranous vesicles are constitutively released by a multitude of cell types. Following fusion of multivesicular bodies with the plasma membrane, endocytic vesicles, 30-90 nm in size termed exosomes are released extracellularly. Whilst several groups have reported the presence of exosomes in cell-culture conditioned medium, their biological and physiological functions still remain unclear. In addition, exosomes have been detected in body fluids associated with disease, further demonstrating their potential as diagnostic biomarkers. This protocol employs size filtration followed by ultracentrifugation to isolate and purify exosomes from the colon carcinoma cell line LIM 1215. Morphological visualisation and characterisation is based on electron microscopy and western blotting, whilst protein identification is achieved using a combination of 1D SDS-PAGE and LC-MS/MS.
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44
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Evaluation of a solution isoelectric focusing protocol as an alternative to ion exchange chromatography for charge-based proteome prefractionation. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:807-13. [DOI: 10.1016/j.jchromb.2009.02.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 12/10/2008] [Accepted: 02/07/2009] [Indexed: 11/19/2022]
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45
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Horká M, Horký J, Matoušková H, Šlais K. Free flow and capillary isoelectric focusing of bacteria from the tomatoes plant tissues. J Chromatogr A 2009; 1216:1019-24. [DOI: 10.1016/j.chroma.2008.12.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 11/16/2022]
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46
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Nissum M, Foucher AL. Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis. Expert Rev Proteomics 2008; 5:571-87. [PMID: 18761468 DOI: 10.1586/14789450.5.4.571] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to ease of accessibility, plasma has become the sample of choice for proteomics studies directed towards biomarker discovery intended for use in diagnostics, prognostics and even in theranostics. The result of these extensive efforts is a long list of potential biomarkers, very few of which have led to clinical utility. Why have so many potential biomarkers failed validation? Herein, we address certain issues encountered, which complicate biomarker discovery efforts originating from plasma. The advantages of stabilizing the sample at collection by the addition of protease inhibitors are discussed. The principles of free-flow electrophoresis (FFE) separation are provided together with examples applying to various studies. Finally, particular attention is given to plasma or serum analysis using multidimensional separation strategies into which the FFE is incorporated. The advantages of using FFE separation in these workflows are discussed.
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Affiliation(s)
- Mikkel Nissum
- BD Diagnostics, Am Klopferspitz 19a, D-82152 Martinsried, Germany.
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47
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Stastna M, Slais K. Single-input divergent flow IEF for preparative analysis of proteins. Electrophoresis 2008; 29:4503-7. [DOI: 10.1002/elps.200800293] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Cargile BJ, Sevinsky JR, Essader AS, Eu JP, Stephenson JL. Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects. Electrophoresis 2008; 29:2768-78. [PMID: 18615785 DOI: 10.1002/elps.200700701] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Current algorithms for the calculation of peptide or protein pI, based on the charge associated with individual amino acids, can calculate pI values to within +/-0.2 pI units. Here, we present a new pI calculation algorithm that takes into account the effect of adjacent amino acids on the pI value. The algorithm accounts for the effect of adjacent amino acids+/-3 residues away from a charged aspartic or glutamic acid, as well as effects on the free C terminus, and applies a correction term to the corresponding pK values. The correction increments are derived from a 5000-peptide training set using a genetic optimization approach. The accuracy of the new pI values obtained with this method approaches the error associated with the manufacture of the IPG strip (<+/-0.03 pI units). The approach is demonstrated for cytosolic cell extracts derived from the breast-cancer cell line DU4475, and from membrane preparations from human lung-tissue samples. One potential application of a more highly accurate pI calculation is data filtering of MS/MS outputs that will allow for more complex database searches including gene finding, and validation, and detection of coding single-nucleotide polymorphisms in their expressed form.
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Affiliation(s)
- Benjamin J Cargile
- Mass Spectrometry Research Program, Research Triangle Institute, Research Triangle Park, NC, USA
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Vaezzadeh AR, Hernandez C, Vadas O, Deshusses JJM, Lescuyer P, Lisacek F, Hochstrasser DF. PICarver: a software tool and strategy for peptides isoelectric focusing. J Proteome Res 2008; 7:4336-45. [PMID: 18783261 DOI: 10.1021/pr8002672] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The use of isoelectric focusing as first dimension of separation is a new trend in shotgun proteomics. In all applications using this approach, peptides are separated into equitable fractions, whereas theoretical distribution of peptides according to p I is heterogeneous. We present the development of a new tool and strategy that generates a fractionation scheme resulting in almost even distribution of peptides per fraction, based on theoretical and experimental data. The "pICarver" software tool also increases the throughput of the approach by reducing the number of fractions and merging the peptide-poor regions. A set of isoelectric point fluorescent peptide markers was also developed in combination with the pICarver program to calibrate the pH gradient of commercially available strips. These markers enhanced the precision of pICarver predications. The overall strategy allowed detecting false positive identification and post-translational modifications. The software tool is freely available on www.expasy.org/tools/pICarver.
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Affiliation(s)
- Ali R Vaezzadeh
- Biomedical Proteomics Research Group, Department of Bioinformatics and Structural Biology, Geneva University, 1 Michel Servet, 1211 Geneva, Switzerland
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Choi CW, Hong YS, Kim SI. Application of free-flow electrophoresis/2-dimentional gel electrophoresis for fractionation and characterization of native proteome of Pseudomonas putida KT2440. J Microbiol 2008; 46:448-55. [DOI: 10.1007/s12275-008-0063-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 06/03/2008] [Indexed: 10/21/2022]
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