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Kim M, Hwang D. Network-Based Protein Biomarker Discovery Platforms. Genomics Inform 2016; 14:2-11. [PMID: 27103885 PMCID: PMC4838525 DOI: 10.5808/gi.2016.14.1.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 02/06/2023] Open
Abstract
The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, compared to control samples. Protein biomarker candidates that can serve as indicators of disease states are then selected as key molecules among these proteins. Recently, it has been addressed that cellular pathways can provide better indications of disease states than individual molecules and also network analysis of the DEPs enables effective identification of cellular pathways altered in disease conditions and key molecules representing the altered cellular pathways. Accordingly, a number of network-based approaches to identify disease-related pathways and representative molecules of such pathways have been developed. In this review, we summarize analytical platforms for network-based protein biomarker discovery and key components in the platforms.
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Affiliation(s)
- Minhyung Kim
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Korea
| | - Daehee Hwang
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Korea
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52
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Rodríguez RA, Urrego WA, Sanabria MC, Sánchez Gómez M, Umaña Perez A. IMPLEMENTACIÓN DE UNA METODOLOGÍA PARA LA SEPARACIÓN DE PROTEOMAS DE PLASMA HUMANO MEDIANTE ELECTROFORESIS BIDIMENSIONAL. REVISTA COLOMBIANA DE QUÍMICA 2016. [DOI: 10.15446/rev.colomb.quim.v44n3.55810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>El análisis proteómico en derivados sanguíneos es una importante herramienta en el descubrimiento de biomarcadores para el diagnóstico de enfermedades, aunque su caracterización exhibe desafíos relacionados con el amplio rango dinámico de las proteínas.<strong> </strong>En este trabajo se implementaron las condiciones para la separación de proteomas de plasma sanguíneo por electroforesis bidimensional. En muestras de plasma de infante y adulto se evaluaron dos sistemas de pretratamiento de la muestra para reducir el rango dinámico de las proteínas: inmunodepleción de proteínas abundantes y enriquecimiento de proteínas de baja abundancia. Los proteomas se separaron por electroforesis bidimensional y las imágenes se analizaron con el programa Melanie 7.0.<strong> </strong>Se encontró que ambos métodos de pretratamiento fueron reproducibles y permitieron ver las diferencias en los proteomas de infante y adulto, como muestran los análisis de componentes principales y de clasificación jerárquica tipo heatmap. El porcentaje de recuperación de proteínas fue mayor con la inmunodepleción en comparación con el enriquecimiento proteico.<strong> </strong>Estos resultados permitieron concluir que con la inmunodepleción, se tiene mayor control de las proteínas eliminadas y por tanto menor pérdida de información, lo que permite su aplicación en estudios exploratorios para la identificación de potenciales biomarcadores de enfermedad.</p>
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53
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Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
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Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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54
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Sample Preparation for Mass Spectrometry-Based Proteomics; from Proteomes to Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:43-62. [DOI: 10.1007/978-3-319-41448-5_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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55
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Enrichment of phosphorylated peptides and proteins by selective precipitation methods. Bioanalysis 2015; 7:243-52. [PMID: 25587840 DOI: 10.4155/bio.14.281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein phosphorylation is one of the most prominent post-translational modifications involved in the regulation of cellular processes. Fundamental understanding of biological processes requires appropriate bioanalytical methods for selectively enriching phosphorylated peptides and proteins. Most of the commonly applied enrichment approaches include chromatographic materials including Fe(3+)-immobilized metal-ion affinity chromatography or metal oxides. In the last years, the introduction of several non-chromatographic isolation technologies has increasingly attracted the interest of many scientists. Such approaches are based on the selective precipitation of phosphorylated peptides and proteins by applying various metal cations. The excellent performance of precipitation-based enrichment methods can be explained by the absence of any stationary phase, resin or sorbent, which usually leads to unspecific binding. This review provides an overview of recently published methods for the selective precipitation of phosphorylated peptides and proteins.
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56
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Development of a high-throughput UHPLC-MS/MS (SRM) method for the quantitation of endogenous glucagon from human plasma. Bioanalysis 2015; 6:3295-309. [PMID: 25534787 DOI: 10.4155/bio.14.226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Published LC-MS/MS methods are not sensitive enough to quantify endogenous levels of glucagon. RESULTS An ultra high performance liquid chromatography-MS/MS (SRM) method for the quantitation of endogenous levels glucagon was successfully developed and qualified. A novel 2D extraction procedure was used to reduce matrix suppression, background noise and interferences. Glucagon levels in samples from healthy volunteers were found to agree with radioimmunoassay (RIA) derived literature values. Bland-Altman analysis showed a concentration-dependent positive bias of the LC/MS-MS assay versus an RIA. Both assays produced similar pharmacokinetic profiles, both of which were feasible considering the nature of the study. CONCLUSION Our method is the first peer reviewed LC-MS/MS method for the quantitation of endogenous levels of glucagon, and offers a viable alternative to RIA-based approaches.
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Filip S, Vougas K, Zoidakis J, Latosinska A, Mullen W, Spasovski G, Mischak H, Vlahou A, Jankowski J. Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine. PLoS One 2015. [PMID: 26208298 PMCID: PMC4514849 DOI: 10.1371/journal.pone.0133773] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.
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Affiliation(s)
- Szymon Filip
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantinos Vougas
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Agnieszka Latosinska
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
- Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - William Mullen
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
| | - Goce Spasovski
- Ss. Cyril and Methodius University in Skopje, Nephrology Department, Skopje, Former Yugoslav Republic of Macedonia
| | - Harald Mischak
- University of Glasgow Institute of Cardiovascular and Medical Sciences, Glasgow, United Kingdom
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Biotechnology Division, Athens, Greece
| | - Joachim Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research, Aachen, Germany
- * E-mail:
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Sundberg M, Bergquist J, Ramström M. High-abundant protein depletion strategies applied on dog cerebrospinal fluid and evaluated by high-resolution mass spectrometry. Biochem Biophys Rep 2015; 3:68-75. [PMID: 30338299 PMCID: PMC6189695 DOI: 10.1016/j.bbrep.2015.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/18/2015] [Accepted: 07/22/2015] [Indexed: 12/27/2022] Open
Abstract
As the number of fully sequenced animal genomes and the performance of advanced mass spectrometry-based proteomics techniques are continuously improving, there is now a great opportunity to increase the knowledge of various animal proteomes. This research area is further stimulated by a growing interest from veterinary medicine and the pharmaceutical industry. Cerebrospinal fluid (CSF) is a good source for better understanding of diseases related to the central nervous system, both in humans and other animals. In this study, four high-abundant protein depletion columns, developed for human or rat serum, were evaluated for dog CSF. For the analysis, a shotgun proteomics approach, based on nanoLC-LTQ Orbitrap MS/MS, was applied. All the selected approaches were shown to deplete dog CSF with different success. It was demonstrated that the columns significantly improved the coverage of the detected dog CSF proteome. An antibody-based column showed the best performance, in terms of efficiency, repeatability and the number of proteins detected in the sample. In total 983 proteins were detected. Of those, 801 proteins were stated as uncharacterized in the UniProt database. To the best of our knowledge, this is the so far largest number of proteins reported for dog CSF in one single study. We evaluated four high-abundant protein depletion kits on dog CSF. High abundant depletion kit developed for humans/rats can be used for dog CSF. Protein depletion of dog CSF gives extended coverage of the CSF proteome. In total, 983 dog proteins were identified in this study.
