1
|
Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
| |
Collapse
|
2
|
Weissinger EM, Basílio-Queirós D, Metzger J, Bieling LM, Ganser A. Proteomics for hematopoietic stem cell transplantation. Expert Rev Proteomics 2020; 17:201-206. [PMID: 32228239 DOI: 10.1080/14789450.2020.1748501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction: After the genomic era, the analysis of the proteome has gained increasing importance. Peptides and/or proteins present in tissue or body fluids can depict health and are prone to change during disease, not only in configuration but also in abundance. Early on, high throughput proteome analysis was implemented in the diagnostic of therapy-linked or induced complications arising after allogeneic hematopoietic stem cell transplantation (HSCT). Several proteomic approaches are currently used in the prediction or diagnosis of acute and/or chronic graft-versus-host disease (GvHD).Areas covered: This review will report on two high throughput proteomics technologies used in the clinical setting to date, namely enzyme-linked-immunosorbent assays (ELISA) for key proteins involved in the pathogenesis of acute GvHD and on capillary electrophoresis coupled on-line to mass spectrometry (CE-MS). Here, we summarize the current data and discuss the strength as well as the limitations of each method and compare the usefulness and practicability in the post-HSCT setting for prediction and diagnosis of acute GvHD.Expert commentary: Both technologies are applied in the clinic and have been tested on several hundred patients after HSCT. The data from both technologies may complement each other in diagnosis of GvHD.
Collapse
Affiliation(s)
- Eva M Weissinger
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Debora Basílio-Queirós
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Lisa M Bieling
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| |
Collapse
|
3
|
Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
|
4
|
Marx D, Metzger J, Olagne J, Belczacka I, Faguer S, Colombat M, Husi H, Mullen W, Gwinner W, Caillard S. Proteomics in Kidney Allograft Transplantation—Application of Molecular Pathway Analysis for Kidney Allograft Disease Phenotypic Biomarker Selection. Proteomics Clin Appl 2019; 13:e1800091. [DOI: 10.1002/prca.201800091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/10/2019] [Indexed: 02/06/2023]
Affiliation(s)
- David Marx
- Nephrology – Transplantation DepartmentUMR_S. INSERM UMR_S 1109ImmunoRhumatologie MoléculaireFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de StrasbourgInstitut d'Immunologie et d'Hématologie 67085 Strasbourg France
- Laboratoire de Spectrométrie de Masse BioOrganiqueUniversity of StrasbourgCentre National de la Recherche ScientifiqueInstitut Pluridisciplinaire Hubert Curien UMR 7178 67037 Strasbourg France
| | | | - Jérôme Olagne
- Nephrology – Transplantation DepartmentUMR_S. INSERM UMR_S 1109ImmunoRhumatologie MoléculaireFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de StrasbourgInstitut d'Immunologie et d'Hématologie 67085 Strasbourg France
- Department of PathologyUniversity Hospital of Strasbourg 67091 Strasbourg France
| | | | - Stanislas Faguer
- Department of Nephrology and Organ TransplantationUniversity Hospital of Toulouse 31059 Toulouse France
- Institut National de la Santé et de la Recherche Médicale (INSERM)Institut of Cardiovascular and Metabolic Disease U1048 31432 Toulouse France
- Université Toulouse III Paul‐Sabatier 31330 Toulouse France
| | - Magali Colombat
- Department of PathologyCancer University Institute of Toulouse 31100 Toulouse France
| | - Holger Husi
- Division of Biomedical SciencesCentre for Health ScienceUniversity of the Highlands and Islands Inverness IV2 3JH UK
| | - William Mullen
- Institute of Cardiovascular and Medical SciencesUniversity of Glasgow Glasgow G12 8TA United Kingdom
| | - Wilfried Gwinner
- Department of NephrologyHannover Medical School 30625 Hannover Germany
| | - Sophie Caillard
- Nephrology – Transplantation DepartmentUMR_S. INSERM UMR_S 1109ImmunoRhumatologie MoléculaireFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de StrasbourgInstitut d'Immunologie et d'Hématologie 67085 Strasbourg France
| |
Collapse
|
5
|
Belczacka I, Pejchinovski M, Krochmal M, Magalhães P, Frantzi M, Mullen W, Vlahou A, Mischak H, Jankowski V. Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers. Proteomics Clin Appl 2018; 13:e1800111. [PMID: 30334612 DOI: 10.1002/prca.201800111] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Indexed: 12/20/2022]
Abstract
PURPOSE Urine is a rich source of potential biomarkers, including glycoproteins. Glycoproteomic analysis remains difficult due to the high heterogeneity of glycans. Nevertheless, recent advances in glycoproteomics software solutions facilitate glycopeptide identification and characterization. The aim is to investigate intact glycopeptides in the urinary peptide profiles of normal subjects using a novel PTM-centric software-Byonic. EXPERIMENTAL DESIGN The urinary peptide profiles of 238 normal subjects, previously analyzed using CE-MS and CE-MS/MS and/or LC-MS/MS, are subjected to glycopeptide analysis. Additionally, glycopeptide distribution is assessed in a set of 969 patients with five different cancer types: bladder, prostate and pancreatic cancer, cholangiocarcinoma, and renal cell carcinoma. RESULTS A total of 37 intact O-glycopeptides and 23 intact N-glycopeptides are identified in the urinary profiles of 238 normal subjects. Among the most commonly identified O-glycoproteins are Apolipoprotein C-III and insulin-like growth factor II, while titin among the N-glycoproteins. Further statistical analysis reveals that three O-glycopeptides and five N-glycopeptides differed significantly in their abundance among the different cancer types, comparing to normal subjects. CONCLUSIONS AND CLINICAL RELEVANCE Through the established glycoproteomics workflow, intact O- and N-glycopeptides in human urine are identified and characterized, providing novel insights for further exploration of the glycoproteome with respect to specific diseases.