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Affiliation(s)
- Mårten Sundberg
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Margareta Ramström
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
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Adav SS, Hwa HH, de Kleijn D, Sze SK. Improving Blood Plasma Glycoproteome Coverage by Coupling Ultracentrifugation Fractionation to Electrostatic Repulsion-Hydrophilic Interaction Chromatography Enrichment. J Proteome Res 2015; 14:2828-38. [PMID: 26044363 DOI: 10.1021/acs.jproteome.5b00102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Blood plasma is considered to be an excellent source of disease biomarkers because it contains proteins, lipids, metabolites, cell, and cell-derived extracellular vesicles from different cellular origins including diseased tissues. Most secretory and membranous proteins that can be found in plasma are glycoproteins; therefore, the plasma glycoproteome is one of the major subproteomes that is highly enriched with disease biomarkers. As a result, the glycoproteome has attracted much attention in clinical proteomic research. The modification of proteins with glycans regulates a wide range of functions in biology, but profiling plasma glycoproteins on a global scale has been hampered by the presence of low stoichiometry of glycoproteins in a complex high abundance plasma proteome background and lack of effective analytical technique. This study aims to improve plasma glycoproteome coverage using pig plasma as a model sample with a two-step strategy. The first step involves fractionation of the plasma proteins using ultracentrifugation into supernatant and pellet that is believed to contain low abundant glycoproteins. In the second step, further enrichment of glycopeptides was achieved in both fractions by adopting electrostatic repulsion hydrophilic interaction chromatography (ERLIC) coupled to tandem mass spectrometry (LC-MS/MS) analysis. The coverage of enriched glycoproteins in supernatant, pellet, and whole plasma sample as control was compared. Using this simple sample fractionation approach by ultracentrifugation and further ERLIC enrichment technique, sample complexity was reduced and glycoproteome coverage was significantly enhanced in supernatant and pellet fractions (by >50%) compared with whole plasma sample. This study showed that when ultracentrifugation is coupled to ERLIC glycopeptides enrichment and glycoproteome identification are significantly improved. This study demonstrates the combination of ultracentrifugation and ERLIC as a useful method for discovering plasma glycoprotein disease biomarkers.
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Affiliation(s)
- Sunil S Adav
- †School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,‡KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Ho Hee Hwa
- §Department of Cardiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
| | | | - Siu Kwan Sze
- †School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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60
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Bormotova EA, Mil’man BL, Gupalova TV. A new approach to the depletion of albumin and immunoglobulin G from human serum. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815030047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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61
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Schoenebeck B, May C, Güldner C, Respondek G, Mollenhauer B, Hoeglinger G, Meyer HE, Marcus K. Improved preparation of nasal lavage fluid (NLF) as a noninvasive sample for proteomic biomarker discovery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:741-5. [PMID: 25680929 DOI: 10.1016/j.bbapap.2015.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Nasal lavage fluid (NLF) becomes more and more important as a noninvasive patient sample serving as a new opportunity to discover new biomarkers in diverse human diseases comprising mainly respiratory disorders. This was supported by the observation that the protein profile of NLF differs from conventional samples of i.e. whole blood, hence being capable to complement or even expand the so far biomarker index. Since sample acquisition and processing are the most crucial steps for a profound and sensitive identification we present here a modified protocol of NLF generation and measurement. We show that mild washing steps for sample generation followed by column-mediated concentration and acetone precipitation are appropriate steps to minimize serum leakage by concomitantly highlighting proteins which represent typical components of NLF. This is shown by separation of proteins via 2D-PAGE followed by LC-MS/MS as well as Gel-LC-MS/MS measurements of cut and digested protein spots/bands. SIGNIFICANCE For a better understanding of the molecular mechanisms underlying respiratory diseases NLF samples are favored sources for protein research. NLF acquisition and sample processing were impaired so far by the problem of blood serum leakage and high salt content. Here, we present a modified protocol of NLF generation leading to the display of typical inventory of NLF proteins combined with reduced salt and serum contaminants. By this, both assay reproducibility and the detection of up- or down-regulated proteins reliably can be discovered in the case of biomarker screenings in a disease versus control design. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Bodo Schoenebeck
- Abteilung für Neuroanatomie und Molekulare Hirnforschung, Medizinische Fakultaet, Ruhr-Universitaet Bochum, 44801 Bochum, Germany
| | - Caroline May
- Abteilung für Medizinische Proteomik/Bioanalytik, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, 44801 Bochum, Germany
| | - Christian Güldner
- Department of Otolaryngology, Phillips Universität, Marburg, Germany
| | - Gesine Respondek
- Department of Neurology, Technische Universität München, Munich, Germany and German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | | | - Guenter Hoeglinger
- Lehrstuhl für Translationale Neurodegeneration, Technische Universität München, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen, 81377 München, Germany
| | - Helmut E Meyer
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - Katrin Marcus
- Abteilung für Funktionelle Proteomik, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, 44801 Bochum, Germany.
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62
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High abundant protein removal from rodent blood for biomarker discovery. Biochem Biophys Res Commun 2015; 455:84-9. [PMID: 25445603 DOI: 10.1016/j.bbrc.2014.09.137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 12/17/2022]
Abstract
In order to realize the goal of stratified and/or personalized medicine in the clinic, significant advances in the field of biomarker discovery are necessary. Adding to the abundance of nucleic acid biomarkers being characterized, additional protein biomarkers will be needed to satisfy diverse clinical needs. An appropriate source for finding these biomarkers is within blood, as it contains tissue leakage factors as well as additional proteins that reside in blood that can be linked to the presence of disease. Unfortunately, high abundant proteins and complexity of the blood proteome present significant challenges for the discovery of protein biomarkers from blood. Animal models often enable the discovery of biomarkers that can later be translated to humans. Therefore, determining appropriate sample preparation of proteomic samples in rodent models is an important research goal. Here, we examined both mouse and rat blood samples (including both serum and plasma), for appropriate high abundant protein removal techniques for subsequent gel-based proteomic experiments. We assessed four methods of albumin removal: antibody-based affinity chromatography (MARS), Cibacron® Blue-based affinity depletion (SwellGel® Blue Albumin Removal Kit), protein-based affinity depletion (ProteaPrep Albumin Depletion Kit) and TCA/acetone precipitation. Albumin removal was quantified for each method and SDS-PAGE and 2-DE gels were used to quantify the number of protein spots obtained following albumin removal. Our results suggest that while all four approaches can effectively remove high abundant proteins, antibody-based affinity chromatography is superior to the other three methods.
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63
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Bladergroen MR, van der Burgt YEM. Solid-phase extraction strategies to surmount body fluid sample complexity in high-throughput mass spectrometry-based proteomics. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:250131. [PMID: 25692071 PMCID: PMC4322654 DOI: 10.1155/2015/250131] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 05/08/2023]
Abstract
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential. Here we present high-throughput sample preparation solutions for balancing the speed of current MS-acquisitions and the time needed for analytical workup of body fluids. The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches. Various sample preparation methods that involve solid-phase extraction (SPE) including affinity enrichment strategies have been automated. Obtained peptide and protein fractions can be mass analyzed by direct infusion into an electrospray ionization (ESI) source or by means of matrix-assisted laser desorption ionization (MALDI) without further need of time-consuming liquid chromatography (LC) separations.
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Affiliation(s)
- Marco R. Bladergroen
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
- *Yuri E. M. van der Burgt:
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Oberbach A, Schlichting N, Neuhaus J, Kullnick Y, Lehmann S, Heinrich M, Dietrich A, Mohr FW, von Bergen M, Baumann S. Establishing a Reliable Multiple Reaction Monitoring-Based Method for the Quantification of Obesity-Associated Comorbidities in Serum and Adipose Tissue Requires Intensive Clinical Validation. J Proteome Res 2014; 13:5784-800. [DOI: 10.1021/pr500722k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andreas Oberbach
- Department
of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Leipzig, Germany
| | | | | | - Yvonne Kullnick
- Department
of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Leipzig, Germany
| | | | | | | | - Friedrich Wilhelm Mohr
- Department
of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Leipzig, Germany
| | - Martin von Bergen
- Department
of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Aalborg, Denmark
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65
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Jauchem JR, Cerna CZ, Lim TY, Seaman RL. Exposures of Sus scrofa to a TASER(®) conducted electrical weapon: no effects on 2-dimensional gel electrophoresis patterns of plasma proteins. Forensic Sci Med Pathol 2014; 10:526-34. [PMID: 25319243 DOI: 10.1007/s12024-014-9606-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
Abstract
In an earlier study, we found significant changes in red-blood-cell, leukocyte, and platelet counts, and in red-blood-cell membrane proteins, following exposures of anesthetized pigs to a conducted electrical weapon. In the current study, we examined potential changes in plasma proteins [analyzed via two-dimensional gel electrophoresis (2-DGE)] following two 30 s exposures of anesthetized pigs (Sus scrofa) to a TASER (®) C2 conducted electrical weapon. Patterns of proteins, separated by 2-DGE, were consistent and reproducible between animals and between times of sampling. We determined that the blood plasma collection, handling, storage, and processing techniques we used are suitable for swine blood. There were no statistically significant changes in plasma proteins following the conducted-electrical-weapon exposures. Overall gel patterns of fibrinogen were similar to results of other studies of both pigs and humans (in control settings, not exposed to conducted electrical weapons). The lack of significant changes in plasma proteins may be added to the body of evidence regarding relative safety of TASER C2 device exposures.
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Affiliation(s)
- James R Jauchem
- Bio-Effects Division, Human Effectiveness Directorate, 711th Human Performance Wing, US Air Force Research Laboratory, 711 HPW/RHDR, 4141 Petroleum Road, Fort Sam Houston, TX, 78234, USA,
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66
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Hepponstall M, Konstantinov IE. Proteomics in paediatric cardiac surgery: is a personalised approach feasible? Proteomics Clin Appl 2014; 8:851-61. [PMID: 25244609 DOI: 10.1002/prca.201400054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/27/2014] [Accepted: 09/17/2014] [Indexed: 11/10/2022]
Abstract
The incidence of congenital cardiac abnormalities remains high. Paediatric patients with congenital cardiac defects often require surgery at a young age. The surgeries are often long and complex, rendering this population particularly vulnerable to the deleterious effects of cardiopulmonary bypass and cardiac surgery. The search for cardioprotective strategies is ongoing in an attempt to reduce the morbidity in this population. In the post-genomic era, it is apparent that simply determining the genomic sequences holds little diagnostic potential and means to determine progression of disease and response to treatment. The field of proteomics is expanding and application of proteomic techniques in the clinical setting holds great potential to advance our understanding of the proteomic changes involved in specific disease stages. This review will assess the application of proteomic techniques in the setting of paediatric cardiac surgery and highlight the need to obtain a clear understanding of the role of various proteins in children with cardiac conditions. The success and challenges of the available proteomic technology will be discussed as well as the future potential of proteomic methods for advancing our understanding of protein changes in children requiring cardiac surgery.
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Affiliation(s)
- Michele Hepponstall
- Murdoch Childrens Research Institute, Melbourne, Australia; Cardiac Surgery Unit and Cardiology, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
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67
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Hyung SW, Piehowski PD, Moore RJ, Orton DJ, Schepmoes AA, Clauss TR, Chu RK, Fillmore TL, Brewer H, Liu T, Zhao R, Smith RD. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid. Anal Bioanal Chem 2014; 406:7117-25. [PMID: 25192788 DOI: 10.1007/s00216-014-8058-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/09/2014] [Accepted: 07/22/2014] [Indexed: 12/30/2022]
Abstract
Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 μL) due to low yields stemming from losses caused by nonspecific binding to the column matrix and concentration of large eluent volumes. Additionally, the cost of the depletion media can be prohibitive for larger-scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large-scale studies. We characterized the performance of a 346 μL column volume microscale depletion system, using four different flow rates to determine the most effective depletion conditions for ∼6-μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10-mL depletion column served as the control. Results showed depletion efficiency of the microscale column increased as flow rate decreased, and that our microdepletion was reproducible. In an initial application, a 600-μL sample of human cerebrospinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.