Collapse
Affiliation(s)
- Iwona Belczacka
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany.,University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
| | | | | | | | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, G128QQ Glasgow, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens (BRFAA), 11527 Athens, Greece
| | | | - Vera Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
| |
Collapse
|
6
|
Stringer KA, McKay RT, Karnovsky A, Quémerais B, Lacy P. Metabolomics and Its Application to Acute Lung Diseases. Front Immunol 2016; 7:44. [PMID: 26973643 PMCID: PMC4770032 DOI: 10.3389/fimmu.2016.00044] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/29/2016] [Indexed: 12/27/2022] Open
Abstract
Metabolomics is a rapidly expanding field of systems biology that is gaining significant attention in many areas of biomedical research. Also known as metabonomics, it comprises the analysis of all small molecules or metabolites that are present within an organism or a specific compartment of the body. Metabolite detection and quantification provide a valuable addition to genomics and proteomics and give unique insights into metabolic changes that occur in tangent to alterations in gene and protein activity that are associated with disease. As a novel approach to understanding disease, metabolomics provides a "snapshot" in time of all metabolites present in a biological sample such as whole blood, plasma, serum, urine, and many other specimens that may be obtained from either patients or experimental models. In this article, we review the burgeoning field of metabolomics in its application to acute lung diseases, specifically pneumonia and acute respiratory disease syndrome (ARDS). We also discuss the potential applications of metabolomics for monitoring exposure to aerosolized environmental toxins. Recent reports have suggested that metabolomics analysis using nuclear magnetic resonance (NMR) and mass spectrometry (MS) approaches may provide clinicians with the opportunity to identify new biomarkers that may predict progression to more severe disease, such as sepsis, which kills many patients each year. In addition, metabolomics may provide more detailed phenotyping of patient heterogeneity, which is needed to achieve the goal of precision medicine. However, although several experimental and clinical metabolomics studies have been conducted assessing the application of the science to acute lung diseases, only incremental progress has been made. Specifically, little is known about the metabolic phenotypes of these illnesses. These data are needed to substantiate metabolomics biomarker credentials so that clinicians can employ them for clinical decision-making and investigators can use them to design clinical trials.
Collapse
Affiliation(s)
- Kathleen A. Stringer
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Paige Lacy
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
7
|
Abstract
Peptides are an important class of analytes in chemistry, biochemistry, food chemistry, as well as medical and pharmaceutical sciences including biomarker analysis in peptidomics and proteomics. As a high-resolution technique, capillary electrophoresis (CE) is well suited for the analysis of polar compounds such as peptides. In addition, CE is orthogonal to high-performance liquid chromatography (HPLC) as both techniques are based on different physicochemical separation principles. For the successful development of peptide separations by CE, operational parameters including puffer pH, buffer concentration and buffer type, applied voltage, capillary dimensions, as well as background electrolyte additives such as detergents, ion-pairing reagents, cyclodextrins, (poly)amines, and soluble polymers have to be considered and optimized.
Collapse
Affiliation(s)
- Gerhard K E Scriba
- Department of Pharmaceutical Chemistry, University of Jena, Philosophenweg 14, Jena, 07743, Germany.
| |
Collapse
|
8
|
Kartsova LA, Bessonova EA. Biomedical applications of capillary electrophoresis. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
9
|
Hou LN, Li F, Zeng QC, Su L, Chen PA, Xu ZH, Zhu DJ, Liu CH, Xu DL. Excretion of urinary orosomucoid 1 protein is elevated in patients with chronic heart failure. PLoS One 2014; 9:e107550. [PMID: 25215505 PMCID: PMC4162620 DOI: 10.1371/journal.pone.0107550] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 08/12/2014] [Indexed: 12/03/2022] Open
Abstract
Easily screening markers for early detection of chronic heart failure (CHF) are lacking. We identified twenty differently expressed proteins including orosomucoid 1(ORM1) in urine between patients with CHF and normal controls by proteomic methods. Bioinformatics analyses suggested ORM1 could be used for further analysis. After verification by western blotting, the urinary levels of ORM1 were quantified with enzyme-linked immunosorbent assay (ELISA) by correcting for creatinine expression. The ORM1-Cr was significantly elevated in CHF patients than normal controls (6498.83±4300.21 versus 2102.26±1069.24 ng/mg). Furthermore, a Spearman analysis indicated that the urinary ORM1 levels had a high positive correlation with the classification of CHF, and the multivariate analysis suggested that the urinary ORM1 content was associated with the plasma amino-terminal pro- brain natriuretic peptide (NT-proBNP) (OR: 2.106, 95% CI: 1.213–3.524, P = 0.002) and the New York Heart Association (NYHA) classification (OR: 3.019, 95% CI: 1.329–4.721, P<0.001). In addition, receiving operating curve (ROC) analyses suggested that an optimum cut-off value of 2484.98 ng/mg with 90.91% sensitivity and 85.48% specificity, respectively, could be used for the diagnosis of CHF. To sum up, our findings indicate that ORM1 could be a potential novel urinary biomarker for the early detection of CHF.