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Affiliation(s)
- Seok-Won Hyung
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA,
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68
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Rohani A, Varhue W, Su YH, Swami NS. Quantifying spatio-temporal dynamics of biomarker pre-concentration and depletion in microfluidic systems by intensity threshold analysis. BIOMICROFLUIDICS 2014; 8:052009. [PMID: 25538800 PMCID: PMC4222295 DOI: 10.1063/1.4897283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/25/2014] [Indexed: 05/05/2023]
Abstract
Microfluidic systems are commonly applied towards pre-concentration of biomarkers for enhancing detection sensitivity. Quantitative information on the spatial and temporal dynamics of pre-concentration, such as its position, extent, and time evolution are essential towards sensor design for coupling pre-concentration to detection. Current quantification methodologies are based on the time evolution of fluorescence signals from biomarkers within a statically defined region of interest, which does not offer information on the spatial dynamics of pre-concentration and leads to significant errors when the pre-concentration zone is delocalized or exhibits wide variations in size, shape, and position over time under the force field. We present a dynamic methodology for quantifying the region of interest by using a statistical description of particle distribution across the device geometry to determine the intensity thresholds for particle pre-concentration. This method is applied to study the delocalized pre-concentration dynamics under an electrokinetic force balance driven by negative dielectrophoresis, for aligning the pre-concentration and detection regions of neuropeptide Y, and for quantifying the polarizability dispersion of silica nano-colloids with frequency of the force field. We envision the application of this automated methodology on data from 2D images and 3D Z-stacks for quantifying pre-concentration dynamics over delocalized regions as a function of the force field.
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Affiliation(s)
- Ali Rohani
- Electrical and Computer Engineering, University of Virginia , Charlottesville, Virginia 22904, USA
| | - Walter Varhue
- Electrical and Computer Engineering, University of Virginia , Charlottesville, Virginia 22904, USA
| | - Yi-Hsuan Su
- Electrical and Computer Engineering, University of Virginia , Charlottesville, Virginia 22904, USA
| | - Nathan S Swami
- Electrical and Computer Engineering, University of Virginia , Charlottesville, Virginia 22904, USA
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69
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Mei N, Seale B, Ng AH, Wheeler AR, Oleschuk R. Digital Microfluidic Platform for Human Plasma Protein Depletion. Anal Chem 2014; 86:8466-72. [DOI: 10.1021/ac5022198] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ningsi Mei
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario K7L
3N6, Canada
| | - Brendon Seale
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Alphonsus H.C. Ng
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Aaron R. Wheeler
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Richard Oleschuk
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario K7L
3N6, Canada
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Fernández-Costa C, Reboiro-Jato M, Fdez-Riverola F, Ruiz-Romero C, Blanco FJ, Capelo-Martínez JL. Sequential depletion coupled to C18 sequential extraction as a rapid tool for human serum multiple profiling. Talanta 2014; 125:189-95. [DOI: 10.1016/j.talanta.2014.02.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/15/2014] [Accepted: 02/20/2014] [Indexed: 01/01/2023]
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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72
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Ahn SB, Khan A. Detection and quantitation of twenty-seven cytokines, chemokines and growth factors pre- and post-high abundance protein depletion in human plasma. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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74
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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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75
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Frantzi M, Bhat A, Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 2014; 3:7. [PMID: 24679154 PMCID: PMC3994249 DOI: 10.1186/2001-1326-3-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/06/2014] [Indexed: 12/11/2022] Open
Abstract
Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
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76
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Pernemalm M, Lehtiö J. Mass spectrometry-based plasma proteomics: state of the art and future outlook. Expert Rev Proteomics 2014; 11:431-48. [PMID: 24661227 DOI: 10.1586/14789450.2014.901157] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mass spectrometry-based plasma proteomics is a field where intense research has been performed during the last decade. Being closely linked to biomarker discovery, the field has received a fair amount of criticism, mostly due to the low number of novel biomarkers reaching the clinic. However, plasma proteomics is under gradual development with improvements on fractionation methods, mass spectrometry instrumentation and analytical approaches. These recent developments have contributed to the revival of plasma proteomics. The goal of this review is to summarize these advances, focusing in particular on fractionation methods, both for targeted and global mass spectrometry-based plasma analysis.
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Affiliation(s)
- Maria Pernemalm
- Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23, 171 65, Solna, Sweden
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77
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Wright EP, Partridge MA, Padula MP, Gauci VJ, Malladi CS, Coorssen JR. Top-down proteomics: enhancing 2D gel electrophoresis from tissue processing to high-sensitivity protein detection. Proteomics 2014; 14:872-89. [PMID: 24452924 DOI: 10.1002/pmic.201300424] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/01/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023]
Abstract
The large-scale resolution and detection of proteins from complex native mixtures is fundamental to quantitative proteomic analyses. Comprehensive analyses depend on careful tissue handling and quantitative protein extraction and assessment. To most effectively link these analyses with an understanding of underlying molecular mechanisms, it is critical that all protein types - isoforms, splice variants and those with functionally important PTMs - are quantitatively extracted with high reproducibility. Methodological details concerning protein extraction and resolution using 2DE are discussed with reference to current in-gel protein detection limits. We confirm a significant increase in total protein, and establish that extraction, resolution and detection of phospho- and glycoproteins are improved following automated frozen disruption relative to manual homogenisation. The quality of 2DE protein resolution is established using third-dimension separations and 'deep imaging'; substantially more proteins/protein species than previously realised are actually resolved by 2DE. Thus, the key issue for effective proteome analyses is most likely to be detection, not resolution. Thus, these systematic methodological and technical advances further solidify the role of 2DE in top-down proteomics. By routinely assessing as much proteomic data from a sample as possible, 2DE enables more detailed and critical insights into molecular mechanisms underlying different physiological states.