Collapse
Affiliation(s)
- Li-na Hou
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
- Department of healthy management, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Fei Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Qing-chun Zeng
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Liang Su
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Ping-an Chen
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Zhi-hao Xu
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Din-ji Zhu
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Chang-hua Liu
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
| | - Ding-li Xu
- State Key Laboratory of Organ Failure Research, Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R.China
- * E-mail:
| |
Collapse
|
10
|
Findeisen P, Peccerella T, Neumaier M, Schadendorf D. Proteomics for biomarker discovery in malignant melanoma. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/17469872.3.2.209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
11
|
Albalat A, Mischak H, Mullen W. Clinical application of urinary proteomics/peptidomics. Expert Rev Proteomics 2014; 8:615-29. [DOI: 10.1586/epr.11.46] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
12
|
Classical MALDI-MS versus CE-based ESI-MS proteomic profiling in urine for clinical applications. Bioanalysis 2014; 6:247-66. [DOI: 10.4155/bio.13.313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human urine is an attractive and informative biofluid for medical diagnosis, which has been shown to reflect the (patho)-physiology of not only the urogenital system, but also others such as the cardiovascular system. For this reason, many studies have concentrated on the study of the urine proteome, aiming to find relevant biomarkers that could be applied in a clinical setting. However, this goal can only be achieved after reliable quantitative and qualitative analysis of the urinary proteome. In the last two decades, MS-based platforms have evolved to become indispensable tools for biomarker research. In this review, we will present and compare two of the most clinically relevant analytical platforms that have been used for the study of the urinary proteome, namely CE-based ESI-MS and classical MALDI-MS. These platforms, although not directly comparable, have been extensively used in proteomic profiling and therefore their comparison is fundamentally relevant to this field.
Collapse
|
13
|
Ibáñez C, Simó C, García-Cañas V, Cifuentes A, Castro-Puyana M. Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: A review. Anal Chim Acta 2013; 802:1-13. [DOI: 10.1016/j.aca.2013.07.042] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/20/2013] [Accepted: 07/17/2013] [Indexed: 01/05/2023]
|
14
|
Stalmach A, Albalat A, Mullen W, Mischak H. Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications. Electrophoresis 2013; 34:1452-64. [DOI: 10.1002/elps.201200708] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Angelique Stalmach
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | - Amaya Albalat
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | - William Mullen
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | | |
Collapse
|
15
|
Kartsova LA, Obedkova EV. Chromatographic and electrophoretic profiles of biologically active compounds for the diagnosis of various diseases. JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1134/s1061934813040035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
16
|
Mischak H, Vlahou A, Ioannidis JP. Technical aspects and inter-laboratory variability in native peptide profiling: The CE–MS experience. Clin Biochem 2013; 46:432-43. [DOI: 10.1016/j.clinbiochem.2012.09.025] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/18/2012] [Accepted: 09/27/2012] [Indexed: 02/08/2023]
|
17
|
Method development and validation for rat serum fingerprinting with CE-MS: application to ventilator-induced-lung-injury study. Anal Bioanal Chem 2013; 405:4849-58. [PMID: 23535741 DOI: 10.1007/s00216-013-6882-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 02/13/2013] [Accepted: 02/27/2013] [Indexed: 02/06/2023]
Abstract
In the search for a noninvasive and reliable rapid screening method to detect biomarkers, a metabolomics fingerprinting approach was developed and applied to rat serum samples using capillary electrophoresis coupled to an electrospray ionization-time of flight-mass spectrometer (CE-TOF-MS). An ultrafiltration method was used for sample pretreatment. To evaluate performance the method was validated with carnitine, choline, ornithine, alanine, acetylcarnitine, betaine, and citrulline, covering the entire electropherogram of pool of rat serum. The linearity for all metabolites was >0.99, with good recovery and precision. Approximately 34 compounds were also confirmed in the pool of rat serum. The method was successfully applied to real serum samples from rats with ventilator-induced lung injury, an experimental rat model for acute lung injury (ALI), giving a total of 1163 molecular features. By use of univariate and multivariate statistics 18 significant compounds were found, of which five were confirmed. The involvement of arginase and nitric oxide synthase has been proved for other lung diseases, meaning the increase of asymmetric dimethyl arginine (ADMA) and ornithine and the decrease of arginine found were in accordance with published literature. Ultimately this fingerprinting approach offers the possibility of identifying biomarkers that could be regularly screened for as part of routine disease control. In this way it might be possible to prevent the development of ALI in patients in critical care units.
Collapse
|
18
|
Mesbah K, Verpillot R, de L'escaille F, Falmagne JB, Taverna M. Contribution of CE to the analysis of protein or peptide biomarkers. Methods Mol Biol 2013; 984:167-190. [PMID: 23386344 DOI: 10.1007/978-1-62703-296-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biomarker analysis is pivotal for disease diagnosis and one important class of biomarkers is constituted by proteins and peptides. This review focuses on protein and peptide analyses from biological fluids performed by capillary electrophoresis. The various strategies that have been reported to prevent difficulties due to the handling of real samples are described. Innovative techniques to overcome the complexity of the sample, to prevent the adsorption of the analytes on the inner capillary wall, and to increase the sensibility of the analysis are summarized and illustrated by different applications. To fully illustrate the contribution of CE to the analysis of biomarkers from human sample, two detailed protocols are given: the analysis from CSF of five amyloid peptide, biomarkers of the Alzheimer disease, and the analysis of sialoforms of transferrin from human serum.
Collapse
Affiliation(s)
- Kiarach Mesbah
- Laboratory of Proteins and Nanotechnologies in Separation Sciences, Faculté de Pharmacie, University of Paris-Sud, UMR-CNRS 8612, Châtenay-Malabry, France
| | | | | | | | | |
Collapse
|
19
|
A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. J Proteomics 2012; 75:5888-97. [DOI: 10.1016/j.jprot.2012.07.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/25/2012] [Accepted: 07/16/2012] [Indexed: 11/22/2022]
|
20
|
Mischak H. How to get proteomics to the clinic? Issues in clinical proteomics, exemplified by CE-MS. Proteomics Clin Appl 2012; 6:437-42. [PMID: 22821927 DOI: 10.1002/prca.201200027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/25/2012] [Accepted: 05/30/2012] [Indexed: 12/19/2022]
Abstract
Clinical proteomics is defined as application of proteome analysis aiming at improving the current clinical situation. As such, the success of clinical proteomics should be assessed based on the clinical impact following implementation of the findings. While we have experienced significant technological advancements in mass spectrometry in the last years, based on the above measure, this has not at all resulted in similar advancements in clinical proteomics. Although a large number of proteomic biomarkers have been described, most of them were not subsequently validated, and certainly have had no impact in clinical decision making as yet. Under the current conditions, it appears likely that the situation will not change significantly: we will be flooded by reports on biomarkers, but not see any implementation. In this article, some key issues in proteomic biomarker research are pinpointed, based on the experience with CE-MS, likely also holding true for biomarkers resulting from other analysis domains.
Collapse
Affiliation(s)
- Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
21
|
Kuznetsova T, Mischak H, Mullen W, Staessen JA. Urinary proteome analysis in hypertensive patients with left ventricular diastolic dysfunction. Eur Heart J 2012; 33:2342-50. [PMID: 22789915 PMCID: PMC3705161 DOI: 10.1093/eurheartj/ehs185] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Despite the significant heart failure (HF) burden on society, easily applicable screening techniques, particularly for the early detection of asymptomatic left ventricular (LV) dysfunction, are lacking. The present study aimed to identify and test a set of urinary polypeptides that may indicate early LV diastolic dysfunction as defined by echocardiography in hypertensive patients in a cross-sectional case-control study nested within the FLEMish study on ENvironment, Genes and Health Outcome (FLEMENGHO). METHODS AND RESULTS To identify potentially discriminating urinary biomarkers for LV diastolic dysfunction, we applied capillary electrophoresis coupled to mass spectrometry. In the discovery set, we compared 19 hypertensive patients with asymptomatic LV diastolic dysfunction with 19 healthy controls. In the absence of adjustment for multiple testing, 85 urinary peptides were different between cases and controls at a P-value of <0.033. With adjustment for multiple testing, three potential biomarkers remained significantly different between cases and controls (P ≤ 0.02). We combined the 85 potential biomarkers in a high-dimensional model (classifier), which we applied in a blinded manner to an independent test set of 16 hypertensive patients with symptomatic HF and 16 healthy controls. Upon unblinding, the area under the receiver operating characteristic curve (AUC) of the HF classification was 0.84 (95% CI: 0.70-0.98; P= 0.001). CONCLUSION In asymptomatic hypertensive patients with LV diastolic dysfunction, we identified a set of urinary polypeptides specific for essential hypertension with LV diastolic dysfunction that subsequently distinguished hypertensive patients with overt HF from healthy controls.
Collapse
Affiliation(s)
- Tatiana Kuznetsova
- Studies Coordinating Centre, Division of Hypertension and Cardiovascular Rehabilitation, Department of Cardiovascular Sciences, University of Leuven, Campus Sint Rafaël, Kapucijnenvoer 35, block d, level 00, Box 7001, B 3000 Leuven, Belgium
| | - Harald Mischak
- Mosaiques Diagnostic and Therapeutics AG, Hannover, Germany
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Jan A. Staessen
- Studies Coordinating Centre, Division of Hypertension and Cardiovascular Rehabilitation, Department of Cardiovascular Sciences, University of Leuven, Campus Sint Rafaël, Kapucijnenvoer 35, block d, level 00, Box 7001, B 3000 Leuven, Belgium
| |
Collapse
|
22
|
Lista S, Faltraco F, Hampel H. Biological and methodical challenges of blood-based proteomics in the field of neurological research. Prog Neurobiol 2012; 101-102:18-34. [PMID: 22743551 DOI: 10.1016/j.pneurobio.2012.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/28/2012] [Accepted: 06/18/2012] [Indexed: 12/17/2022]
Abstract
Biomarker discovery is an application of major importance in today's proteomic research. There is an urgent need for suitable biomarkers to improve diagnostic tools and treatment in various neurological diseases, such as neurodegenerative disorders. Recent years have witnessed an enormous interest in proteomics, which is currently seen as an invaluable tool to shed more light on complex interacting signalling pathways and molecular networks involved in several neuropathological conditions. However, while first results of proteomic research studies have sparked much public attention, the momentum of further proteomic biomarker research in neurological disorders may suffer by its very complex methodology which is sensitive to various sources of artefacts. A major source of variability is proteome perturbation caused by sample handling/preservation (preanalytical phase) and processing/measurement (analytical phase). The aim of the present review is to summarize the current literature focusing on the crucial role played by preanalytical and analytical factors that affect the quality of samples and the reliability of the data produced in blood-based proteomic biomarker research in neurology, which may apply to Alzheimer's disease (AD) as well as other neurological disorders. Procedures for sample preparation and protocols for the analysis of serum and plasma samples will be delineated. Finally, the potential usefulness of bioinformatics--allowing for the assembly, store, and processing of data--as well as its contribution to the execution of proteomic studies will be critically discussed.
Collapse
Affiliation(s)
- Simone Lista
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe-University of Frankfurt, Frankfurt am Main, Germany.
| | | | | |
Collapse
|
23
|
Mullen W, Albalat A, Gonzalez J, Zerefos P, Siwy J, Franke J, Mischak H. Performance of different separation methods interfaced in the same MS-reflection TOF detector: A comparison of performance between CE versus HPLC for biomarker analysis. Electrophoresis 2012; 33:567-74. [DOI: 10.1002/elps.201100415] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
24
|
Ryvolova M, Adam V, Kizek R. Analysis of metallothionein by capillary electrophoresis. J Chromatogr A 2012; 1226:31-42. [DOI: 10.1016/j.chroma.2011.10.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/30/2011] [Accepted: 10/01/2011] [Indexed: 02/05/2023]
|
25
|
Siwy J, Mullen W, Golovko I, Franke J, Zürbig P. Human urinary peptide database for multiple disease biomarker discovery. Proteomics Clin Appl 2011; 5:367-74. [PMID: 21591268 DOI: 10.1002/prca.201000155] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/04/2011] [Accepted: 03/09/2011] [Indexed: 11/07/2022]
Abstract
PURPOSE Human urine is an ideal candidate for use in clinical diagnostics. It is easily available, as untrained personnel can collect it. It correlates well with the pathophysiology of a number of diseases, making it a useful source for clinical proteomics. EXPERIMENTAL DESIGN In this article, we give an update of the human urinary peptide database derived from over 13,000 data sets of CE-MS by now. RESULTS Urine samples from both patients and healthy subjects were analyzed by CE-MS; these included 47 different pathophysiological conditions. Besides defining biomarkers by their experimental parameters, information on their sequences provides fundamental data into the pathological pathways of diseases. Therefore, we have sequenced 953 urinary peptides by using state-of-the-art top-down MS/MS. Identified biomarkers of all clinical proteomic CE-MS studies including their regulation are also listed in this work. CONCLUSIONS AND CLINICAL RELEVANCE Biomarker discovery can be used in the management of a wide range of diseases, by combining these data sets of the database. Taking this approach, we can reveal details, at a molecular level, on the pathogenesis of a number of diseases, in particular those associated with urine production and excretion.