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Affiliation(s)
- Elise P Wright
- Department of Molecular Physiology, Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW, Australia
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78
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Siripornadulsil S, Thanwisai L, Siripornadulsil W. Changes in the proteome of the cadmium-tolerant bacteria Cupriavidus taiwanensis KKU2500-3 in response to cadmium toxicity. Can J Microbiol 2014; 60:121-31. [DOI: 10.1139/cjm-2013-0713] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cupriavidus taiwanensis KKU2500-3 is a cadmium (Cd)-tolerant bacterial strain that was previously isolated from rice fields contaminated with high levels of Cd. In 500 μmol/L CdCl2, the KKU2500-3 strain grew slower and with a more prolonged lag-phase than when grown in the absence of Cd. A proteomic approach was used to characterize the protein expression in the Cd-tolerant bacteria C. taiwanensis KKU2500-3 during growth under Cd stress. When compared with the untreated cells, a total of 982 differentially expressed protein spots were observed in the CdCl2-treated cells, and 59 and 10 spots exhibited >2- and >4-fold changes, respectively. The level of up- and downregulation varied from 2.01- to 11.26-fold and from 2.01- to 5.34-fold, respectively. Of the 33 differentially expressed protein spots analyzed by MALDI TOF MS/MS, 19 spots were successfully identified, many of which were involved in stress responses. The most highly upregulated protein (+7.95-fold) identified was the chaperone GroEL, which indicated that this factor likely contributed to the bacterial survival and growth in response to Cd toxicity. Detection of the downregulated protein flagellin (–3.52-fold) was consistent with the less effective ATP-mediated and flagella-driven motility. The flagella-losing cells were also observed in the Cd-treated bacteria when analyzed by scanning electron microscopy. Thus, the Cd-stressed cells may downregulate pathways involving ATP utilization in favor of other mechanisms in response to Cd toxicity. When the KKU2500-3 strain was grown in the presence of Cd, H2S was not detected, suggesting a possible role of the sulfur in precipitation with Cd. Apart from a general response, no specific process could be determined using the present proteomic approach. However, the potential role of protein folding-mediated GroEL, flagella-mediated motility and CdS biotransformation in Cd toxicity response observed in this study as well as the extent of Cd-tolerant mechanisms using other methods could facilitate the future application of this strain in addressing Cd environmental contamination.
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Affiliation(s)
- Surasak Siripornadulsil
- Department of Microbiology, Faculty of Science, Khon Kaen University, 123 Mittapap Road, Tambon Nai-Muang, Muang District, Khon Kaen, 40002 Thailand
- Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Lalita Thanwisai
- Department of Microbiology, Faculty of Science, Khon Kaen University, 123 Mittapap Road, Tambon Nai-Muang, Muang District, Khon Kaen, 40002 Thailand
| | - Wilailak Siripornadulsil
- Department of Microbiology, Faculty of Science, Khon Kaen University, 123 Mittapap Road, Tambon Nai-Muang, Muang District, Khon Kaen, 40002 Thailand
- Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen, 40002 Thailand
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79
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Chromy BA, Eldridge A, Forsberg JA, Brown TS, Kirkup BC, Elster E, Luciw P. Proteomic sample preparation for blast wound characterization. Proteome Sci 2014; 12:10. [PMID: 24529238 PMCID: PMC3943455 DOI: 10.1186/1477-5956-12-10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 02/03/2014] [Indexed: 01/04/2023] Open
Abstract
Background Blast wounds often involve diverse tissue types and require substantial time and treatment for appropriate healing. Some of these subsequent wounds become colonized with bacteria requiring a better understanding of how the host responds to these bacteria and what proteomic factors contribute wound healing outcome. In addition, using reliable and effective proteomic sample preparation procedures can lead to novel biomarkers for improved diagnosis and therapy. Results To address this need, suitable sample preparation for 2-D DIGE proteomic characterization of wound effluent and serum samples from combat-wounded patients was investigated. Initial evaluation of crude effluent and serum proved the necessity of high abundant protein depletion. Subsequently, both samples were successfully depleted using Agilent Multiple Affinity Removal system and showed greatly improved 2-D spot maps, comprising 1,800 and 1,200 protein spots, respectively. Conclusion High abundant protein removal was necessary for both wound effluent and serum. This is the first study to show a successful method for high abundant protein depletion from wound effluent which is compatible with downstream 2-D DIGE analysis. This development allows for improved biomarker discovery in wound effluent and serum samples.
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Affiliation(s)
- Brett A Chromy
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California at Davis, Davis, CA, USA.
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80
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Krüger T, Lautenschläger J, Grosskreutz J, Rhode H. Proteome analysis of body fluids for amyotrophic lateral sclerosis biomarker discovery. Proteomics Clin Appl 2014; 7:123-35. [PMID: 23129563 DOI: 10.1002/prca.201200067] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/28/2012] [Accepted: 10/22/2012] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder of motor neurons leading to death of the patients, mostly within 2-5 years after disease onset. The pathomechanism of motor neuron degeneration is only partially understood and therapeutic strategies based on mechanistic insights are largely ineffective. The discovery of reliable biomarkers of disease diagnosis and progression is the sine qua non of both the revelation of insights into the ALS pathomechanism and the assessment of treatment efficacies. Proteomic approaches are an important pillar in ALS biomarker discovery. Cerebrospinal fluid is the most promising body fluid for differential proteome analyses, followed by blood (serum, plasma), and even urine and saliva. The present study provides an overview about reported peptide/protein biomarker candidates that showed significantly altered levels in certain body fluids of ALS patients. These findings have to be discussed according to proposed pathomechanisms to identify modifiers of disease progression and to pave the way for the development of potential therapeutic strategies. Furthermore, limitations and advantages of proteomic approaches for ALS biomarker discovery in different body fluids and reliable validation of biomarker candidates have been addressed.
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Affiliation(s)
- Thomas Krüger
- Institute of Biochemistry 1, University Hospital, Jena, Germany.
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81
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Such-Sanmartín G, Ventura-Espejo E, Jensen ON. Depletion of abundant plasma proteins by poly(N-isopropylacrylamide-acrylic acid) hydrogel particles. Anal Chem 2014; 86:1543-50. [PMID: 24428553 DOI: 10.1021/ac403749j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein and proteome analysis of human blood plasma presents a challenge to current analytical platforms such as mass spectrometry (MS). High abundance plasma proteins interfere with detection of potential protein biomarkers that are often 3-10 orders of magnitude lower in concentration. We report the application of pH-sensitive poly(N-isopropylacrylamide-acrylic acid) hydrogel particles for removal of abundant plasma proteins, prior to proteome analysis by MS. Protein depletion occurs by two separate mechanisms: (1) hydrogel particles incubated with low concentrations of plasma capture abundant proteins at higher efficiency than low abundance proteins, which are enriched in the supernatants, whereas (2) hydrogel particles incubated with high concentrations of plasma capture and irreversibly trap abundant proteins. During the elution step, irreversibly trapped proteins remain captured while low abundance proteins are released and recovered in the eluate. We developed a series of distinct depletion protocols that proved useful for sample depletion and fractionation and facilitated targeted analysis of putative biomarkers such as IGF1-2, IBP2-7, ALS, KLK6-7, ISK5, and PLF4 by selected reaction monitoring (SRM) liquid chromatography (LC)-MS/MS. This novel use of hydrogel particles opens new perspectives for biomarker analysis based on mass spectrometry.