Collapse
|
26
|
Borchers S, Provasi E, Silvani A, Radrizzani M, Benati C, Dammann E, Krons A, Kontsendorn J, Schmidtke J, Kuehnau W, von Neuhoff N, Stadler M, Ciceri F, Bonini C, Ganser A, Hertenstein B, Weissinger EM. Genetically modified donor leukocyte transfusion and graft-versus-leukemia effect after allogeneic stem cell transplantation. Hum Gene Ther 2011; 22:829-41. [PMID: 21091264 DOI: 10.1089/hum.2010.162] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Seven patients with acute myeloid leukemia (AML) and two patients with chronic myelogenous leukemia (CML) were transplanted from HLA-identical sibling donors with CD34(+) cell-enriched stem cells (HSCTs) without further immunosuppression. The myeloablative standard transplantation protocol was adapted to include transfusion of gene-modified donor T cells after HSCT. Donor T cells were transduced with the replication-deficient retrovirus SFCMM-3, which expresses herpes simplex thymidine kinase (HSV-Tk) and a truncated version of low-affinity nerve growth factor receptor (ΔLNGFR) for selection and characterization of transduced cells. Transduced T cells were detectable in all patients during follow-up for up to 5 years after transfusion. Proteomic screening for development of acute graft-versus-host disease (aGvHD) was applied to five of the seven patients with AML. No positivity for the aGvHD grade II-specific proteomic pattern was observed. Only one patient developed aGvHD grade I. To date, three of the patients with AML relapsed; one responded to three escalating transfusions of lymphocytes from the original donor and is in complete remission. Two were retransplanted with non-T cell-depleted peripheral blood stem cells from their original donors and died after retransplantation of septic complications or relapse, respectively. In one patient with CML, loss of bcr-abl gene expression was observed after an expansion of transduced cells. Seven of nine patients are alive and in complete remission.
Collapse
Affiliation(s)
- Sylvia Borchers
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover 30625, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Advances in proteomic prostate cancer biomarker discovery. J Proteomics 2010; 73:1839-50. [PMID: 20398807 DOI: 10.1016/j.jprot.2010.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 01/15/2010] [Accepted: 04/06/2010] [Indexed: 11/21/2022]
Abstract
Prostate cancer is the most common non-cutaneous cancer in men in the United States. For reasons largely unknown, the incidence of prostate cancer has increased in the last two decades, in spite or perhaps because of a concomitant increase in serum prostate-specific antigen (PSA) screening. While PSA is acknowledged not to be an ideal biomarker for prostate cancer detection, it is however widely used by physicians due to lack of an alternative. Thus, the identification of a biomarker(s) that can complement or replace PSA represents a major goal for prostate cancer research. Screening complex biological specimens such as blood, urine, and tissue to identify protein biomarkers has become increasingly popular over the last decade thanks to advances in proteomic discovery methods. The completion of human genome sequence together with new development in mass spectrometry instrumentation and bioinformatics has been a major driving force in biomarker discovery research. Here we review the current state of proteomic applications as applied to various sample sources including blood, urine, tissue, and "secretome" for the purpose of prostate cancer biomarker discovery. Additionally, we review recent developments in validation of putative markers, efforts at systems biology approach, and current challenges of proteomics in biomarker discovery.
Collapse
|
28
|
Sobhani K. Urine proteomic analysis: use of two-dimensional gel electrophoresis, isotope coded affinity tags, and capillary electrophoresis. Methods Mol Biol 2010; 641:325-346. [PMID: 20407955 DOI: 10.1007/978-1-60761-711-2_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The identities and abundance levels of proteins excreted in urine are not only key indicators of diseases associated with renal function but are also indicators of the overall health of individuals. Urine specimens are readily available and provide a noninvasive means to assess and diagnose many disease states. Proteins in urine originate from two sources: the ultrafiltrate of plasma, and those that are shed from the urinary tract. The protein concentration in urine excreted from a normal adult is approximately 150 mg/day, and is typically not greater than 10 mg/100 mL in any single specimen. Following precipitation, concentration, and fractionation methods, proteins of interest from urine samples can be separated, identified, and quantified. One of the most commonly used techniques in the field of urine proteomics is gel electrophoresis followed by identification with mass spectrometry and protein database search algorithms. In this chapter, two-dimensional gel electrophoresis (2-DE) will be discussed, along with less frequently applied techniques, such as isotope coded affinity tags (ICAT) and capillary electrophoresis (CE). Publications discussing the application of these techniques to urine proteomic analyses of healthy individuals and urinary disease biomarker discovery will also be summarized.
Collapse
Affiliation(s)
- Kimia Sobhani
- Department of Clinical Pathology, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
29
|
Findeisen P, Neumaier M. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective. Clin Chem Lab Med 2009; 47:666-84. [PMID: 19445650 DOI: 10.1515/cclm.2009.159] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proteomics analysis has been heralded as a novel tool for identifying new and specific biomarkers that may improve diagnosis and monitoring of various disease states. Recent years have brought a number of proteomics profiling technologies. Although proteomics profiling has resulted in the detection of disease-associated differences and modification of proteins, current proteomics technologies display certain limitations that are hampering the introduction of these new technologies into clinical laboratory diagnostics and routine applications. In this review, we summarize current advances in mass spectrometry based biomarker discovery. The promises and challenges of this new technology are discussed with particular emphasis on diagnostic perspectives of mass-spectrometry based proteomics profiling for malignant diseases.