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Affiliation(s)
- Gerard Such-Sanmartín
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Odense M, DK-5230, Denmark
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82
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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83
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Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K. Systems Approach to Neurodegenerative Disease Biomarker Discovery. Annu Rev Pharmacol Toxicol 2014; 54:457-81. [DOI: 10.1146/annurev-pharmtox-011613-135928] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Inyoul Lee
- Institute for Systems Biology, Seattle, Washington 98109; , , , , , ,
| | - Yong Zhou
- Institute for Systems Biology, Seattle, Washington 98109; , , , , , ,
| | - Shizhen Qin
- Institute for Systems Biology, Seattle, Washington 98109; , , , , , ,
| | - Jaeyun Sung
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 790-784, Republic of Korea;
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, Washington 98109; , , , , , ,
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington 98109; , , , , , ,
| | - Kai Wang
- Institute for Systems Biology, Seattle, Washington 98109; , , , , , ,
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84
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Prieto DA, Johann DJ, Wei BR, Ye X, Chan KC, Nissley DV, Simpson RM, Citrin DE, Mackall CL, Linehan WM, Blonder J. Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens. Biomark Med 2014; 8:269-86. [PMID: 24521024 PMCID: PMC4201940 DOI: 10.2217/bmm.13.101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The discovery of clinically relevant cancer biomarkers using mass spectrometry (MS)-based proteomics has proven difficult, primarily because of the enormous dynamic range of blood-derived protein concentrations and the fact that the 22 most abundant blood-derived proteins constitute approximately 99% of the total plasma protein mass. Immunodepletion of clinical body fluid specimens (e.g., serum/plasma) for the removal of highly abundant proteins is a reasonable and reproducible solution. Often overlooked, clinical tissue specimens also contain a formidable amount of highly abundant blood-derived proteins present in tissue-embedded networks of blood/lymph capillaries and interstitial fluid. Hence, the dynamic range impediment to biomarker discovery remains a formidable obstacle, regardless of clinical sample type (solid tissue and/or body fluid). Thus, we optimized and applied simultaneous immunodepletion of blood-derived proteins from solid tissue and peripheral blood, using clear cell renal cell carcinoma as a model disease. Integrative analysis of data from this approach and genomic data obtained from the same type of tumor revealed concordant key pathways and protein targets germane to clear cell renal cell carcinoma. This includes the activation of the lipogenic pathway characterized by increased expression of adipophilin (PLIN2) along with 'cadherin switching', a phenomenon indicative of transcriptional reprogramming linked to renal epithelial dedifferentiation. We also applied immunodepletion of abundant blood-derived proteins to various tissue types (e.g., adipose tissue and breast tissue) showing unambiguously that the removal of abundant blood-derived proteins represents a powerful tool for the reproducible profiling of tissue proteomes. Herein, we show that the removal of abundant blood-derived proteins from solid tissue specimens is of equal importance to depletion of body fluids and recommend its routine use in the context of biological discovery and/or cancer biomarker research. Finally, this perspective presents the background, rationale and strategy for using tissue-directed high-resolution/accuracy MS-based shotgun proteomics to detect genuine tumor proteins in the peripheral blood of a patient diagnosed with nonmetastatic cancer, employing concurrent liquid chromatography-MS analysis of immunodepleted clinical tissue and blood specimens.
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Affiliation(s)
- DaRue A Prieto
- Laboratory of Proteomics & Analytical Technologies, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - Donald J Johann
- University of Arkansas for Medical Sciences, 4301 West Markham, Slot 816 Little Rock, AR, USA
| | - Bih-Rong Wei
- Laboratory of Cancer Biology & Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xiaoying Ye
- Laboratory of Proteomics & Analytical Technologies, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - King C Chan
- Laboratory of Proteomics & Analytical Technologies, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - Dwight V Nissley
- Laboratory of Proteomics & Analytical Technologies, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
| | - R Mark Simpson
- Laboratory of Cancer Biology & Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Deborah E Citrin
- Immunology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Crystal L Mackall
- Section of Translational Radiation Oncology Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - W Marston Linehan
- Urologic Surgery & the Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Josip Blonder
- Laboratory of Proteomics & Analytical Technologies, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702, USA
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85
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Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 2013; 5:2837-56. [DOI: 10.4155/bio.13.245] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Quantitative plasma proteomics, through the use of targeted MRM-MS and isotopically labeled standards, is emerging as a popular technique to address biological- and biomedical-centered queries. High precision and accuracy are essential in such measurements, particularly in protein biomarker research where translation to the clinic is sought. Standardized procedures and routine performance evaluation of all stages of the workflow (both pre-analytical and analytical) are therefore imperative to satisfy these requisites and enable high inter-laboratory reproducibility and transferability. In this review, we first discuss the pre-analytical and analytical variables that can affect the precision and accuracy of ‘absolute’ quantitative plasma proteomic measurements. Proposed strategies to limit such variability will then be highlighted and unmet needs for future exploration will be noted. Although there is no way to conduct a truly comprehensive review on this broad, rapidly changing topic, we have highlighted key aspects and included references to review articles on various sub-topics.
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86
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Ji J, Nie L, Li Y, Yang P, Liu B. Simultaneous Online Enrichment and Identification of Trace Species Based on Microfluidic Droplets. Anal Chem 2013; 85:9617-22. [DOI: 10.1021/ac4018082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ji Ji
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| | - Lei Nie
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
- Shanghai Institute of Quality Inspection and Technical Research, Shanghai 201114, China
| | - Yixin Li
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| | - Pengyuan Yang
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
| | - Baohong Liu
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, 220
HanDan Road, Shanghai 200433, China
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87
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Xiang F, Guo X, Chen W, Wang J, Zhou T, Huang F, Cao C, Chen X. Proteomics analysis of human pericardial fluid. Proteomics 2013; 13:2692-5. [PMID: 23797974 DOI: 10.1002/pmic.201200317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 05/18/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Fei Xiang
- Department of Thoracic and Cardiovascular Surgery; Nanjing First Hospital Affiliated to Nanjing Medical University; Nanjing P. R. China
| | - Xuejiang Guo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing P. R. China
| | - Wen Chen
- Department of Thoracic and Cardiovascular Surgery; Nanjing First Hospital Affiliated to Nanjing Medical University; Nanjing P. R. China
| | - Jing Wang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing P. R. China
| | - Tao Zhou
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing P. R. China
| | - Fuhua Huang
- Department of Thoracic and Cardiovascular Surgery; Nanjing First Hospital Affiliated to Nanjing Medical University; Nanjing P. R. China
| | - Changchun Cao
- Department of Nephrology; Nanjing First Hospital Affiliated to Nanjing Medical University; Nanjing P. R. China
| | - Xin Chen
- Department of Thoracic and Cardiovascular Surgery; Nanjing First Hospital Affiliated to Nanjing Medical University; Nanjing P. R. China
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88
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Startsev MA, Inglis DW, Baker MS, Goldys EM. Nanochannel pH gradient electrofocusing of proteins. Anal Chem 2013; 85:7133-8. [PMID: 23819922 DOI: 10.1021/ac4014447] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate matrix-free pH gradient electrofocusing of proteins within an 85 nm deep nanochannel. In contrast to conventional isoelectric focusing where the fluid does not move, this pH gradient method traps protein molecules flowing through a channel by balancing electric forces due to pH-dependent protein charge and viscous drag forces caused by electro-osmosis. The nanoscale depth of the device and the low voltage used limit convection relative to diffusion, thus producing a stable focused band of protein. R-Phycoerythrin (RPE) and Dylight labeled streptavidin (Dyl-Strep) were focused within a nanochannel using applied voltages between 0.4 and 1.6 V. Concentration enhancement factors of over 380 have been achieved within 5 min. Varying the buffer pH (between 2.7 and 7.2) at the boundaries of the nanochannel affected the shape of the focused bands. For RPE, a pH span of 4.5 (pH 2.7 to 7.2) yielded the narrowest peak while a span of 2.4 (pH 2.7 to 5.1) produced a significantly wider peak. Such matrix-free nanofluidic devices with pH gradient electrofocusing may enable on-chip integration of orthogonal separation techniques with mass spectrometry offering labor savings and enhanced performance.
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Affiliation(s)
- Michael A Startsev
- Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109, Australia.
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89
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Bennett S, Grant M, Creese AJ, Mangialasche F, Cecchetti R, Cooper HJ, Mecocci P, Aldred S. Plasma levels of complement 4a protein are increased in Alzheimer's disease. Alzheimer Dis Assoc Disord 2013; 26:329-34. [PMID: 22052466 DOI: 10.1097/wad.0b013e318239dcbd] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder that has been predicted to affect 106.2 million people worldwide by 2050. Currently, definitive diagnosis for this disease is given post mortem, and there is a need for biomarker identification to enable earlier diagnosis of this disease. Biomarkers of AD would ideally represent early disease process and will be present in peripheral tissue before cognitive decline develops in this population. Proteomic technologies offer a strategy to undertake such work. In recent times, research in this field has moved away from classical 2-dimensional gel-based proteomics toward more sensitive, non-gel-based proteomic methodologies. In the study presented here, isobaric labeling for relative and absolute quantification was used to assess plasma protein expression in a small group of AD and control samples. Several proteins were identified as being differentially expressed between these 2 populations. Complement 4a plasma protein was identified as increased in AD by isobaric labeling for relative and absolute quantification, and this finding was further validated by Western blotting and enzyme-linked immunosorbent assay. These data suggest that inflammatory processes, which have been shown to be involved in AD pathology in the brain, are also present in plasma.
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Affiliation(s)
- Stuart Bennett
- School of Sport and Exercise Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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90
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Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:917-26. [PMID: 23806606 DOI: 10.1016/j.bbapap.2013.06.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/27/2013] [Accepted: 06/14/2013] [Indexed: 11/23/2022]
Abstract
Accurate and rapid protein quantitation is essential for screening biomarkers for disease stratification and monitoring, and to validate the hundreds of putative markers in human biofluids, including blood plasma. An analytical method that utilizes stable isotope-labeled standard (SIS) peptides and selected/multiple reaction monitoring-mass spectrometry (SRM/MRM-MS) has emerged as a promising technique for determining protein concentrations. This targeted approach has analytical merit, but its true potential (in terms of sensitivity and multiplexing) has yet to be realized. Described herein is a method that extends the multiplexing ability of the MRM method to enable the quantitation 142 high-to-moderate abundance proteins (from 31mg/mL to 44ng/mL) in undepleted and non-enriched human plasma in a single run. The proteins have been reported to be associated to a wide variety of non-communicable diseases (NCDs), from cardiovascular disease (CVD) to diabetes. The concentrations of these proteins in human plasma are inferred from interference-free peptides functioning as molecular surrogates (2 peptides per protein, on average). A revised data analysis strategy, involving the linear regression equation of normal control plasma, has been instituted to enable the facile application to patient samples, as demonstrated in separate nutrigenomics and CVD studies. The exceptional robustness of the LC/MS platform and the quantitative method, as well as its high throughput, makes the assay suitable for application to patient samples for the verification of a condensed or complete protein panel. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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91
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Percy AJ, Chambers AG, Yang J, Borchers CH. Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013; 13:2202-15. [DOI: 10.1002/pmic.201200316] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/06/2013] [Accepted: 03/26/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Andrew G. Chambers
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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92
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Tan SH, Mohamedali A, Kapur A, Baker MS. Ultradepletion of human plasma using chicken antibodies: a proof of concept study. J Proteome Res 2013; 12:2399-413. [PMID: 23082986 DOI: 10.1021/pr3007182] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human plasma arguably represents the most comprehensive version of the human proteome. Despite its immense theoretical discovery potential, plasma has many high and medium abundance proteins that mask low abundance protein disease biomarkers of relevance, making the discovery of novel diagnostic markers particularly difficult. Some form of protein depletion and/or fractionation is essential in order to detect markers of low abundance. Here, we describe a "proof of concept" two-pronged approach to immunodeplete abundant proteins from human plasma. The method, called API (Abundant Protein Immunodepletion), involves the fractionation of plasma using dual ion exchange columns (protein repetitive orthogonal offline fractionation (PROOF)) to simplify the proteome, the production of polyclonal IgY against each fraction and finally using the purified antibodies in a immunodepletion column. We explored the use of this product for immunodepletion of human plasma and identified a total of 165 nonredundant proteins after depletion. Of these, 38 proteins that were not previously identified in nondepleted plasma were now detected. It is envisaged that further optimization of the method as well as its cyclic implementation (by reinjecting depleted plasma into chickens for second round of antibody production) can make this technology highly robust, extremely cost-effective, and ideal for high throughput biomarker discovery.
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Affiliation(s)
- Sock-Hwee Tan
- Department of Chemistry and Biomolecular Sciences and Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
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93
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Anguizola J, Joseph K, Barnaby OS, Matsuda R, Alvarado G, Clarke W, Cerny RL, Hage DS. Development of affinity microcolumns for drug-protein binding studies in personalized medicine: interactions of sulfonylurea drugs with in vivo glycated human serum albumin. Anal Chem 2013; 85:4453-60. [PMID: 23544441 PMCID: PMC3696407 DOI: 10.1021/ac303734c] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This report used high-performance affinity microcolumns to examine the changes in binding by sulfonylurea drugs to in vivo glycated HSA that had been isolated from individual patients with diabetes. An immunoextraction approach was developed to isolate HSA and glycated HSA from clinical samples, using only 20 μL of plasma or serum and 6-12 nmol of protein to prepare each affinity microcolumn. It was found that the affinity microcolumns could be used in either frontal analysis or zonal elution studies, which typically required only 4-8 min per run. The microcolumns had good stability and allowed data to be obtained for multiple drugs and experimental conditions over hundreds of sample application cycles. Both the overall binding, as measured by frontal analysis, and site-specific interactions, as examined by zonal elution, showed good agreement with previous data that had been obtained for in vitro glycated HSA with similar levels of modification. It was also possible to directly compare the changes in site-specific binding that occurred between sulfonylurea drugs or as the level of HSA glycation was varied. This method is not limited to clinical samples of glycated HSA but could be adapted for work with other modified proteins of interest in personalized medicine.