Collapse
Affiliation(s)
- Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany.
| | | |
Collapse
|
30
|
Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
|
31
|
Staub A, Schappler J, Rudaz S, Veuthey JL. CE-TOF/MS: Fundamental concepts, instrumental considerations and applications. Electrophoresis 2009; 30:1610-23. [DOI: 10.1002/elps.200800782] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
32
|
Kistler AD, Mischak H, Poster D, Dakna M, Wüthrich RP, Serra AL. Identification of a unique urinary biomarker profile in patients with autosomal dominant polycystic kidney disease. Kidney Int 2009; 76:89-96. [PMID: 19340089 DOI: 10.1038/ki.2009.93] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To gain some insight into early disease progression in human autosomal dominant polycystic kidney disease (ADPKD), we analyzed the urine proteome of 41 young patients with ADPKD whose renal function was relatively preserved. Using capillary electrophoresis and mass spectrometry, we compared these results to those from age-matched healthy controls and patients with other renal diseases. There were 197 proteins with significantly altered urinary excretion; and 38 of them could be sequenced, most of which were collagen fragments. This suggests that there is high turnover of extracellular matrix proteins. Uromodulin peptides, previously implicated in tubular injury, were also found in the urine specimens. These marker proteins were found to distinguish patients from controls with a high degree of accuracy. The sensitivity and specificity of this marker set remained high in an independent validation cohort of 24 patients with ADPKD and 35 healthy controls, and even in comparisons of patients with a variety of other renal diseases or patients with kidney or bladder cancer. These findings present a potential hypothesis for the mechanisms of disease progression in ADPKD which will need to be confirmed by further studies.
Collapse
|
33
|
von Zur Muhlen C, Schiffer E, Zuerbig P, Kellmann M, Brasse M, Meert N, Vanholder RC, Dominiczak AF, Chen YC, Mischak H, Bode C, Peter K. Evaluation of urine proteome pattern analysis for its potential to reflect coronary artery atherosclerosis in symptomatic patients. J Proteome Res 2009; 8:335-45. [PMID: 19053529 DOI: 10.1021/pr800615t] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coronary artery disease (CAD) is a major cause of mortality and morbidity. Noninvasive proteome analysis could guide clinical evaluation and early/preventive treatment. Under routine clinical conditions, urine of 67 patients presenting with symptoms suspicious for CAD were analyzed by capillary electrophoresis directly coupled with mass spectrometry (CE-MS). All patients were subjected to coronary angiography and either assigned to a CAD or non-CAD group. A training set of 29 patients was used to establish CAD and non-CAD-associated proteome patterns of plasma as well as urine. Significant discriminatory power was achieved in urine but not in plasma. Therefore, urine proteomic analysis of further 38 patients was performed in a blinded study. A combination of 17 urinary polypeptides allowed separation of both groups in the test set with a sensitivity of 81%, a specificity of 92%, and an accuracy of 84%. Sequencing of urinary marker peptides identified fragments of collagen alpha1 (I and III), which we furthermore demonstrated to be expressed in atherosclerotic plaques of human aorta. In conclusion, specific CE-MS polypeptide patterns in urine were associated with significant CAD in patients with angina-typical symptoms. These promising findings need to be further evaluated in regard to reliability of a urine-based screening method with the potential of improving the diagnostic approaches for CAD.
Collapse
|
34
|
Abstract
Complex biological samples hold significant information on the health status and on development of disease. Approximately 35,000 human genes give rise to more than 1,000,000 functional entities at the protein level. Thus, the proteome provides a much richer source of information than the genome for describing the state of health or disease of humans. The composition body fluids comprise a rich source of information on changes of protein and peptide expression. Here we describe the application of capillary electrophoresis (CE) coupled online to an electrospray-ionization time-of-flight mass spectrometer (ESI-TOF-MS) to analyze human urine for the identification of biomarkers specific for complications after allogeneic hematopoietic stem cell transplantation (HSCT). Sequencing of native proteins/peptides is necessary for the identification of possible new therapeutic targets.
Collapse
|
35
|
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med 2009; 47:724-44. [DOI: 10.1515/cclm.2009.167] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
36
|
Metzger J, Luppa PB, Good DM, Mischak H. Adapting mass spectrometry-based platforms for clinical proteomics applications: The capillary electrophoresis coupled mass spectrometry paradigm. Crit Rev Clin Lab Sci 2009; 46:129-52. [PMID: 19404829 PMCID: PMC5769463 DOI: 10.1080/10408360902805261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single biomarker detection is common in clinical laboratories due to the currently available method spectrum. For various diseases, however, no specific single biomarker could be identified. A strategy to overcome this diagnostic void is to shift from single analyte detection to multiplexed biomarker profiling. Mass spectrometric methods were employed for biomarker discovery in body fluids. The enormous complexity of biofluidic proteome compartments implies upstream fractionation. For this reason, mass spectrometry (MS) was coupled to two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization, or capillary electrophoresis (CE). Differences in performance and operating characteristics make them differentially suited for routine laboratory applications. Progress in the field of clinical proteomics relies not only on the use of an adequate technological platform, but also on a fast and efficient proteomic workflow including standardized sample preparation, proteomic data processing, statistical validation of biomarker selection, and sample classification. Based on CE-MS analysis, we describe how proteomic technology can be implemented in a clinical laboratory environment. In the last part of this review, we give an overview of CE-MS-based clinical studies and present information on identity and biological significance of the identified peptide biomarkers providing evidence of disease-induced changes in proteolytic processing and posttranslational modification.