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Affiliation(s)
| | - K.S. Joseph
- Chemistry Department, University of Nebraska, Lincoln, NE 68588, USA
| | - Omar S. Barnaby
- Chemistry Department, University of Nebraska, Lincoln, NE 68588, USA
| | - Ryan Matsuda
- Chemistry Department, University of Nebraska, Lincoln, NE 68588, USA
| | | | - William Clarke
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Ronald L. Cerny
- Chemistry Department, University of Nebraska, Lincoln, NE 68588, USA
| | - David S. Hage
- Chemistry Department, University of Nebraska, Lincoln, NE 68588, USA
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94
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Krüger T, Lehmann T, Rhode H. Effect of quality characteristics of single sample preparation steps in the precision and coverage of proteomic studies—A review. Anal Chim Acta 2013; 776:1-10. [DOI: 10.1016/j.aca.2013.01.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 11/25/2022]
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95
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Wang XP, Wang QX, Lin HP, Wang YL, Yang Y. Glycoprotein 96 and α-fetoprotein cross-linking complexes elicited specific antitumor immunity. Cancer Biother Radiopharm 2013; 28:406-14. [PMID: 23484810 DOI: 10.1089/cbr.2012.1404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant gastroenterological cancers over the world. α-fetoprotein (AFP) is an oncofetal protein produced during HCC development that could generate weaker and less reproducible antitumor protection, and it may serve as a target for immunotherapy. Therefore, it is imperative to enhance its immunogenicity and develop therapeutic vaccines to eliminate AFP-expressing tumors. In this study, by way of glutaraldehyde cross-linking, we constructed a potential therapeutic protein vaccine, glycoprotein 96 (gp96)/AFP. Our results demonstrated that AFP and gp96 synergistically exhibited significant increase in AFP-specific CD8⁺ T-cell responses and impressive cytotoxic antitumor effect against AFP-expressing tumors. Priming mice with the reconstructed vaccine, we elicited robust strong protective immunity. Our study suggests that tumor vaccine by cross-linking tumor antigen and gp96 is a promising approach to cancer therapy.
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Affiliation(s)
- Xiao-Ping Wang
- Laboratory of Molecular Biology & Pathology, Shaanxi University of Chinese Medicine, Xianyang, China.
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96
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Scaling down constriction-based (electrodeless) dielectrophoresis devices for trapping nanoscale bioparticles in physiological media of high-conductivity. Electrophoresis 2013; 34:1097-104. [DOI: 10.1002/elps.201200456] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/07/2022]
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97
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Kočevar N, Hudler P, Komel R. The progress of proteomic approaches in searching for cancer biomarkers. N Biotechnol 2013; 30:319-26. [DOI: 10.1016/j.nbt.2012.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/05/2012] [Indexed: 12/28/2022]
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98
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von Toerne C, Kahle M, Schäfer A, Ispiryan R, Blindert M, Hrabe De Angelis M, Neschen S, Ueffing M, Hauck SM. Apoe, Mbl2, and Psp Plasma Protein Levels Correlate with Diabetic Phenotype in NZO Mice—An Optimized Rapid Workflow for SRM-Based Quantification. J Proteome Res 2013; 12:1331-43. [DOI: 10.1021/pr3009836] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Marius Ueffing
- Centre of Ophthalmology, Institute
for Ophthalmic Research, University of Tübingen, Tübingen, Germany
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99
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Koutroukides TA, Jaros JAJ, Amess B, Martins-de-Souza D, Guest PC, Rahmoune H, Levin Y, Deery M, Charles PD, Hester S, Groen A, Christoforou A, Howard J, Bond N, Bahn S, Lilley KS. Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry. Methods Mol Biol 2013; 1061:291-307. [PMID: 23963945 DOI: 10.1007/978-1-62703-589-7_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Blood serum is one of the easiest accessible sources of biomarkers and its proteome presents a significant parcel of immune system proteins. These proteins can provide not only biological explanation but also diagnostic and drug response answers independently of the type of disease or condition in question. Shotgun mass spectrometry has profoundly contributed to proteome analysis and is presently considered as an indispensible tool in the field of biomarker discovery. In addition, the multiplexing potential of isotopic labeling techniques such as iTRAQ can increase statistical relevance and accuracy of proteomic data through the simultaneous analysis of different biological samples. Here, we describe a complete protocol using iTRAQ in a shotgun proteomics workflow along with data analysis steps, customized for the challenges associated with the serum proteome.
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Affiliation(s)
- Theodoros A Koutroukides
- Department of Chemical Engineering and Biotechnology, Cambridge Centre for Neuropsychiatric Research, University of Cambridge, Cambridge, UK
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100
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Calvo E, Martínez-Pinna R, Ramos-Mozo P, Pastor-Vargas C, Camafeita E, Egido J, Martin-Ventura JL, Lopez JA. Unraveling biomarkers of abdominal aortic aneurisms by iTRAQ analysis of depleted plasma. Methods Mol Biol 2013; 1000:157-166. [PMID: 23585091 DOI: 10.1007/978-1-62703-405-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Abdominal aortic aneurysm (AAA) is a significant health problem in Western countries. The diameter of AAA is a surrogate marker of its growth rate that reflects the magnitude of the degenerative process in the vascular wall, although most AAAs show discontinuous growth patterns and alternate periods of stability and nongrowth with periods of acute expansion and occasionally ruptures. Thus, the identification of biomarkers of AAA in plasma could aid in the diagnosis, prognosis, and therapy of AAA progression. However, owing to the complex composition of plasma, depletion methods must be applied before the analytical approaches for detecting low-abundant plasma protein components. In the present work, we describe a proteomic study on MARS 14-depleted plasma based on mass spectrometry (MS) which combines peptide labelling (isobaric tagging for relative and absolute quantification, iTRAQ) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). This quantitative approach revealed altered levels of several proteins related to the complement system in AAA patients.
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Affiliation(s)
- Enrique Calvo
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
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