Collapse
Affiliation(s)
- Jochen Metzger
- Mosaiques Diagnostics and Terapeutics AG, Mellendorfer Str. 7-9, Hannover 30625, Germany.
| | | | | | | |
Collapse
|
37
|
Weissinger EM, Dickinson AM. Immunogenomics and proteomics in hematopoietic stem cell transplantation: predicting post-hematopoietic stem cell transplant complications. Cancer Treat Res 2009; 144:95-129. [PMID: 19779872 DOI: 10.1007/978-0-387-78580-6_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Eva M Weissinger
- Hannover Medical School, Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Carl-Neuberg-Str.1, 30625 Hannover, Germany.
| | | |
Collapse
|
38
|
Zürbig P, Schiffer E, Mischak H. Capillary Electrophoresis Coupled to Mass Spectrometry for Proteomic Profiling of Human Urine and Biomarker Discovery. Proteomics 2009; 564:105-21. [DOI: 10.1007/978-1-60761-157-8_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
39
|
Jantos-Siwy J, Schiffer E, Brand K, Schumann G, Rossing K, Delles C, Mischak H, Metzger J. Quantitative Urinary Proteome Analysis for Biomarker Evaluation in Chronic Kidney Disease. J Proteome Res 2008; 8:268-81. [DOI: 10.1021/pr800401m] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Justyna Jantos-Siwy
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Eric Schiffer
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Korbinian Brand
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Gerhard Schumann
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Kasper Rossing
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Christian Delles
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Harald Mischak
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Jochen Metzger
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany, Institut für Klinische Chemie, Medizinische Hochschule Hannover, Hannover, Germany, Steno Diabetes Center, Gentofe, Denmark, and BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
40
|
Benavente F, Andón B, Giménez E, Olivieri AC, Barbosa J, Sanz-Nebot V. A multiway approach for classification and characterization of rabbit liver apothioneins by CE-ESI-MS. Electrophoresis 2008; 29:4355-67. [DOI: 10.1002/elps.200800212] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
41
|
Herrero M, Ibañez E, Cifuentes A. Capillary electrophoresis-electrospray-mass spectrometry in peptide analysis and peptidomics. Electrophoresis 2008; 29:2148-60. [DOI: 10.1002/elps.200700404] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
42
|
Schiffer E, Mischak H, Vanholder RC. Biomarkers for Renal Disease and Uremic Toxins. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
43
|
Theodorescu D, Schiffer E, Bauer HW, Douwes F, Eichhorn F, Polley R, Schmidt T, Schöfer W, Zürbig P, Good DM, Coon JJ, Mischak H. Discovery and validation of urinary biomarkers for prostate cancer. Proteomics Clin Appl 2008; 2:556-570. [PMID: 19759844 DOI: 10.1002/prca.200780082] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Only 30% of patients with elevated serum prostate specific antigen (PSA) levels who undergo prostate biopsy are diagnosed with prostate cancer (PCa). Novel methods are needed to reduce the number of unnecessary biopsies. We report on the identification and validation of a panel of 12 novel biomarkers for prostate cancer (PCaP), using CE coupled MS. The biomarkers could be defined by comparing first void urine of 51 men with PCa and 35 with negative prostate biopsy. In contrast, midstream urine samples did not allow the identification of discriminatory molecules, suggesting that prostatic fluids may be the source of the defined biomarkers. Consequently, first void urine samples were tested for sufficient amounts of prostatic fluid, using a prostatic fluid indicative panel ("informative" polypeptide panel; IPP). A combination of IPP and PCaP to predict positive prostate biopsy was evaluated in a blinded prospective study. Two hundred thirteen of 264 samples matched the IPP criterion. PCa was detected with 89% sensitivity, 51% specificity. Including age and percent free PSA to the proteomic signatures resulted in 91% sensitivity, 69% specificity.
Collapse
Affiliation(s)
- Dan Theodorescu
- Department of Urology, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Haselberg R, de Jong GJ, Somsen GW. Capillary electrophoresis–mass spectrometry for the analysis of intact proteins. J Chromatogr A 2007; 1159:81-109. [PMID: 17560583 DOI: 10.1016/j.chroma.2007.05.048] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/01/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Developments in the fields of protein chemistry, proteomics and biotechnology have increased the demand for suitable analytical techniques for the analysis of intact proteins. In 1989, capillary electrophoresis (CE) was combined with mass spectrometry (MS) for the first time and its potential usefulness for the analysis of intact (i.e. non-digested) proteins was shown. This article provides an overview of the applications of CE-MS within the field of intact protein analysis. The principles of the applied CE modes and ionization techniques used for CE-MS of intact proteins are shortly described. It is shown that separations are predominantly carried out by capillary zone electrophoresis and capillary isoelectric focusing, whereas electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) are the most popular ionization techniques used for interfacing. The combination of CE with inductively coupled plasma (ICP) MS for the analysis of metalloproteins is also discussed. The various CE-MS combinations are systematically outlined and tables provide extensive overviews of the applications of each technique for intact protein analysis. Selected examples are given to illustrate the usefulness of the CE-MS techniques. Examples include protein isoform assignment, single cell analysis, metalloprotein characterization, proteomics and biomarker screening. Finally, chip-based electrophoresis combined with MS is shortly treated and some of its applications are described. It is concluded that CE-MS represents a powerful tool for the analysis of intact proteins yielding unique separations and information.
Collapse
Affiliation(s)
- Rob Haselberg
- Department of Biomedical Analysis, Utrecht University, 3508 TB Utrecht, The Netherlands.
| | | | | |
Collapse
|
45
|
Thongboonkerd V. Recent progress in urinary proteomics. Proteomics Clin Appl 2007; 1:780-91. [PMID: 21136734 DOI: 10.1002/prca.200700035] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Indexed: 11/08/2022]
Abstract
Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.
Collapse
Affiliation(s)
- Visith Thongboonkerd
- Medical Molecular Biology Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. ,
| |
Collapse
|
46
|
Luque-Garcia JL, Neubert TA. Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry. J Chromatogr A 2007; 1153:259-76. [PMID: 17166507 PMCID: PMC7094463 DOI: 10.1016/j.chroma.2006.11.054] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/06/2006] [Accepted: 11/16/2006] [Indexed: 01/14/2023]
Abstract
In this article, we present an overview of the different strategies for sample preparation for identification by mass spectrometry (MS) of biomarkers from serum and/or plasma. We consider the effects of the variables involved in sample collection, handling and storage, and describe different approaches for removal of high abundance proteins and serum/plasma fractionation. We review the advantages and disadvantages of such techniques as centrifugal ultrafiltration, different formats for solid phase extraction, organic solvent extraction, gel and capillary electrophoresis, and liquid chromatography. We also discuss a variety of current proteomic methods and their main applications for biomarker-related studies.
Collapse
Affiliation(s)
| | - Thomas A. Neubert
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
47
|
Frommberger M, Zürbig P, Jantos J, Krahn T, Mischak H, Pich A, Just I, Schmitt-Kopplin P, Schiffer E. Peptidomic analysis of rat urine using capillary electrophoresis coupled to mass spectrometry. Proteomics Clin Appl 2007; 1:650-60. [PMID: 21136720 DOI: 10.1002/prca.200700195] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Indexed: 11/10/2022]
Abstract
We have established and validated a protocol for the peptidomic analysis of rat urine using CE coupled to MS (CE-MS). In the first experiments, the reproducibility of the CE-MS set-up and of the established preparation procedure were assessed. To establish a first rat urinary peptidome map, samples were also analyzed using CE-FT-ICR. The subsequent analysis of independent samples from two different strains (WISTAR and CD) indicated strain-specific differences, which were validated in a blinded assessment. MS/MS revealed the presence of specific fragments from well-known urinary rat peptides, such as collagens, alpha-1-antitrypsin, and serum albumin. The CE-MS-based peptidomics platform may provide novel insights into body fluids of animal models, such as rat or mice. Together with peptide identification, the technology appears to be an excellent, complimentary, and non-invasive tool to analyze toxicological or other (patho)physiological effects of pharmaceutical compounds in animal models.
Collapse
Affiliation(s)
- Moritz Frommberger
- Institute of Ecological Chemistry, GSF - National Research Center for Environment and Health, Neuherberg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Sniehotta M, Schiffer E, Zürbig P, Novak J, Mischak H. CE – a multifunctional application for clinical diagnosis. Electrophoresis 2007; 28:1407-17. [PMID: 17427258 DOI: 10.1002/elps.200600581] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
CE has been used widely as an analytical tool with high separation power taking advantage of size, charge-to-size ratio, or isoelectric point of various analytes. In combination with detection methods, such as UV absorption, electrochemical detection, fluorescence, or mass spectrometry (MS), it allows the separation and detection of inorganic and organic ions, as well as complex compounds, such as polypeptides, nucleic acids, including PCR amplicons from viruses or bacteria. Recent interest in identification of biomarkers of diseases using body fluids leads to development of CE-MS techniques. These applications allowed identification of new potential biomarkers for clinical diagnosis and monitoring of therapeutic interventions. In this report, we present a technical overview of various CE techniques and discuss their applications in clinical medicine.
Collapse
Affiliation(s)
- Maike Sniehotta
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
| | | | | | | | | |
Collapse
|
49
|
Abstract
A new method for displaying CE-MALDI-MS data for proteolytic digests is described. This data display mode yields distinct charge-based trends for plots of mass-to-charge (m/z) versus CE migration time. These trends arise owing to the in-solution charge state of the peptides, and this interpretation was confirmed by using empirical peptide electromigration models and peptide standards as charge-state markers. These charge-state specific trends exhibit analytical utility by providing additional chemical information about the peptides, which increases the confidence level of peptide identification and provides a rapid means for screening for posttranslationally modified peptides.
Collapse
Affiliation(s)
- Brad J Williams
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | | | | |
Collapse
|
50
|
Weissinger EM, Schiffer E, Hertenstein B, Ferrara JL, Holler E, Stadler M, Kolb HJ, Zander A, Zürbig P, Kellmann M, Ganser A. Proteomic patterns predict acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation. Blood 2007; 109:5511-9. [PMID: 17339419 DOI: 10.1182/blood-2007-01-069757] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute graft-versus-host disease (aGvHD) contributes significantly to morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Diagnosis of GvHD is mainly based on clinical features and tissue biopsies. A noninvasive, unbiased laboratory test for GvHD diagnosis does not exist. Here we describe the application of capillary electrophoresis coupled online with mass spectrometry (CE-MS) to 13 samples from 10 patients with aGvHD of grade II or more and 50 control samples from 23 patients without GvHD. About 170 GvHD-specific polypeptides were detected and a tentatively aGvHD-specific model consisting of 31 polypeptides was chosen, allowing correct classification of 13 of 13 (sensitivity 100.0% [95% confidence interval {CI} 75.1 to 100.0]) aGvHD samples and 49 of 50 (specificity 98.0% [95% CI 89.3 to 99.7]) control samples of the training set. The subsequent blinded evaluation of 599 samples enabled diagnosis of aGvHD greater than grade II, even prior to clinical diagnosis, with a sensitivity of 83.1% (95% CI 73.1 to 87.9) and a specificity of 75.6% (95% CI 71.6 to 79.4). Thus, high-resolution proteome analysis represents an unbiased laboratory-based screening method, enabling diagnosis, and possibly enabling preemptive therapy.
Collapse
Affiliation(s)
- Eva M Weissinger
- Hannover Medical School, Department of Hematology, Hemostasis, and Oncology, Hannover, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|